Starting phenix.real_space_refine on Sat Dec 16 19:04:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr5_40720/12_2023/8sr5_40720.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr5_40720/12_2023/8sr5_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_40720/12_2023/8sr5_40720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr5_40720/12_2023/8sr5_40720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr5_40720/12_2023/8sr5_40720.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr5_40720/12_2023/8sr5_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-1.21rc1-5172/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: 9.80, per 1000 atoms: 0.53 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: 7.50 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: 1.77 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: 5.91 Time building geometry restraints manager: 7.88 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: 11.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 27.960 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 53.510 Find NCS groups from input model: 1.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.460 ------------------------------------------------------------------------------- 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 : 2.098 Fit side-chains outliers start: 15 outliers final: 1 residues processed: 401 average time/residue: 0.3678 time to fit residues: 213.7447 Evaluate side-chains 269 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 1.978 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1965 time to fit residues: 3.0894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 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: 0.7980 chunk 133 optimal weight: 0.0980 chunk 207 optimal weight: 1.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1458 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= 0.189 Angle : 0.563 7.903 26139 Z= 0.292 Chirality : 0.043 0.161 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.445 23.331 2520 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.99 % Rotamer: Outliers : 1.18 % Allowed : 7.74 % Favored : 91.08 % 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: 0.45 (0.18), residues: 2274 helix: 1.17 (0.16), residues: 993 sheet: -0.09 (0.29), residues: 342 loop : -0.39 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 206 HIS 0.007 0.001 HIS E 137 PHE 0.013 0.001 PHE J 27 TYR 0.033 0.002 TYR J 37 ARG 0.006 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 308 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 285 time to evaluate : 2.038 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 303 average time/residue: 0.3129 time to fit residues: 144.2267 Evaluate side-chains 275 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 264 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2338 time to fit residues: 7.2757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 224 optimal weight: 0.0270 chunk 184 optimal weight: 0.6980 chunk 205 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.4842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN B 245 GLN 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** F 187 ASN ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN J 245 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19173 Z= 0.325 Angle : 0.596 8.685 26139 Z= 0.310 Chirality : 0.045 0.163 2841 Planarity : 0.004 0.037 3240 Dihedral : 4.532 22.105 2520 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.97 % Favored : 94.90 % Rotamer: Outliers : 0.72 % Allowed : 10.31 % Favored : 88.97 % 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: 1.12 (0.16), residues: 990 sheet: -0.25 (0.29), residues: 348 loop : -0.47 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 206 HIS 0.008 0.002 HIS E 137 PHE 0.015 0.001 PHE J 31 TYR 0.034 0.002 TYR F 37 ARG 0.005 0.001 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 285 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 271 time to evaluate : 2.054 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 278 average time/residue: 0.3158 time to fit residues: 134.1849 Evaluate side-chains 257 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 253 time to evaluate : 2.007 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1667 time to fit residues: 3.9555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 208 optimal weight: 0.9990 chunk 220 optimal weight: 0.4980 chunk 108 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** 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: 0.7985 moved from start: 0.2334 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= 0.205 Angle : 0.544 8.688 26139 Z= 0.281 Chirality : 0.043 0.161 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.440 22.015 2520 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 0.92 % Allowed : 11.64 % Favored : 87.44 % 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: 0.42 (0.18), residues: 2274 helix: 1.26 (0.16), residues: 990 sheet: -0.11 (0.29), residues: 330 loop : -0.55 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.006 0.001 HIS F 11 PHE 0.021 0.001 PHE B 31 TYR 0.023 0.002 TYR G 184 ARG 0.005 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 276 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 258 time to evaluate : 1.985 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 272 average time/residue: 0.3118 time to fit residues: 130.9499 Evaluate side-chains 259 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 248 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1781 time to fit residues: 6.6788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 197 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 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 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 245 GLN E 108 GLN ** 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** F 184 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2508 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= 0.212 Angle : 0.543 9.817 26139 Z= 0.280 Chirality : 0.043 0.159 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.383 23.060 2520 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.07 % Rotamer: Outliers : 0.67 % Allowed : 13.49 % Favored : 85.85 % 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: 0.45 (0.18), residues: 2274 helix: 1.32 (0.16), residues: 987 sheet: -0.11 (0.29), residues: 330 loop : -0.56 (0.21), residues: 957 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 0.017 0.001 PHE B 31 TYR 0.023 0.002 TYR K 184 ARG 0.006 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 269 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 256 time to evaluate : 2.260 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 263 average time/residue: 0.3350 time to fit residues: 133.9421 Evaluate side-chains 252 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1757 time to fit residues: 4.6932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.2980 chunk 198 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 184 GLN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19173 Z= 0.196 Angle : 0.530 10.752 26139 Z= 0.273 Chirality : 0.043 0.159 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.334 21.305 2520 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.66 % Favored : 95.21 % Rotamer: Outliers : 0.82 % Allowed : 14.36 % Favored : 84.82 % 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: 1.36 (0.16), residues: 987 sheet: -0.11 (0.29), residues: 330 loop : -0.52 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 112 HIS 0.007 0.001 HIS E 137 PHE 0.014 0.001 PHE B 31 TYR 0.022 0.001 TYR C 184 ARG 0.007 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 262 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 246 time to evaluate : 1.996 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 258 average time/residue: 0.3062 time to fit residues: 122.0461 Evaluate side-chains 242 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 235 time to evaluate : 1.918 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1666 time to fit residues: 5.0302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 185 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 219 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 184 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19173 Z= 0.196 Angle : 0.532 11.463 26139 Z= 0.272 Chirality : 0.043 0.158 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.308 21.093 2520 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 0.72 % Allowed : 14.46 % Favored : 84.82 % 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: 0.54 (0.18), residues: 2274 helix: 1.40 (0.16), residues: 987 sheet: -0.14 (0.29), residues: 330 loop : -0.50 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 237 HIS 0.003 0.001 HIS J 11 PHE 0.013 0.001 PHE B 31 TYR 0.022 0.001 TYR C 184 ARG 0.004 0.000 ARG F 242 *********************** 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 267 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 253 time to evaluate : 2.066 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 264 average time/residue: 0.3427 time to fit residues: 135.9794 Evaluate side-chains 242 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 235 time to evaluate : 2.041 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1887 time to fit residues: 5.1925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 184 GLN ** 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** F 184 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19173 Z= 0.273 Angle : 0.570 13.023 26139 Z= 0.291 Chirality : 0.044 0.246 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.401 22.373 2520 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 0.72 % Allowed : 14.92 % 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: 0.38 (0.18), residues: 2274 helix: 1.27 (0.16), residues: 987 sheet: -0.34 (0.29), residues: 345 loop : -0.52 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 237 HIS 0.009 0.001 HIS E 137 PHE 0.015 0.001 PHE B 31 TYR 0.037 0.002 TYR G 210 ARG 0.007 0.000 ARG F 9 *********************** 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 258 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 244 time to evaluate : 2.025 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 252 average time/residue: 0.3281 time to fit residues: 126.0667 Evaluate side-chains 245 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 238 time to evaluate : 2.161 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1754 time to fit residues: 5.1256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 192 optimal weight: 0.5980 chunk 204 optimal weight: 0.0370 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19173 Z= 0.184 Angle : 0.538 13.709 26139 Z= 0.273 Chirality : 0.043 0.213 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.335 21.567 2520 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 0.31 % Allowed : 15.44 % 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: 0.47 (0.18), residues: 2274 helix: 1.39 (0.16), residues: 984 sheet: -0.36 (0.28), residues: 345 loop : -0.50 (0.21), residues: 945 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 B 31 TYR 0.027 0.001 TYR G 210 ARG 0.007 0.000 ARG F 9 *********************** 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 260 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 254 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 257 average time/residue: 0.3325 time to fit residues: 129.1125 Evaluate side-chains 251 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 248 time to evaluate : 1.976 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1946 time to fit residues: 3.7233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 209 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 184 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** J 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19173 Z= 0.270 Angle : 0.571 14.413 26139 Z= 0.289 Chirality : 0.044 0.218 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.400 20.809 2520 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 0.26 % Allowed : 16.00 % Favored : 83.74 % 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: 0.40 (0.18), residues: 2274 helix: 1.35 (0.16), residues: 984 sheet: -0.39 (0.28), residues: 348 loop : -0.56 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 237 HIS 0.005 0.001 HIS J 11 PHE 0.015 0.001 PHE B 31 TYR 0.033 0.002 TYR G 210 ARG 0.007 0.000 ARG F 9 ********************** 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 250 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 246 average time/residue: 0.3588 time to fit residues: 131.3362 Evaluate side-chains 246 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1998 time to fit residues: 3.7324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 181 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 159 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 184 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112780 restraints weight = 23129.820| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.94 r_work: 0.3038 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3046 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= 0.189 Angle : 0.545 15.008 26139 Z= 0.275 Chirality : 0.043 0.202 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.340 21.264 2520 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 0.15 % Allowed : 15.79 % Favored : 84.05 % 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: 1.43 (0.16), residues: 984 sheet: -0.38 (0.28), residues: 342 loop : -0.49 (0.21), residues: 948 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 B 31 TYR 0.027 0.001 TYR G 210 ARG 0.007 0.000 ARG F 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4422.66 seconds wall clock time: 81 minutes 29.22 seconds (4889.22 seconds total)