Starting phenix.real_space_refine on Fri Feb 16 14:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1m_27135/02_2024/8d1m_27135.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1m_27135/02_2024/8d1m_27135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1m_27135/02_2024/8d1m_27135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1m_27135/02_2024/8d1m_27135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1m_27135/02_2024/8d1m_27135.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1m_27135/02_2024/8d1m_27135.pdb" } resolution = 3.11 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= 0.005 sd= 0.095 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 10260 2.51 5 N 2550 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 302": "OD1" <-> "OD2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 302": "OD1" <-> "OD2" Residue "E GLU 306": "OE1" <-> "OE2" Residue "E ASP 323": "OD1" <-> "OD2" Residue "E ASP 335": "OD1" <-> "OD2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 302": "OD1" <-> "OD2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B ASP 335": "OD1" <-> "OD2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 302": "OD1" <-> "OD2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "D ASP 323": "OD1" <-> "OD2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 302": "OD1" <-> "OD2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C ASP 335": "OD1" <-> "OD2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15590 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "E" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "B" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Time building chain proxies: 7.90, per 1000 atoms: 0.51 Number of scatterers: 15590 At special positions: 0 Unit cell: (109.56, 106.24, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2700 8.00 N 2550 7.00 C 10260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.35 Conformation dependent library (CDL) restraints added in 2.7 seconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 5 sheets defined 68.0% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 27 through 53 removed outlier: 3.553A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 removed outlier: 3.510A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.571A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.713A pdb=" N ALA A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.567A pdb=" N LYS A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.640A pdb=" N LEU A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.700A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.741A pdb=" N LEU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.923A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.766A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.550A pdb=" N ASP A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'E' and resid 17 through 23 Processing helix chain 'E' and resid 27 through 53 removed outlier: 3.554A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 removed outlier: 3.511A pdb=" N TYR E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 99 Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.572A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.713A pdb=" N ALA E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 removed outlier: 3.567A pdb=" N LYS E 149 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.640A pdb=" N LEU E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.699A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.741A pdb=" N LEU E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.922A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.765A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 removed outlier: 3.550A pdb=" N ASP E 323 " --> pdb=" O LEU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'B' and resid 17 through 23 Processing helix chain 'B' and resid 27 through 52 removed outlier: 3.552A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 removed outlier: 3.510A pdb=" N TYR B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.571A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.713A pdb=" N ALA B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.566A pdb=" N LYS B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.640A pdb=" N LEU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.699A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.741A pdb=" N LEU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.923A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.765A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 removed outlier: 3.550A pdb=" N ASP B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 27 through 53 removed outlier: 3.553A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.510A pdb=" N TYR D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 99 Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.572A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.713A pdb=" N ALA D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 removed outlier: 3.567A pdb=" N LYS D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.640A pdb=" N LEU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.699A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.741A pdb=" N LEU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.922A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.766A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 removed outlier: 3.551A pdb=" N ASP D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 52 removed outlier: 3.554A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 removed outlier: 3.511A pdb=" N TYR C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 99 Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.571A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.713A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.567A pdb=" N LYS C 149 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.640A pdb=" N LEU C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.699A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.741A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.923A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.765A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 removed outlier: 3.550A pdb=" N ASP C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 348 removed outlier: 4.202A pdb=" N TYR A 347 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 375 through 376 removed outlier: 4.213A pdb=" N TYR B 347 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 347 through 348 removed outlier: 4.220A pdb=" N TYR E 347 " --> pdb=" O GLN D 376 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 375 through 376 removed outlier: 4.223A pdb=" N TYR C 347 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 347 through 348 removed outlier: 4.204A pdb=" N TYR D 347 " --> pdb=" O GLN C 376 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.17 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3103 1.33 - 1.45: 4143 1.45 - 1.57: 8679 1.57 - 1.69: 5 1.69 - 1.81: 135 Bond restraints: 16065 Sorted by residual: bond pdb=" CA LEU A 75 " pdb=" C LEU A 75 " ideal model delta sigma weight residual 1.523 1.574 -0.050 1.34e-02 5.57e+03 1.41e+01 bond pdb=" CA LEU B 75 " pdb=" C LEU B 75 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.41e+01 bond pdb=" CA LEU C 75 " pdb=" C LEU C 75 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.38e+01 bond pdb=" CA LEU E 75 " pdb=" C LEU E 75 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.37e+01 bond pdb=" CA LEU D 75 " pdb=" C LEU D 75 " ideal model delta sigma weight residual 1.523 1.573 -0.049 1.34e-02 5.57e+03 1.36e+01 ... (remaining 16060 not shown) Histogram of bond angle deviations from ideal: 97.44 - 104.76: 350 104.76 - 112.09: 7675 112.09 - 119.42: 5588 119.42 - 126.74: 7946 126.74 - 134.07: 326 Bond angle restraints: 21885 Sorted by residual: angle pdb=" N ASP D 301 " pdb=" CA ASP D 301 " pdb=" C ASP D 301 " ideal model delta sigma weight residual 109.79 97.82 11.97 1.56e+00 4.11e-01 5.88e+01 angle pdb=" N ASP C 301 " pdb=" CA ASP C 301 " pdb=" C ASP C 301 " ideal model delta sigma weight residual 109.79 97.83 11.96 1.56e+00 4.11e-01 5.88e+01 angle pdb=" N ASP B 301 " pdb=" CA ASP B 301 " pdb=" C ASP B 301 " ideal model delta sigma weight residual 109.79 97.84 11.95 1.56e+00 4.11e-01 5.87e+01 angle pdb=" N ASP A 301 " pdb=" CA ASP A 301 " pdb=" C ASP A 301 " ideal model delta sigma weight residual 109.79 97.84 11.95 1.56e+00 4.11e-01 5.87e+01 angle pdb=" N ASP E 301 " pdb=" CA ASP E 301 " pdb=" C ASP E 301 " ideal model delta sigma weight residual 109.79 97.85 11.94 1.56e+00 4.11e-01 5.86e+01 ... (remaining 21880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 8370 17.76 - 35.52: 780 35.52 - 53.28: 170 53.28 - 71.04: 25 71.04 - 88.80: 30 Dihedral angle restraints: 9375 sinusoidal: 3810 harmonic: 5565 Sorted by residual: dihedral pdb=" CA ARG C 313 " pdb=" CB ARG C 313 " pdb=" CG ARG C 313 " pdb=" CD ARG C 313 " ideal model delta sinusoidal sigma weight residual -180.00 -122.62 -57.38 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA ARG A 313 " pdb=" CB ARG A 313 " pdb=" CG ARG A 313 " pdb=" CD ARG A 313 " ideal model delta sinusoidal sigma weight residual -180.00 -122.62 -57.38 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA ARG D 313 " pdb=" CB ARG D 313 " pdb=" CG ARG D 313 " pdb=" CD ARG D 313 " ideal model delta sinusoidal sigma weight residual -180.00 -122.65 -57.35 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 9372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1746 0.050 - 0.100: 429 0.100 - 0.150: 128 0.150 - 0.200: 47 0.200 - 0.250: 25 Chirality restraints: 2375 Sorted by residual: chirality pdb=" CA ILE C 28 " pdb=" N ILE C 28 " pdb=" C ILE C 28 " pdb=" CB ILE C 28 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE B 28 " pdb=" N ILE B 28 " pdb=" C ILE B 28 " pdb=" CB ILE B 28 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ILE E 28 " pdb=" N ILE E 28 " pdb=" C ILE E 28 " pdb=" CB ILE E 28 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2372 not shown) Planarity restraints: 2750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 29 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C TYR E 29 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR E 29 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS E 30 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 29 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C TYR C 29 " -0.036 2.00e-02 2.50e+03 pdb=" O TYR C 29 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS C 30 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 29 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C TYR A 29 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR A 29 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 30 " -0.012 2.00e-02 2.50e+03 ... (remaining 2747 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 6141 2.90 - 3.40: 16376 3.40 - 3.90: 27431 3.90 - 4.40: 31976 4.40 - 4.90: 53230 Nonbonded interactions: 135154 Sorted by model distance: nonbonded pdb=" N ASP B 301 " pdb=" O ASP B 301 " model vdw 2.396 2.496 nonbonded pdb=" N ASP A 301 " pdb=" O ASP A 301 " model vdw 2.397 2.496 nonbonded pdb=" N ASP C 301 " pdb=" O ASP C 301 " model vdw 2.397 2.496 nonbonded pdb=" N ASP D 301 " pdb=" O ASP D 301 " model vdw 2.397 2.496 nonbonded pdb=" N ASP E 301 " pdb=" O ASP E 301 " model vdw 2.397 2.496 ... (remaining 135149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 6.560 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 40.740 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.006 0.050 16065 Z= 0.382 Angle : 0.865 11.965 21885 Z= 0.584 Chirality : 0.057 0.250 2375 Planarity : 0.005 0.040 2750 Dihedral : 15.342 88.804 5785 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.67 % Favored : 97.06 % Rotamer: Outliers : 1.18 % Allowed : 2.36 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 1870 helix: 1.48 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.17 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 93 HIS 0.005 0.001 HIS B 178 PHE 0.021 0.002 PHE C 248 TYR 0.032 0.002 TYR B 236 ARG 0.009 0.001 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 316 time to evaluate : 1.834 Fit side-chains REVERT: A 331 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7245 (ttp80) REVERT: E 262 LYS cc_start: 0.8124 (mmtp) cc_final: 0.7898 (mmtm) REVERT: B 331 ARG cc_start: 0.7519 (ttp80) cc_final: 0.7174 (ttp80) REVERT: B 344 GLN cc_start: 0.7810 (mt0) cc_final: 0.7569 (mm-40) REVERT: C 173 LYS cc_start: 0.8744 (tmmt) cc_final: 0.8516 (tttm) REVERT: C 331 ARG cc_start: 0.7555 (ttp80) cc_final: 0.7185 (ttp80) REVERT: C 360 MET cc_start: 0.8182 (mmt) cc_final: 0.7716 (mmt) outliers start: 20 outliers final: 10 residues processed: 334 average time/residue: 0.3112 time to fit residues: 147.4876 Evaluate side-chains 231 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 221 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN E 256 GLN E 296 ASN B 256 GLN D 256 GLN C 256 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16065 Z= 0.227 Angle : 0.524 7.968 21885 Z= 0.278 Chirality : 0.038 0.149 2375 Planarity : 0.004 0.026 2750 Dihedral : 4.016 16.603 2095 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.77 % Allowed : 8.55 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.19), residues: 1870 helix: 1.66 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -0.04 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 93 HIS 0.004 0.001 HIS D 178 PHE 0.019 0.002 PHE B 248 TYR 0.018 0.002 TYR C 236 ARG 0.006 0.001 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 229 time to evaluate : 1.801 Fit side-chains REVERT: A 209 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8447 (p) REVERT: E 209 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8403 (p) REVERT: E 331 ARG cc_start: 0.7589 (ttp80) cc_final: 0.7175 (ttp80) REVERT: B 62 PHE cc_start: 0.8183 (t80) cc_final: 0.7981 (t80) REVERT: B 209 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8391 (p) REVERT: B 331 ARG cc_start: 0.7514 (ttp80) cc_final: 0.7196 (ttp80) REVERT: B 344 GLN cc_start: 0.7778 (mt0) cc_final: 0.7516 (mm-40) REVERT: D 331 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7415 (ttp80) REVERT: D 344 GLN cc_start: 0.7894 (mt0) cc_final: 0.7548 (mm-40) REVERT: C 360 MET cc_start: 0.8171 (mmt) cc_final: 0.7697 (mmt) outliers start: 30 outliers final: 22 residues processed: 253 average time/residue: 0.3479 time to fit residues: 122.3965 Evaluate side-chains 233 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 208 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 296 ASN D 296 ASN C 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16065 Z= 0.166 Angle : 0.475 6.716 21885 Z= 0.250 Chirality : 0.036 0.144 2375 Planarity : 0.004 0.030 2750 Dihedral : 3.785 15.344 2090 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.89 % Allowed : 11.68 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.19), residues: 1870 helix: 1.60 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.20 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.002 0.001 HIS A 178 PHE 0.015 0.001 PHE C 248 TYR 0.014 0.001 TYR E 97 ARG 0.004 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 221 time to evaluate : 1.685 Fit side-chains revert: symmetry clash REVERT: E 331 ARG cc_start: 0.7569 (ttp80) cc_final: 0.7251 (ttp80) REVERT: B 344 GLN cc_start: 0.7763 (mt0) cc_final: 0.7473 (mm-40) REVERT: D 344 GLN cc_start: 0.7904 (mt0) cc_final: 0.7573 (mm-40) REVERT: C 68 TYR cc_start: 0.5254 (t80) cc_final: 0.4816 (t80) REVERT: C 344 GLN cc_start: 0.7812 (mt0) cc_final: 0.7520 (mm-40) REVERT: C 360 MET cc_start: 0.8134 (mmt) cc_final: 0.7667 (mmt) outliers start: 32 outliers final: 18 residues processed: 248 average time/residue: 0.3543 time to fit residues: 121.6287 Evaluate side-chains 218 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16065 Z= 0.280 Angle : 0.526 6.631 21885 Z= 0.275 Chirality : 0.038 0.150 2375 Planarity : 0.004 0.045 2750 Dihedral : 3.900 16.198 2090 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.89 % Allowed : 12.63 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 1870 helix: 1.50 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : 0.15 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 93 HIS 0.005 0.001 HIS D 178 PHE 0.022 0.002 PHE B 248 TYR 0.020 0.002 TYR D 236 ARG 0.006 0.000 ARG D 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 217 time to evaluate : 1.659 Fit side-chains REVERT: A 331 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7286 (ttp80) REVERT: A 344 GLN cc_start: 0.7811 (mt0) cc_final: 0.7568 (mm-40) REVERT: E 331 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7226 (ttp80) REVERT: B 262 LYS cc_start: 0.8412 (mptt) cc_final: 0.8182 (mmtp) REVERT: B 331 ARG cc_start: 0.7541 (ttp80) cc_final: 0.7160 (ttp80) REVERT: B 344 GLN cc_start: 0.7770 (mt0) cc_final: 0.7509 (mm-40) REVERT: D 62 PHE cc_start: 0.8172 (t80) cc_final: 0.7946 (t80) REVERT: D 68 TYR cc_start: 0.5432 (t80) cc_final: 0.5114 (t80) REVERT: D 344 GLN cc_start: 0.7877 (mt0) cc_final: 0.7559 (mm-40) REVERT: C 344 GLN cc_start: 0.7858 (mt0) cc_final: 0.7537 (mm-40) REVERT: C 360 MET cc_start: 0.8122 (mmt) cc_final: 0.7630 (mmt) outliers start: 32 outliers final: 28 residues processed: 242 average time/residue: 0.3530 time to fit residues: 117.4076 Evaluate side-chains 236 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16065 Z= 0.278 Angle : 0.516 6.705 21885 Z= 0.271 Chirality : 0.038 0.148 2375 Planarity : 0.004 0.051 2750 Dihedral : 3.912 16.174 2090 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.18 % Allowed : 13.98 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 1870 helix: 1.35 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : 0.04 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 93 HIS 0.004 0.001 HIS D 178 PHE 0.022 0.002 PHE B 248 TYR 0.018 0.002 TYR E 97 ARG 0.006 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 216 time to evaluate : 1.844 Fit side-chains REVERT: A 344 GLN cc_start: 0.7841 (mt0) cc_final: 0.7608 (mm-40) REVERT: E 262 LYS cc_start: 0.8243 (mmtp) cc_final: 0.8024 (mmtm) REVERT: B 262 LYS cc_start: 0.8406 (mptt) cc_final: 0.8168 (mmtp) REVERT: B 331 ARG cc_start: 0.7558 (ttp80) cc_final: 0.7149 (ttp80) REVERT: B 344 GLN cc_start: 0.7783 (mt0) cc_final: 0.7547 (mm-40) REVERT: D 62 PHE cc_start: 0.8199 (t80) cc_final: 0.7952 (t80) REVERT: D 344 GLN cc_start: 0.7890 (mt0) cc_final: 0.7563 (mm-40) REVERT: C 344 GLN cc_start: 0.7859 (mt0) cc_final: 0.7536 (mm-40) REVERT: C 360 MET cc_start: 0.8085 (mmt) cc_final: 0.7582 (mmt) outliers start: 37 outliers final: 29 residues processed: 244 average time/residue: 0.3674 time to fit residues: 123.8979 Evaluate side-chains 238 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 353 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 215 ASN B 120 GLN D 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16065 Z= 0.210 Angle : 0.486 6.697 21885 Z= 0.254 Chirality : 0.037 0.145 2375 Planarity : 0.004 0.051 2750 Dihedral : 3.816 16.074 2090 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.01 % Allowed : 14.69 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 1870 helix: 1.43 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : 0.03 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 93 HIS 0.003 0.001 HIS D 178 PHE 0.025 0.001 PHE E 80 TYR 0.016 0.001 TYR E 97 ARG 0.008 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 217 time to evaluate : 1.744 Fit side-chains REVERT: A 344 GLN cc_start: 0.7833 (mt0) cc_final: 0.7599 (mm-40) REVERT: B 207 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8281 (tt) REVERT: B 262 LYS cc_start: 0.8454 (mptt) cc_final: 0.8222 (mmtp) REVERT: B 331 ARG cc_start: 0.7539 (ttp80) cc_final: 0.7203 (ttp80) REVERT: B 344 GLN cc_start: 0.7777 (mt0) cc_final: 0.7544 (mm-40) REVERT: D 62 PHE cc_start: 0.8188 (t80) cc_final: 0.7950 (t80) REVERT: D 344 GLN cc_start: 0.7880 (mt0) cc_final: 0.7553 (mm-40) REVERT: C 344 GLN cc_start: 0.7847 (mt0) cc_final: 0.7520 (mm-40) outliers start: 34 outliers final: 30 residues processed: 240 average time/residue: 0.3688 time to fit residues: 121.5002 Evaluate side-chains 241 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 210 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN C 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16065 Z= 0.279 Angle : 0.519 6.777 21885 Z= 0.271 Chirality : 0.038 0.150 2375 Planarity : 0.004 0.052 2750 Dihedral : 3.897 16.440 2090 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.30 % Allowed : 14.57 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 1870 helix: 1.35 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : 0.00 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 93 HIS 0.004 0.001 HIS D 178 PHE 0.022 0.002 PHE B 248 TYR 0.014 0.001 TYR A 97 ARG 0.007 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 222 time to evaluate : 1.857 Fit side-chains REVERT: A 331 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7271 (ttp80) REVERT: A 344 GLN cc_start: 0.7853 (mt0) cc_final: 0.7600 (mm-40) REVERT: B 60 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7953 (tt) REVERT: B 203 ASP cc_start: 0.7871 (p0) cc_final: 0.7658 (p0) REVERT: B 262 LYS cc_start: 0.8485 (mptt) cc_final: 0.8263 (mmtp) REVERT: B 331 ARG cc_start: 0.7582 (ttp80) cc_final: 0.7237 (ttp80) REVERT: B 344 GLN cc_start: 0.7796 (mt0) cc_final: 0.7569 (mm-40) REVERT: D 331 ARG cc_start: 0.7580 (ttp80) cc_final: 0.7096 (ttp80) REVERT: D 344 GLN cc_start: 0.7891 (mt0) cc_final: 0.7550 (mm-40) REVERT: C 344 GLN cc_start: 0.7865 (mt0) cc_final: 0.7537 (mm-40) outliers start: 39 outliers final: 31 residues processed: 252 average time/residue: 0.3502 time to fit residues: 121.7374 Evaluate side-chains 246 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 214 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16065 Z= 0.316 Angle : 0.534 6.766 21885 Z= 0.280 Chirality : 0.039 0.150 2375 Planarity : 0.005 0.054 2750 Dihedral : 3.968 16.796 2090 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.54 % Allowed : 14.75 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.19), residues: 1870 helix: 1.30 (0.15), residues: 1230 sheet: None (None), residues: 0 loop : -0.06 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 93 HIS 0.005 0.001 HIS D 178 PHE 0.025 0.002 PHE B 248 TYR 0.019 0.002 TYR E 97 ARG 0.008 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 217 time to evaluate : 1.603 Fit side-chains REVERT: A 331 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7290 (ttp80) REVERT: A 344 GLN cc_start: 0.7883 (mt0) cc_final: 0.7614 (mm-40) REVERT: B 60 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7986 (tt) REVERT: B 262 LYS cc_start: 0.8523 (mptt) cc_final: 0.8310 (mmtp) REVERT: B 331 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7203 (ttp80) REVERT: B 344 GLN cc_start: 0.7808 (mt0) cc_final: 0.7570 (mm-40) REVERT: D 344 GLN cc_start: 0.7872 (mt0) cc_final: 0.7528 (mm-40) REVERT: C 344 GLN cc_start: 0.7843 (mt0) cc_final: 0.7538 (mm-40) outliers start: 43 outliers final: 36 residues processed: 248 average time/residue: 0.3480 time to fit residues: 119.5130 Evaluate side-chains 250 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 213 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 100 optimal weight: 0.1980 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16065 Z= 0.152 Angle : 0.471 6.611 21885 Z= 0.246 Chirality : 0.035 0.143 2375 Planarity : 0.004 0.062 2750 Dihedral : 3.720 15.343 2090 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.59 % Allowed : 15.69 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 1870 helix: 1.46 (0.15), residues: 1230 sheet: None (None), residues: 0 loop : -0.06 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 93 HIS 0.002 0.001 HIS D 178 PHE 0.020 0.001 PHE D 62 TYR 0.011 0.001 TYR A 97 ARG 0.009 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 208 time to evaluate : 2.204 Fit side-chains REVERT: A 331 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7276 (ttp80) REVERT: B 60 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7899 (tt) REVERT: B 331 ARG cc_start: 0.7524 (ttp80) cc_final: 0.7249 (ttp80) REVERT: B 344 GLN cc_start: 0.7768 (mt0) cc_final: 0.7538 (mm-40) REVERT: D 344 GLN cc_start: 0.7875 (mt0) cc_final: 0.7525 (mm-40) REVERT: C 344 GLN cc_start: 0.7886 (mt0) cc_final: 0.7549 (mm-40) outliers start: 27 outliers final: 23 residues processed: 228 average time/residue: 0.3635 time to fit residues: 114.1909 Evaluate side-chains 227 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 116 optimal weight: 0.0040 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16065 Z= 0.231 Angle : 0.501 6.826 21885 Z= 0.261 Chirality : 0.037 0.148 2375 Planarity : 0.005 0.062 2750 Dihedral : 3.766 16.032 2090 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.89 % Allowed : 15.69 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.19), residues: 1870 helix: 1.41 (0.15), residues: 1230 sheet: None (None), residues: 0 loop : -0.06 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 93 HIS 0.003 0.001 HIS D 178 PHE 0.018 0.001 PHE D 62 TYR 0.016 0.001 TYR A 97 ARG 0.010 0.000 ARG A 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 203 time to evaluate : 1.730 Fit side-chains REVERT: A 331 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7277 (ttp80) REVERT: A 344 GLN cc_start: 0.7840 (mt0) cc_final: 0.7582 (mm-40) REVERT: B 60 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7917 (tt) REVERT: B 331 ARG cc_start: 0.7541 (ttp80) cc_final: 0.7215 (ttp80) REVERT: B 344 GLN cc_start: 0.7775 (mt0) cc_final: 0.7553 (mm-40) REVERT: D 344 GLN cc_start: 0.7887 (mt0) cc_final: 0.7533 (mm-40) REVERT: C 344 GLN cc_start: 0.7889 (mt0) cc_final: 0.7550 (mm-40) outliers start: 32 outliers final: 29 residues processed: 226 average time/residue: 0.3608 time to fit residues: 112.2855 Evaluate side-chains 230 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 61 optimal weight: 0.4980 chunk 150 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110751 restraints weight = 18165.713| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.93 r_work: 0.3091 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16065 Z= 0.156 Angle : 0.471 6.702 21885 Z= 0.245 Chirality : 0.035 0.144 2375 Planarity : 0.004 0.064 2750 Dihedral : 3.650 15.009 2090 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.71 % Allowed : 15.69 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.19), residues: 1870 helix: 1.50 (0.15), residues: 1230 sheet: None (None), residues: 0 loop : -0.07 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.002 0.001 HIS D 178 PHE 0.018 0.001 PHE D 62 TYR 0.029 0.001 TYR B 97 ARG 0.010 0.000 ARG A 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3371.48 seconds wall clock time: 61 minutes 47.60 seconds (3707.60 seconds total)