Starting phenix.real_space_refine on Mon Apr 15 21:57:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr5_40720/04_2024/8sr5_40720.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr5_40720/04_2024/8sr5_40720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr5_40720/04_2024/8sr5_40720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr5_40720/04_2024/8sr5_40720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr5_40720/04_2024/8sr5_40720.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr5_40720/04_2024/8sr5_40720.pdb" } resolution = 3.22 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17727 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Cu 6 5.60 5 S 87 5.16 5 C 12246 2.51 5 N 3042 2.21 5 O 3207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 276": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 172": "OE1" <-> "OE2" Residue "J PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18588 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "C" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain breaks: 3 Chain: "G" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain breaks: 3 Chain: "K" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain breaks: 3 Chain: "F" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.55, per 1000 atoms: 0.51 Number of scatterers: 18588 At special positions: 0 Unit cell: (106.349, 104.762, 119.577, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 6 28.99 S 87 16.00 O 3207 8.00 N 3042 7.00 C 12246 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: 6.97 Conformation dependent library (CDL) restraints added in 3.4 seconds 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 49.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 184 through 206 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 257 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.969A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 45 Processing helix chain 'B' and resid 45 through 51 removed outlier: 4.024A pdb=" N ASP B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TRP B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 69 through 84 removed outlier: 3.913A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 107 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 140 through 165 removed outlier: 4.251A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 211 through 239 removed outlier: 3.736A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 206 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 231 through 257 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.969A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 184 through 206 Processing helix chain 'I' and resid 212 through 221 Processing helix chain 'I' and resid 231 through 257 Processing helix chain 'I' and resid 337 through 339 No H-bonds generated for 'chain 'I' and resid 337 through 339' Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'I' and resid 376 through 381 removed outlier: 3.970A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.991A pdb=" N LEU C 51 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 114 Processing helix chain 'C' and resid 123 through 150 removed outlier: 3.805A pdb=" N THR C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.579A pdb=" N ASP C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 199 Processing helix chain 'C' and resid 208 through 220 Proline residue: C 217 - end of helix Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.527A pdb=" N TRP C 253 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'G' and resid 48 through 52 removed outlier: 3.991A pdb=" N LEU G 51 " --> pdb=" O LYS G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 114 Processing helix chain 'G' and resid 123 through 150 removed outlier: 3.806A pdb=" N THR G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS G 134 " --> pdb=" O ARG G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 159 removed outlier: 3.579A pdb=" N ASP G 156 " --> pdb=" O PHE G 152 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 199 Processing helix chain 'G' and resid 208 through 220 Proline residue: G 217 - end of helix Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.528A pdb=" N TRP G 253 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 256 No H-bonds generated for 'chain 'G' and resid 254 through 256' Processing helix chain 'G' and resid 257 through 270 Processing helix chain 'K' and resid 48 through 52 removed outlier: 3.990A pdb=" N LEU K 51 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 114 Processing helix chain 'K' and resid 123 through 150 removed outlier: 3.806A pdb=" N THR K 133 " --> pdb=" O ARG K 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS K 134 " --> pdb=" O ARG K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 159 removed outlier: 3.580A pdb=" N ASP K 156 " --> pdb=" O PHE K 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY K 157 " --> pdb=" O THR K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 199 Processing helix chain 'K' and resid 208 through 220 Proline residue: K 217 - end of helix Processing helix chain 'K' and resid 248 through 253 removed outlier: 3.527A pdb=" N TRP K 253 " --> pdb=" O VAL K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 256 No H-bonds generated for 'chain 'K' and resid 254 through 256' Processing helix chain 'K' and resid 257 through 270 Processing helix chain 'F' and resid 10 through 45 Processing helix chain 'F' and resid 45 through 51 removed outlier: 4.024A pdb=" N ASP F 49 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 69 Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 69 through 84 removed outlier: 3.913A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 107 Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 140 through 165 removed outlier: 4.252A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET F 150 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Proline residue: F 162 - end of helix Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 180 through 188 Processing helix chain 'F' and resid 211 through 239 removed outlier: 3.737A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 45 Processing helix chain 'J' and resid 45 through 51 removed outlier: 4.024A pdb=" N ASP J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 69 Proline residue: J 65 - end of helix Processing helix chain 'J' and resid 69 through 84 removed outlier: 3.913A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 107 Processing helix chain 'J' and resid 115 through 120 Processing helix chain 'J' and resid 124 through 137 Processing helix chain 'J' and resid 140 through 165 removed outlier: 4.251A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET J 150 " --> pdb=" O ILE J 146 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Proline residue: J 158 - end of helix Proline residue: J 162 - end of helix Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 211 through 239 removed outlier: 3.736A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.188A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 108 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 348 removed outlier: 5.552A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 301 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 342 removed outlier: 6.551A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA8, first strand: chain 'B' and resid 243 through 244 Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.188A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AB2, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AB3, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB4, first strand: chain 'E' and resid 346 through 348 removed outlier: 5.551A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS E 301 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 341 through 342 removed outlier: 6.552A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.188A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 58 through 60 Processing sheet with id=AB8, first strand: chain 'I' and resid 87 through 88 Processing sheet with id=AB9, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AC1, first strand: chain 'I' and resid 346 through 348 removed outlier: 5.552A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS I 301 " --> pdb=" O ASP I 288 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 341 through 342 removed outlier: 6.552A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 206 through 207 Processing sheet with id=AC4, first strand: chain 'K' and resid 206 through 207 Processing sheet with id=AC5, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AC6, first strand: chain 'J' and resid 170 through 173 927 hydrogen bonds defined for protein. 2691 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: 5.80 Time building geometry restraints manager: 7.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 3 1.20 - 1.35: 5673 1.35 - 1.50: 6240 1.50 - 1.66: 7089 1.66 - 1.81: 168 Bond restraints: 19173 Sorted by residual: bond pdb=" C LEU F 244 " pdb=" N GLN F 245 " ideal model delta sigma weight residual 1.334 1.045 0.290 1.52e-02 4.33e+03 3.63e+02 bond pdb=" C LEU J 244 " pdb=" N GLN J 245 " ideal model delta sigma weight residual 1.334 1.045 0.289 1.52e-02 4.33e+03 3.62e+02 bond pdb=" C LEU B 244 " pdb=" N GLN B 245 " ideal model delta sigma weight residual 1.334 1.045 0.289 1.52e-02 4.33e+03 3.62e+02 bond pdb=" C GLN F 245 " pdb=" N SER F 246 " ideal model delta sigma weight residual 1.335 1.261 0.074 1.35e-02 5.49e+03 3.01e+01 bond pdb=" C GLN B 245 " pdb=" N SER B 246 " ideal model delta sigma weight residual 1.335 1.261 0.074 1.35e-02 5.49e+03 2.99e+01 ... (remaining 19168 not shown) Histogram of bond angle deviations from ideal: 99.25 - 111.20: 8146 111.20 - 123.14: 16772 123.14 - 135.09: 1218 135.09 - 147.04: 0 147.04 - 158.99: 3 Bond angle restraints: 26139 Sorted by residual: angle pdb=" C LEU F 244 " pdb=" N GLN F 245 " pdb=" CA GLN F 245 " ideal model delta sigma weight residual 122.24 158.99 -36.75 1.57e+00 4.06e-01 5.48e+02 angle pdb=" C LEU B 244 " pdb=" N GLN B 245 " pdb=" CA GLN B 245 " ideal model delta sigma weight residual 122.24 158.96 -36.72 1.57e+00 4.06e-01 5.47e+02 angle pdb=" C LEU J 244 " pdb=" N GLN J 245 " pdb=" CA GLN J 245 " ideal model delta sigma weight residual 122.24 158.93 -36.69 1.57e+00 4.06e-01 5.46e+02 angle pdb=" O LEU F 244 " pdb=" C LEU F 244 " pdb=" N GLN F 245 " ideal model delta sigma weight residual 122.86 107.44 15.42 1.18e+00 7.18e-01 1.71e+02 angle pdb=" O LEU B 244 " pdb=" C LEU B 244 " pdb=" N GLN B 245 " ideal model delta sigma weight residual 122.86 107.47 15.39 1.18e+00 7.18e-01 1.70e+02 ... (remaining 26134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 9852 17.23 - 34.47: 879 34.47 - 51.70: 168 51.70 - 68.94: 18 68.94 - 86.17: 9 Dihedral angle restraints: 10926 sinusoidal: 4278 harmonic: 6648 Sorted by residual: dihedral pdb=" CA MET J 45 " pdb=" C MET J 45 " pdb=" N GLY J 46 " pdb=" CA GLY J 46 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA MET F 45 " pdb=" C MET F 45 " pdb=" N GLY F 46 " pdb=" CA GLY F 46 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA MET B 45 " pdb=" C MET B 45 " pdb=" N GLY B 46 " pdb=" CA GLY B 46 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 10923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2013 0.042 - 0.083: 568 0.083 - 0.125: 230 0.125 - 0.167: 24 0.167 - 0.208: 6 Chirality restraints: 2841 Sorted by residual: chirality pdb=" CA HIS E 137 " pdb=" N HIS E 137 " pdb=" C HIS E 137 " pdb=" CB HIS E 137 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA HIS A 137 " pdb=" N HIS A 137 " pdb=" C HIS A 137 " pdb=" CB HIS A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA HIS I 137 " pdb=" N HIS I 137 " pdb=" C HIS I 137 " pdb=" CB HIS I 137 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2838 not shown) Planarity restraints: 3240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " 0.038 2.00e-02 2.50e+03 2.91e-02 1.70e+01 pdb=" CG TYR F 37 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 37 " 0.038 2.00e-02 2.50e+03 2.91e-02 1.70e+01 pdb=" CG TYR B 37 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR B 37 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 37 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 37 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 37 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 37 " 0.039 2.00e-02 2.50e+03 2.90e-02 1.69e+01 pdb=" CG TYR J 37 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR J 37 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR J 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR J 37 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR J 37 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR J 37 " 0.004 2.00e-02 2.50e+03 ... (remaining 3237 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 203 2.54 - 3.13: 14735 3.13 - 3.72: 30349 3.72 - 4.31: 42922 4.31 - 4.90: 71654 Nonbonded interactions: 159863 Sorted by model distance: nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.949 2.320 nonbonded pdb=" ND1 HIS E 33 " pdb="CU CU E 501 " model vdw 1.950 2.320 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 501 " model vdw 1.951 2.320 nonbonded pdb=" ND1 HIS A 48 " pdb="CU CU A 502 " model vdw 1.982 2.320 nonbonded pdb=" ND1 HIS I 48 " pdb="CU CU I 502 " model vdw 1.982 2.320 ... (remaining 159858 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } 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: 11.060 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.020 Extract box with map and model: 27.430 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 49.160 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.130 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 92.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 0.290 19173 Z= 0.369 Angle : 0.784 36.751 26139 Z= 0.471 Chirality : 0.045 0.208 2841 Planarity : 0.004 0.038 3240 Dihedral : 13.263 86.169 6672 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.85 % Favored : 93.76 % Rotamer: Outliers : 0.77 % Allowed : 0.67 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.25 (0.18), residues: 2274 helix: 0.94 (0.16), residues: 981 sheet: 0.73 (0.35), residues: 246 loop : -0.67 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 206 HIS 0.004 0.001 HIS I 139 PHE 0.013 0.001 PHE J 50 TYR 0.070 0.002 TYR B 37 ARG 0.006 0.001 ARG K 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 389 time to evaluate : 2.231 Fit side-chains REVERT: A 137 HIS cc_start: 0.6408 (OUTLIER) cc_final: 0.5974 (m170) REVERT: A 237 MET cc_start: 0.7828 (mtm) cc_final: 0.7541 (mtp) REVERT: A 368 ASP cc_start: 0.8396 (t70) cc_final: 0.8131 (t0) REVERT: A 375 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7211 (mtp-110) REVERT: B 113 TYR cc_start: 0.7869 (m-80) cc_final: 0.7518 (m-80) REVERT: B 199 MET cc_start: 0.6549 (mtm) cc_final: 0.6254 (mtm) REVERT: E 237 MET cc_start: 0.7804 (mtm) cc_final: 0.7498 (mtp) REVERT: E 251 MET cc_start: 0.7541 (ttp) cc_final: 0.7299 (ttt) REVERT: E 368 ASP cc_start: 0.8412 (t70) cc_final: 0.8119 (t0) REVERT: E 375 ARG cc_start: 0.7480 (mtp85) cc_final: 0.7178 (mtp-110) REVERT: I 117 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7530 (mm-30) REVERT: I 137 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.6029 (m170) REVERT: I 237 MET cc_start: 0.7836 (mtm) cc_final: 0.7506 (mtp) REVERT: I 251 MET cc_start: 0.7538 (ttp) cc_final: 0.7302 (ttt) REVERT: I 285 LYS cc_start: 0.8370 (tmmt) cc_final: 0.7878 (tttp) REVERT: I 316 GLU cc_start: 0.8370 (tt0) cc_final: 0.8155 (tt0) REVERT: I 368 ASP cc_start: 0.8431 (t70) cc_final: 0.8208 (t0) REVERT: I 375 ARG cc_start: 0.7452 (mtp85) cc_final: 0.7166 (mtp-110) REVERT: F 113 TYR cc_start: 0.7902 (m-80) cc_final: 0.7535 (m-80) REVERT: F 199 MET cc_start: 0.6562 (mtm) cc_final: 0.6254 (mtm) REVERT: J 199 MET cc_start: 0.6645 (mtm) cc_final: 0.6338 (mtm) REVERT: J 242 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7791 (mtp85) outliers start: 15 outliers final: 1 residues processed: 401 average time/residue: 0.3645 time to fit residues: 210.9640 Evaluate side-chains 276 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 273 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain I residue 137 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 0.0270 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 HIS ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19173 Z= 0.266 Angle : 0.583 7.774 26139 Z= 0.304 Chirality : 0.044 0.163 2841 Planarity : 0.004 0.037 3240 Dihedral : 4.875 52.842 2526 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.99 % Rotamer: Outliers : 1.28 % Allowed : 8.21 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.33 (0.18), residues: 2274 helix: 1.07 (0.16), residues: 990 sheet: -0.26 (0.29), residues: 348 loop : -0.40 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 206 HIS 0.006 0.001 HIS E 139 PHE 0.012 0.001 PHE J 31 TYR 0.037 0.002 TYR B 37 ARG 0.004 0.000 ARG K 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 293 time to evaluate : 2.158 Fit side-chains REVERT: A 137 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6635 (m170) REVERT: A 237 MET cc_start: 0.7873 (mtm) cc_final: 0.7618 (mtt) REVERT: A 358 GLU cc_start: 0.8251 (tt0) cc_final: 0.7807 (tt0) REVERT: A 375 ARG cc_start: 0.7576 (mtp85) cc_final: 0.7205 (mtp-110) REVERT: B 113 TYR cc_start: 0.7926 (m-80) cc_final: 0.7530 (m-80) REVERT: B 199 MET cc_start: 0.6538 (mtm) cc_final: 0.6085 (mtm) REVERT: E 137 HIS cc_start: 0.6887 (OUTLIER) cc_final: 0.6607 (m170) REVERT: E 163 MET cc_start: 0.8518 (ttt) cc_final: 0.8277 (ttt) REVERT: E 239 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.6801 (t80) REVERT: E 251 MET cc_start: 0.7751 (ttp) cc_final: 0.7539 (ttt) REVERT: E 368 ASP cc_start: 0.8454 (t70) cc_final: 0.8123 (t0) REVERT: E 375 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7199 (mtp-110) REVERT: I 137 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.6449 (m170) REVERT: I 237 MET cc_start: 0.7900 (mtm) cc_final: 0.7530 (mtp) REVERT: I 239 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.6839 (t80) REVERT: I 251 MET cc_start: 0.7774 (ttp) cc_final: 0.7447 (ttt) REVERT: I 285 LYS cc_start: 0.8442 (tmmt) cc_final: 0.7899 (tttp) REVERT: I 316 GLU cc_start: 0.8383 (tt0) cc_final: 0.8045 (tt0) REVERT: I 368 ASP cc_start: 0.8531 (t70) cc_final: 0.8256 (t0) REVERT: I 375 ARG cc_start: 0.7546 (mtp85) cc_final: 0.7240 (mtp-110) REVERT: C 114 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8113 (p) REVERT: C 263 THR cc_start: 0.8788 (t) cc_final: 0.8359 (m) REVERT: G 114 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.8026 (p) REVERT: K 114 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8067 (p) REVERT: K 198 ARG cc_start: 0.8162 (mmt90) cc_final: 0.7708 (mmt90) REVERT: F 113 TYR cc_start: 0.7918 (m-80) cc_final: 0.7505 (m-80) REVERT: F 199 MET cc_start: 0.6522 (mtm) cc_final: 0.6177 (mtm) REVERT: J 199 MET cc_start: 0.6656 (mtm) cc_final: 0.6334 (mtm) outliers start: 25 outliers final: 10 residues processed: 311 average time/residue: 0.3282 time to fit residues: 153.2035 Evaluate side-chains 291 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 273 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 172 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 224 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 166 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19173 Z= 0.190 Angle : 0.542 8.130 26139 Z= 0.281 Chirality : 0.043 0.156 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.760 51.862 2526 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.25 % Rotamer: Outliers : 0.87 % Allowed : 10.41 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2274 helix: 1.24 (0.16), residues: 990 sheet: -0.16 (0.29), residues: 348 loop : -0.40 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 206 HIS 0.004 0.001 HIS J 11 PHE 0.011 0.001 PHE A 71 TYR 0.024 0.002 TYR J 37 ARG 0.005 0.000 ARG F 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 273 time to evaluate : 1.563 Fit side-chains REVERT: A 137 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6605 (m170) REVERT: A 237 MET cc_start: 0.7862 (mtm) cc_final: 0.7610 (mtt) REVERT: A 375 ARG cc_start: 0.7564 (mtp85) cc_final: 0.7184 (mtp-110) REVERT: B 24 MET cc_start: 0.8279 (mtp) cc_final: 0.8054 (mtm) REVERT: B 113 TYR cc_start: 0.7882 (m-80) cc_final: 0.7479 (m-80) REVERT: B 199 MET cc_start: 0.6416 (mtm) cc_final: 0.6102 (mtm) REVERT: E 137 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6674 (m170) REVERT: E 237 MET cc_start: 0.7790 (mtm) cc_final: 0.7556 (mtt) REVERT: E 239 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.6768 (t80) REVERT: E 251 MET cc_start: 0.7742 (ttp) cc_final: 0.7537 (ttt) REVERT: E 368 ASP cc_start: 0.8358 (t70) cc_final: 0.8052 (t0) REVERT: I 137 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.6556 (m170) REVERT: I 237 MET cc_start: 0.7889 (mtm) cc_final: 0.7520 (mtp) REVERT: I 239 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.6727 (t80) REVERT: I 251 MET cc_start: 0.7753 (ttp) cc_final: 0.7435 (ttt) REVERT: I 285 LYS cc_start: 0.8472 (tmmt) cc_final: 0.7868 (tttp) REVERT: I 316 GLU cc_start: 0.8350 (tt0) cc_final: 0.7980 (tt0) REVERT: I 375 ARG cc_start: 0.7523 (mtp85) cc_final: 0.7219 (mtp-110) REVERT: K 198 ARG cc_start: 0.8133 (mmt90) cc_final: 0.7883 (mmt90) REVERT: F 113 TYR cc_start: 0.7879 (m-80) cc_final: 0.7497 (m-80) REVERT: F 199 MET cc_start: 0.6484 (mtm) cc_final: 0.6115 (mtm) REVERT: J 93 VAL cc_start: 0.8101 (t) cc_final: 0.7794 (m) REVERT: J 199 MET cc_start: 0.6629 (mtm) cc_final: 0.6263 (mtm) REVERT: J 241 GLU cc_start: 0.8748 (mp0) cc_final: 0.8545 (mp0) outliers start: 17 outliers final: 9 residues processed: 286 average time/residue: 0.3090 time to fit residues: 134.6893 Evaluate side-chains 282 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 268 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 0.3980 chunk 22 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 208 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN B 245 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19173 Z= 0.261 Angle : 0.561 9.053 26139 Z= 0.292 Chirality : 0.044 0.152 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.793 52.182 2526 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.15 % Favored : 94.72 % Rotamer: Outliers : 1.64 % Allowed : 10.97 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2274 helix: 1.22 (0.16), residues: 990 sheet: -0.16 (0.28), residues: 348 loop : -0.39 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.005 0.001 HIS J 11 PHE 0.014 0.001 PHE J 31 TYR 0.025 0.002 TYR C 210 ARG 0.006 0.000 ARG F 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 267 time to evaluate : 1.884 Fit side-chains REVERT: A 137 HIS cc_start: 0.6932 (OUTLIER) cc_final: 0.6719 (m170) REVERT: A 237 MET cc_start: 0.7883 (mtm) cc_final: 0.7603 (mtt) REVERT: A 368 ASP cc_start: 0.8576 (t0) cc_final: 0.8358 (t0) REVERT: A 375 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7244 (mtp-110) REVERT: B 199 MET cc_start: 0.6520 (mtm) cc_final: 0.6202 (mtm) REVERT: E 137 HIS cc_start: 0.6937 (OUTLIER) cc_final: 0.6709 (m170) REVERT: E 251 MET cc_start: 0.7877 (ttp) cc_final: 0.7630 (ttt) REVERT: E 252 SER cc_start: 0.8137 (t) cc_final: 0.7935 (m) REVERT: E 368 ASP cc_start: 0.8373 (t70) cc_final: 0.8081 (t0) REVERT: I 137 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.6642 (m170) REVERT: I 237 MET cc_start: 0.7889 (mtm) cc_final: 0.7482 (mtp) REVERT: I 251 MET cc_start: 0.7910 (ttp) cc_final: 0.7529 (ttt) REVERT: I 252 SER cc_start: 0.8143 (t) cc_final: 0.7939 (m) REVERT: I 285 LYS cc_start: 0.8539 (tmmt) cc_final: 0.7870 (tttp) REVERT: I 316 GLU cc_start: 0.8401 (tt0) cc_final: 0.8032 (tt0) REVERT: I 368 ASP cc_start: 0.8562 (t0) cc_final: 0.8335 (t0) REVERT: I 375 ARG cc_start: 0.7556 (mtp85) cc_final: 0.7216 (mtp-110) REVERT: C 114 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7971 (p) REVERT: G 114 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7894 (p) REVERT: K 114 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7889 (p) REVERT: K 198 ARG cc_start: 0.8110 (mmt90) cc_final: 0.7512 (mmt90) REVERT: F 24 MET cc_start: 0.8208 (mtp) cc_final: 0.7997 (mtm) REVERT: F 113 TYR cc_start: 0.7934 (m-80) cc_final: 0.7503 (m-80) REVERT: F 199 MET cc_start: 0.6586 (mtm) cc_final: 0.6177 (mtm) REVERT: J 199 MET cc_start: 0.6712 (mtm) cc_final: 0.6284 (mtm) outliers start: 32 outliers final: 20 residues processed: 289 average time/residue: 0.3202 time to fit residues: 141.1306 Evaluate side-chains 285 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 259 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19173 Z= 0.288 Angle : 0.566 9.886 26139 Z= 0.293 Chirality : 0.044 0.156 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.853 52.540 2526 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 1.79 % Allowed : 11.95 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.39 (0.18), residues: 2274 helix: 1.22 (0.16), residues: 990 sheet: -0.16 (0.29), residues: 327 loop : -0.53 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.005 0.001 HIS J 11 PHE 0.016 0.001 PHE J 31 TYR 0.030 0.002 TYR K 210 ARG 0.009 0.000 ARG F 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 260 time to evaluate : 2.189 Fit side-chains REVERT: A 137 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6842 (m170) REVERT: A 237 MET cc_start: 0.7879 (mtm) cc_final: 0.7594 (mtt) REVERT: A 368 ASP cc_start: 0.8580 (t0) cc_final: 0.8299 (t0) REVERT: A 375 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7203 (mtp-110) REVERT: B 199 MET cc_start: 0.6593 (mtm) cc_final: 0.6209 (mtm) REVERT: E 137 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6814 (m170) REVERT: E 237 MET cc_start: 0.7829 (mtm) cc_final: 0.7370 (mtt) REVERT: E 251 MET cc_start: 0.8010 (ttp) cc_final: 0.7716 (ttt) REVERT: E 368 ASP cc_start: 0.8388 (t70) cc_final: 0.8113 (t0) REVERT: I 137 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6823 (m170) REVERT: I 237 MET cc_start: 0.7880 (mtm) cc_final: 0.7466 (mtp) REVERT: I 251 MET cc_start: 0.8042 (ttp) cc_final: 0.7606 (ttt) REVERT: I 252 SER cc_start: 0.8182 (t) cc_final: 0.7962 (m) REVERT: I 285 LYS cc_start: 0.8560 (tmmt) cc_final: 0.7965 (tttp) REVERT: I 316 GLU cc_start: 0.8402 (tt0) cc_final: 0.8010 (tt0) REVERT: I 368 ASP cc_start: 0.8580 (t0) cc_final: 0.8249 (t0) REVERT: I 375 ARG cc_start: 0.7539 (mtp85) cc_final: 0.7186 (mtp-110) REVERT: G 114 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7921 (p) REVERT: K 114 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7957 (p) REVERT: K 198 ARG cc_start: 0.8087 (mmt90) cc_final: 0.7476 (mmt90) REVERT: F 24 MET cc_start: 0.8307 (mtp) cc_final: 0.8091 (mtm) REVERT: F 113 TYR cc_start: 0.7974 (m-80) cc_final: 0.7561 (m-80) REVERT: J 47 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7315 (t0) REVERT: J 199 MET cc_start: 0.6772 (mtm) cc_final: 0.6303 (mtm) outliers start: 35 outliers final: 24 residues processed: 284 average time/residue: 0.3199 time to fit residues: 138.6093 Evaluate side-chains 280 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 250 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 274 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 239 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19173 Z= 0.199 Angle : 0.530 11.068 26139 Z= 0.273 Chirality : 0.043 0.160 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.751 51.415 2526 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.19 % Favored : 94.68 % Rotamer: Outliers : 1.54 % Allowed : 13.59 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2274 helix: 1.32 (0.16), residues: 990 sheet: -0.20 (0.29), residues: 327 loop : -0.49 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 237 HIS 0.004 0.001 HIS J 11 PHE 0.018 0.001 PHE F 31 TYR 0.022 0.001 TYR G 184 ARG 0.006 0.000 ARG F 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 254 time to evaluate : 1.852 Fit side-chains REVERT: A 237 MET cc_start: 0.7873 (mtm) cc_final: 0.7587 (mtt) REVERT: A 368 ASP cc_start: 0.8533 (t0) cc_final: 0.8250 (t0) REVERT: A 375 ARG cc_start: 0.7538 (mtp85) cc_final: 0.7193 (mtp-110) REVERT: B 199 MET cc_start: 0.6583 (mtm) cc_final: 0.6194 (mtm) REVERT: E 237 MET cc_start: 0.7826 (mtm) cc_final: 0.7392 (mtt) REVERT: E 251 MET cc_start: 0.7977 (ttp) cc_final: 0.7676 (ttt) REVERT: E 368 ASP cc_start: 0.8324 (t70) cc_final: 0.8080 (t0) REVERT: I 137 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.6908 (m170) REVERT: I 237 MET cc_start: 0.7857 (mtm) cc_final: 0.7493 (mtp) REVERT: I 251 MET cc_start: 0.7995 (ttp) cc_final: 0.7550 (ttt) REVERT: I 285 LYS cc_start: 0.8567 (tmmt) cc_final: 0.7992 (tttp) REVERT: I 368 ASP cc_start: 0.8531 (t0) cc_final: 0.8238 (t0) REVERT: I 375 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7157 (mtp-110) REVERT: G 114 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7876 (p) REVERT: K 198 ARG cc_start: 0.8104 (mmt90) cc_final: 0.7670 (mmt90) REVERT: F 24 MET cc_start: 0.8273 (mtp) cc_final: 0.8069 (mtm) REVERT: F 113 TYR cc_start: 0.7930 (m-80) cc_final: 0.7512 (m-80) REVERT: F 176 MET cc_start: 0.8467 (mtm) cc_final: 0.8250 (mtm) REVERT: F 197 ILE cc_start: 0.4506 (OUTLIER) cc_final: 0.4160 (mt) REVERT: J 47 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7240 (t0) REVERT: J 199 MET cc_start: 0.6696 (mtm) cc_final: 0.6190 (mtm) outliers start: 30 outliers final: 20 residues processed: 278 average time/residue: 0.3199 time to fit residues: 135.1751 Evaluate side-chains 273 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 249 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 124 optimal weight: 0.0980 chunk 185 optimal weight: 0.0170 chunk 123 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19173 Z= 0.158 Angle : 0.515 11.797 26139 Z= 0.264 Chirality : 0.042 0.158 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.535 50.775 2524 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.66 % Favored : 95.21 % Rotamer: Outliers : 1.90 % Allowed : 13.69 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.56 (0.18), residues: 2274 helix: 1.42 (0.16), residues: 987 sheet: -0.18 (0.29), residues: 327 loop : -0.46 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 237 HIS 0.003 0.001 HIS J 11 PHE 0.012 0.001 PHE F 31 TYR 0.022 0.001 TYR C 184 ARG 0.003 0.000 ARG I 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 257 time to evaluate : 2.152 Fit side-chains REVERT: A 237 MET cc_start: 0.7851 (mtm) cc_final: 0.7576 (mtt) REVERT: A 368 ASP cc_start: 0.8474 (t0) cc_final: 0.8227 (t0) REVERT: A 375 ARG cc_start: 0.7483 (mtp85) cc_final: 0.7131 (mtp-110) REVERT: B 47 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7068 (t0) REVERT: B 93 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7828 (m) REVERT: B 199 MET cc_start: 0.6564 (mtm) cc_final: 0.6143 (mtm) REVERT: E 237 MET cc_start: 0.7799 (mtm) cc_final: 0.7380 (mtt) REVERT: E 239 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.6855 (t80) REVERT: E 251 MET cc_start: 0.7875 (ttp) cc_final: 0.7584 (ttt) REVERT: I 237 MET cc_start: 0.7836 (mtm) cc_final: 0.7475 (mtp) REVERT: I 239 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.6788 (t80) REVERT: I 251 MET cc_start: 0.7924 (ttp) cc_final: 0.7509 (ttt) REVERT: I 285 LYS cc_start: 0.8542 (tmmt) cc_final: 0.7891 (tttp) REVERT: I 316 GLU cc_start: 0.8433 (tt0) cc_final: 0.7995 (tt0) REVERT: I 368 ASP cc_start: 0.8477 (t0) cc_final: 0.8205 (t0) REVERT: I 375 ARG cc_start: 0.7490 (mtp85) cc_final: 0.7125 (mtp-110) REVERT: G 114 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7839 (p) REVERT: K 198 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7592 (mmt90) REVERT: F 24 MET cc_start: 0.8239 (mtp) cc_final: 0.8037 (mtm) REVERT: F 113 TYR cc_start: 0.7878 (m-80) cc_final: 0.7463 (m-80) REVERT: J 47 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7158 (t0) outliers start: 37 outliers final: 20 residues processed: 283 average time/residue: 0.3120 time to fit residues: 135.1356 Evaluate side-chains 274 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 248 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 210 TYR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 47 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 139 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19173 Z= 0.274 Angle : 0.555 12.173 26139 Z= 0.285 Chirality : 0.044 0.158 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.529 52.422 2522 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 1.90 % Allowed : 13.69 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2274 helix: 1.34 (0.16), residues: 987 sheet: -0.01 (0.30), residues: 309 loop : -0.59 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 237 HIS 0.005 0.001 HIS J 11 PHE 0.015 0.001 PHE J 31 TYR 0.024 0.002 TYR G 210 ARG 0.005 0.000 ARG F 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 242 time to evaluate : 2.255 Fit side-chains REVERT: A 237 MET cc_start: 0.7861 (mtm) cc_final: 0.7577 (mtt) REVERT: A 368 ASP cc_start: 0.8533 (t0) cc_final: 0.8261 (t0) REVERT: A 375 ARG cc_start: 0.7532 (mtp85) cc_final: 0.7104 (mtp85) REVERT: B 199 MET cc_start: 0.6694 (mtm) cc_final: 0.6414 (mtm) REVERT: E 237 MET cc_start: 0.7806 (mtm) cc_final: 0.7373 (mtt) REVERT: E 251 MET cc_start: 0.8022 (ttp) cc_final: 0.7725 (ttt) REVERT: I 237 MET cc_start: 0.7861 (mtm) cc_final: 0.7485 (mtp) REVERT: I 251 MET cc_start: 0.8064 (ttp) cc_final: 0.7610 (ttt) REVERT: I 285 LYS cc_start: 0.8566 (tmmt) cc_final: 0.7987 (tttp) REVERT: I 368 ASP cc_start: 0.8541 (t0) cc_final: 0.8230 (t0) REVERT: I 375 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7152 (mtp-110) REVERT: G 198 ARG cc_start: 0.8260 (mmt90) cc_final: 0.7787 (mmt90) REVERT: K 198 ARG cc_start: 0.8035 (mmt90) cc_final: 0.7634 (mmt90) REVERT: F 24 MET cc_start: 0.8304 (mtp) cc_final: 0.8084 (mtm) REVERT: F 113 TYR cc_start: 0.7956 (m-80) cc_final: 0.7513 (m-80) REVERT: J 199 MET cc_start: 0.6891 (mtm) cc_final: 0.6504 (mtm) outliers start: 37 outliers final: 29 residues processed: 271 average time/residue: 0.3248 time to fit residues: 133.6123 Evaluate side-chains 270 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 241 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 210 TYR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain K residue 274 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 239 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 134 optimal weight: 0.0270 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19173 Z= 0.210 Angle : 0.535 12.853 26139 Z= 0.273 Chirality : 0.043 0.159 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.500 51.878 2522 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 1.59 % Allowed : 14.15 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 2274 helix: 1.39 (0.16), residues: 987 sheet: -0.24 (0.29), residues: 327 loop : -0.51 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 237 HIS 0.004 0.001 HIS J 11 PHE 0.013 0.001 PHE F 31 TYR 0.022 0.001 TYR C 184 ARG 0.005 0.000 ARG F 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 246 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.7850 (mtm) cc_final: 0.7578 (mtt) REVERT: A 368 ASP cc_start: 0.8513 (t0) cc_final: 0.8238 (t0) REVERT: A 375 ARG cc_start: 0.7472 (mtp85) cc_final: 0.7048 (mtp85) REVERT: B 199 MET cc_start: 0.6666 (mtm) cc_final: 0.6372 (mtm) REVERT: E 237 MET cc_start: 0.7808 (mtm) cc_final: 0.7386 (mtt) REVERT: E 251 MET cc_start: 0.8004 (ttp) cc_final: 0.7697 (ttt) REVERT: I 237 MET cc_start: 0.7831 (mtm) cc_final: 0.7473 (mtp) REVERT: I 251 MET cc_start: 0.8040 (ttp) cc_final: 0.7584 (ttt) REVERT: I 285 LYS cc_start: 0.8558 (tmmt) cc_final: 0.7984 (tttp) REVERT: I 368 ASP cc_start: 0.8523 (t0) cc_final: 0.8222 (t0) REVERT: I 375 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7116 (mmm160) REVERT: K 126 GLU cc_start: 0.8290 (tp30) cc_final: 0.7897 (tp30) REVERT: K 198 ARG cc_start: 0.8002 (mmt90) cc_final: 0.7612 (mmt90) REVERT: F 24 MET cc_start: 0.8301 (mtp) cc_final: 0.8085 (mtm) REVERT: F 113 TYR cc_start: 0.7938 (m-80) cc_final: 0.7511 (m-80) REVERT: J 199 MET cc_start: 0.6773 (mtm) cc_final: 0.6391 (mtm) outliers start: 31 outliers final: 28 residues processed: 271 average time/residue: 0.3321 time to fit residues: 136.2007 Evaluate side-chains 269 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 241 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 210 TYR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain K residue 274 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 209 optimal weight: 0.4980 chunk 180 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19173 Z= 0.196 Angle : 0.533 13.621 26139 Z= 0.271 Chirality : 0.042 0.158 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.451 52.005 2522 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 1.38 % Allowed : 14.15 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.56 (0.18), residues: 2274 helix: 1.44 (0.16), residues: 987 sheet: -0.22 (0.29), residues: 321 loop : -0.48 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 237 HIS 0.004 0.001 HIS J 11 PHE 0.013 0.001 PHE J 31 TYR 0.022 0.001 TYR C 184 ARG 0.006 0.000 ARG F 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 245 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.7878 (mtm) cc_final: 0.7566 (mtt) REVERT: A 368 ASP cc_start: 0.8504 (t0) cc_final: 0.8231 (t0) REVERT: A 375 ARG cc_start: 0.7452 (mtp85) cc_final: 0.7089 (mmm160) REVERT: B 199 MET cc_start: 0.6675 (mtm) cc_final: 0.6362 (mtm) REVERT: E 251 MET cc_start: 0.7985 (ttp) cc_final: 0.7684 (ttt) REVERT: I 237 MET cc_start: 0.7835 (mtm) cc_final: 0.7471 (mtp) REVERT: I 251 MET cc_start: 0.8015 (ttp) cc_final: 0.7556 (ttt) REVERT: I 285 LYS cc_start: 0.8557 (tmmt) cc_final: 0.7994 (tttp) REVERT: I 368 ASP cc_start: 0.8510 (t0) cc_final: 0.8210 (t0) REVERT: I 375 ARG cc_start: 0.7486 (mtp85) cc_final: 0.7107 (mmm160) REVERT: G 126 GLU cc_start: 0.8253 (tp30) cc_final: 0.8034 (tp30) REVERT: G 198 ARG cc_start: 0.8194 (mmt90) cc_final: 0.7950 (mmt90) REVERT: K 126 GLU cc_start: 0.8285 (tp30) cc_final: 0.7862 (tp30) REVERT: K 198 ARG cc_start: 0.7991 (mmt90) cc_final: 0.7596 (mmt90) REVERT: F 24 MET cc_start: 0.8288 (mtp) cc_final: 0.8074 (mtm) REVERT: F 113 TYR cc_start: 0.7929 (m-80) cc_final: 0.7509 (m-80) outliers start: 27 outliers final: 26 residues processed: 268 average time/residue: 0.3271 time to fit residues: 132.2888 Evaluate side-chains 268 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 242 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 210 TYR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111965 restraints weight = 23294.505| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.95 r_work: 0.2881 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19173 Z= 0.212 Angle : 0.540 13.986 26139 Z= 0.274 Chirality : 0.043 0.158 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.476 52.365 2522 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.97 % Favored : 94.99 % Rotamer: Outliers : 1.59 % Allowed : 14.05 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.57 (0.18), residues: 2274 helix: 1.47 (0.16), residues: 987 sheet: -0.23 (0.29), residues: 324 loop : -0.49 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 237 HIS 0.004 0.001 HIS J 11 PHE 0.013 0.001 PHE J 31 TYR 0.022 0.001 TYR C 184 ARG 0.006 0.000 ARG F 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4520.43 seconds wall clock time: 83 minutes 15.81 seconds (4995.81 seconds total)