Starting phenix.real_space_refine on Mon Apr 8 01:30:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/04_2024/8sgp_40463_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/04_2024/8sgp_40463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/04_2024/8sgp_40463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/04_2024/8sgp_40463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/04_2024/8sgp_40463_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/04_2024/8sgp_40463_updated.pdb" } resolution = 2.69 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 72 5.16 5 C 7632 2.51 5 N 2080 2.21 5 O 2308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12100 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2972 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 370} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2972 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 370} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2972 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 370} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2972 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 370} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.84, per 1000 atoms: 0.57 Number of scatterers: 12100 At special positions: 0 Unit cell: (96.5835, 93.2815, 98.2345, 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) S 72 16.00 P 8 15.00 O 2308 8.00 N 2080 7.00 C 7632 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: 4.57 Conformation dependent library (CDL) restraints added in 2.3 seconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 12 sheets defined 57.4% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 43 through 70 removed outlier: 5.267A pdb=" N ILE A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Proline residue: A 62 - end of helix removed outlier: 4.467A pdb=" N ALA A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 83 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 102 through 115 Processing helix chain 'A' and resid 117 through 135 removed outlier: 4.119A pdb=" N ASN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 139 through 151 removed outlier: 4.133A pdb=" N ARG A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N MET A 149 " --> pdb=" O TYR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 269 through 303 removed outlier: 3.786A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 317 through 345 Processing helix chain 'A' and resid 351 through 376 removed outlier: 3.551A pdb=" N ASN A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 386 through 398 removed outlier: 4.221A pdb=" N LYS A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 removed outlier: 3.682A pdb=" N TYR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 70 removed outlier: 5.267A pdb=" N ILE B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Proline residue: B 62 - end of helix removed outlier: 4.468A pdb=" N ALA B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU B 66 " --> pdb=" O PRO B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 102 through 115 Processing helix chain 'B' and resid 117 through 135 removed outlier: 4.119A pdb=" N ASN B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Proline residue: B 132 - end of helix Processing helix chain 'B' and resid 139 through 151 removed outlier: 4.132A pdb=" N ARG B 148 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N MET B 149 " --> pdb=" O TYR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 269 through 303 removed outlier: 3.786A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Proline residue: B 282 - end of helix Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 317 through 345 Processing helix chain 'B' and resid 351 through 376 removed outlier: 3.551A pdb=" N ASN B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 381 No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 386 through 398 removed outlier: 4.221A pdb=" N LYS B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR B 397 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.682A pdb=" N TYR B 419 " --> pdb=" O HIS B 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 70 removed outlier: 5.268A pdb=" N ILE C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 4.467A pdb=" N ALA C 65 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU C 66 " --> pdb=" O PRO C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 102 through 115 Processing helix chain 'C' and resid 117 through 135 removed outlier: 4.119A pdb=" N ASN C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Proline residue: C 132 - end of helix Processing helix chain 'C' and resid 139 through 151 removed outlier: 4.133A pdb=" N ARG C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N MET C 149 " --> pdb=" O TYR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 269 through 303 removed outlier: 3.786A pdb=" N PHE C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS C 279 " --> pdb=" O GLY C 275 " (cutoff:3.500A) Proline residue: C 282 - end of helix Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 317 through 345 Processing helix chain 'C' and resid 351 through 376 removed outlier: 3.551A pdb=" N ASN C 366 " --> pdb=" O GLY C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 381 No H-bonds generated for 'chain 'C' and resid 378 through 381' Processing helix chain 'C' and resid 386 through 398 removed outlier: 4.221A pdb=" N LYS C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR C 397 " --> pdb=" O ASP C 393 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 419 removed outlier: 3.682A pdb=" N TYR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 70 removed outlier: 5.267A pdb=" N ILE D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Proline residue: D 62 - end of helix removed outlier: 4.467A pdb=" N ALA D 65 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU D 66 " --> pdb=" O PRO D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 83 Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 102 through 115 Processing helix chain 'D' and resid 117 through 135 removed outlier: 4.118A pdb=" N ASN D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Proline residue: D 132 - end of helix Processing helix chain 'D' and resid 139 through 151 removed outlier: 4.132A pdb=" N ARG D 148 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N MET D 149 " --> pdb=" O TYR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 269 through 303 removed outlier: 3.786A pdb=" N PHE D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP D 278 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS D 279 " --> pdb=" O GLY D 275 " (cutoff:3.500A) Proline residue: D 282 - end of helix Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 317 through 345 Processing helix chain 'D' and resid 351 through 376 removed outlier: 3.550A pdb=" N ASN D 366 " --> pdb=" O GLY D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 381 No H-bonds generated for 'chain 'D' and resid 378 through 381' Processing helix chain 'D' and resid 386 through 398 removed outlier: 4.221A pdb=" N LYS D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR D 397 " --> pdb=" O ASP D 393 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 419 removed outlier: 3.682A pdb=" N TYR D 419 " --> pdb=" O HIS D 415 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 156 through 159 removed outlier: 7.024A pdb=" N TRP A 200 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N CYS A 159 " --> pdb=" O TRP A 200 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE A 202 " --> pdb=" O CYS A 159 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 175 through 179 Processing sheet with id= C, first strand: chain 'A' and resid 187 through 189 Processing sheet with id= D, first strand: chain 'B' and resid 156 through 159 removed outlier: 7.024A pdb=" N TRP B 200 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N CYS B 159 " --> pdb=" O TRP B 200 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE B 202 " --> pdb=" O CYS B 159 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 175 through 179 Processing sheet with id= F, first strand: chain 'B' and resid 187 through 189 Processing sheet with id= G, first strand: chain 'C' and resid 156 through 159 removed outlier: 7.024A pdb=" N TRP C 200 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N CYS C 159 " --> pdb=" O TRP C 200 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE C 202 " --> pdb=" O CYS C 159 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 175 through 179 Processing sheet with id= I, first strand: chain 'C' and resid 187 through 189 Processing sheet with id= J, first strand: chain 'D' and resid 156 through 159 removed outlier: 7.024A pdb=" N TRP D 200 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N CYS D 159 " --> pdb=" O TRP D 200 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE D 202 " --> pdb=" O CYS D 159 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 175 through 179 Processing sheet with id= L, first strand: chain 'D' and resid 187 through 189 636 hydrogen bonds defined for protein. 1848 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4011 1.34 - 1.46: 2522 1.46 - 1.58: 5679 1.58 - 1.69: 8 1.69 - 1.81: 120 Bond restraints: 12340 Sorted by residual: bond pdb=" O3P FAD D 501 " pdb=" P FAD D 501 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" O3P FAD B 501 " pdb=" P FAD B 501 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3P FAD C 501 " pdb=" P FAD C 501 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O5B FAD C 501 " pdb=" PA FAD C 501 " ideal model delta sigma weight residual 1.634 1.569 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 12335 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.17: 354 107.17 - 113.88: 6734 113.88 - 120.58: 5157 120.58 - 127.28: 4331 127.28 - 133.98: 104 Bond angle restraints: 16680 Sorted by residual: angle pdb=" O1P FAD D 501 " pdb=" P FAD D 501 " pdb=" O2P FAD D 501 " ideal model delta sigma weight residual 122.50 115.35 7.15 3.00e+00 1.11e-01 5.68e+00 angle pdb=" O1P FAD C 501 " pdb=" P FAD C 501 " pdb=" O2P FAD C 501 " ideal model delta sigma weight residual 122.50 115.35 7.15 3.00e+00 1.11e-01 5.68e+00 angle pdb=" O1P FAD B 501 " pdb=" P FAD B 501 " pdb=" O2P FAD B 501 " ideal model delta sigma weight residual 122.50 115.36 7.14 3.00e+00 1.11e-01 5.66e+00 angle pdb=" O1P FAD A 501 " pdb=" P FAD A 501 " pdb=" O2P FAD A 501 " ideal model delta sigma weight residual 122.50 115.38 7.12 3.00e+00 1.11e-01 5.63e+00 angle pdb=" P FAD B 501 " pdb=" O3P FAD B 501 " pdb=" PA FAD B 501 " ideal model delta sigma weight residual 130.34 123.88 6.46 3.00e+00 1.11e-01 4.64e+00 ... (remaining 16675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.08: 7301 27.08 - 54.16: 143 54.16 - 81.24: 32 81.24 - 108.32: 0 108.32 - 135.40: 4 Dihedral angle restraints: 7480 sinusoidal: 3108 harmonic: 4372 Sorted by residual: dihedral pdb=" O5' FAD C 501 " pdb=" O3P FAD C 501 " pdb=" P FAD C 501 " pdb=" PA FAD C 501 " ideal model delta sinusoidal sigma weight residual 298.23 162.83 135.40 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" O5' FAD A 501 " pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " pdb=" PA FAD A 501 " ideal model delta sinusoidal sigma weight residual 298.23 162.85 135.38 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" O5' FAD B 501 " pdb=" O3P FAD B 501 " pdb=" P FAD B 501 " pdb=" PA FAD B 501 " ideal model delta sinusoidal sigma weight residual 298.23 162.85 135.38 1 3.00e+01 1.11e-03 1.83e+01 ... (remaining 7477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1217 0.033 - 0.066: 402 0.066 - 0.100: 120 0.100 - 0.133: 45 0.133 - 0.166: 4 Chirality restraints: 1788 Sorted by residual: chirality pdb=" C2B FAD D 501 " pdb=" C1B FAD D 501 " pdb=" C3B FAD D 501 " pdb=" O2B FAD D 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" C2B FAD A 501 " pdb=" C1B FAD A 501 " pdb=" C3B FAD A 501 " pdb=" O2B FAD A 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" C2B FAD B 501 " pdb=" C1B FAD B 501 " pdb=" C3B FAD B 501 " pdb=" O2B FAD B 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 1785 not shown) Planarity restraints: 2152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 281 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.23e+00 pdb=" N PRO D 282 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 282 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 282 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 281 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 282 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 281 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO C 282 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 282 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 282 " -0.016 5.00e-02 4.00e+02 ... (remaining 2149 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 384 2.72 - 3.26: 12166 3.26 - 3.81: 20427 3.81 - 4.35: 26460 4.35 - 4.90: 44266 Nonbonded interactions: 103703 Sorted by model distance: nonbonded pdb=" OH TYR A 419 " pdb=" OD1 ASP D 297 " model vdw 2.171 2.440 nonbonded pdb=" OH TYR B 419 " pdb=" OD1 ASP C 297 " model vdw 2.173 2.440 nonbonded pdb=" OD1 ASP B 297 " pdb=" OH TYR C 419 " model vdw 2.179 2.440 nonbonded pdb=" OD1 ASP A 297 " pdb=" OH TYR D 419 " model vdw 2.182 2.440 nonbonded pdb=" OE1 GLU D 110 " pdb=" OH TYR D 337 " model vdw 2.186 2.440 ... (remaining 103698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.520 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 35.280 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.004 0.079 12340 Z= 0.251 Angle : 0.506 7.151 16680 Z= 0.239 Chirality : 0.040 0.166 1788 Planarity : 0.003 0.028 2152 Dihedral : 11.583 135.399 4704 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.33 % Allowed : 6.64 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.21), residues: 1532 helix: 2.50 (0.17), residues: 812 sheet: 0.09 (0.38), residues: 180 loop : 0.27 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 342 HIS 0.001 0.000 HIS D 316 PHE 0.005 0.001 PHE C 321 TYR 0.016 0.001 TYR A 337 ARG 0.002 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.422 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 180 average time/residue: 1.6502 time to fit residues: 317.1999 Evaluate side-chains 92 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 194 ASN A 199 ASN A 261 ASN A 293 GLN A 317 GLN A 338 GLN A 398 GLN A 405 GLN B 45 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 194 ASN B 199 ASN B 261 ASN B 293 GLN B 317 GLN B 338 GLN B 398 GLN B 405 GLN C 45 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 194 ASN C 199 ASN C 261 ASN C 293 GLN C 317 GLN C 338 GLN C 398 GLN C 405 GLN D 45 GLN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN D 194 ASN D 199 ASN D 261 ASN D 293 GLN D 317 GLN D 338 GLN D 398 GLN D 405 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12340 Z= 0.223 Angle : 0.487 7.015 16680 Z= 0.245 Chirality : 0.041 0.162 1788 Planarity : 0.003 0.028 2152 Dihedral : 10.928 128.718 1860 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.74 % Allowed : 11.54 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.21), residues: 1532 helix: 2.47 (0.17), residues: 812 sheet: -0.42 (0.36), residues: 188 loop : 0.43 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 200 HIS 0.001 0.000 HIS B 316 PHE 0.011 0.001 PHE A 381 TYR 0.019 0.002 TYR A 337 ARG 0.002 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 86 time to evaluate : 1.430 Fit side-chains outliers start: 33 outliers final: 20 residues processed: 111 average time/residue: 1.4572 time to fit residues: 174.9927 Evaluate side-chains 97 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 335 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 0.0670 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12340 Z= 0.218 Angle : 0.465 6.095 16680 Z= 0.236 Chirality : 0.040 0.144 1788 Planarity : 0.003 0.028 2152 Dihedral : 10.667 121.528 1860 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.90 % Allowed : 9.22 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.21), residues: 1532 helix: 2.47 (0.17), residues: 812 sheet: -0.55 (0.35), residues: 188 loop : 0.47 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 191 HIS 0.001 0.000 HIS D 316 PHE 0.010 0.001 PHE D 381 TYR 0.018 0.002 TYR C 337 ARG 0.002 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 87 time to evaluate : 1.403 Fit side-chains REVERT: C 401 GLU cc_start: 0.6609 (tp30) cc_final: 0.6351 (mm-30) outliers start: 47 outliers final: 24 residues processed: 117 average time/residue: 1.5915 time to fit residues: 199.9839 Evaluate side-chains 105 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 131 optimal weight: 0.0040 chunk 39 optimal weight: 4.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12340 Z= 0.170 Angle : 0.446 5.717 16680 Z= 0.225 Chirality : 0.040 0.142 1788 Planarity : 0.003 0.027 2152 Dihedral : 10.164 114.234 1860 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.16 % Allowed : 10.47 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.21), residues: 1532 helix: 2.48 (0.17), residues: 816 sheet: -0.48 (0.35), residues: 188 loop : 0.49 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 191 HIS 0.001 0.000 HIS C 415 PHE 0.007 0.001 PHE D 381 TYR 0.016 0.001 TYR D 337 ARG 0.001 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 94 time to evaluate : 1.458 Fit side-chains REVERT: B 149 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.5697 (mmm) REVERT: C 149 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.5692 (mmm) REVERT: C 401 GLU cc_start: 0.6579 (tp30) cc_final: 0.6343 (mm-30) outliers start: 38 outliers final: 17 residues processed: 118 average time/residue: 1.6030 time to fit residues: 203.1798 Evaluate side-chains 110 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12340 Z= 0.352 Angle : 0.514 6.134 16680 Z= 0.262 Chirality : 0.042 0.135 1788 Planarity : 0.003 0.030 2152 Dihedral : 10.263 112.002 1860 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.41 % Allowed : 11.13 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.21), residues: 1532 helix: 2.33 (0.17), residues: 816 sheet: -0.47 (0.34), residues: 188 loop : 0.43 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 191 HIS 0.001 0.001 HIS D 316 PHE 0.011 0.001 PHE A 381 TYR 0.022 0.002 TYR A 337 ARG 0.002 0.000 ARG D 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 88 time to evaluate : 1.321 Fit side-chains REVERT: A 149 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.5793 (mmm) REVERT: A 325 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6158 (mt-10) REVERT: B 325 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6160 (mt-10) REVERT: C 325 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6143 (mt-10) REVERT: D 325 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6159 (mt-10) outliers start: 41 outliers final: 25 residues processed: 117 average time/residue: 1.5818 time to fit residues: 198.6465 Evaluate side-chains 113 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 147 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12340 Z= 0.193 Angle : 0.470 5.475 16680 Z= 0.235 Chirality : 0.040 0.137 1788 Planarity : 0.003 0.028 2152 Dihedral : 9.881 105.485 1860 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.49 % Allowed : 13.29 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.21), residues: 1532 helix: 2.42 (0.17), residues: 816 sheet: -0.45 (0.35), residues: 188 loop : 0.38 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 191 HIS 0.001 0.000 HIS D 415 PHE 0.007 0.001 PHE C 381 TYR 0.017 0.001 TYR A 337 ARG 0.001 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.449 Fit side-chains REVERT: C 401 GLU cc_start: 0.6645 (tp30) cc_final: 0.6392 (mm-30) outliers start: 30 outliers final: 24 residues processed: 105 average time/residue: 1.5712 time to fit residues: 178.0821 Evaluate side-chains 108 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 0.0270 chunk 146 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12340 Z= 0.144 Angle : 0.444 5.544 16680 Z= 0.221 Chirality : 0.039 0.136 1788 Planarity : 0.003 0.027 2152 Dihedral : 9.529 99.672 1860 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.74 % Allowed : 12.79 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.21), residues: 1532 helix: 2.53 (0.17), residues: 812 sheet: -0.14 (0.35), residues: 180 loop : 0.33 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 191 HIS 0.001 0.000 HIS C 415 PHE 0.006 0.001 PHE C 381 TYR 0.016 0.001 TYR B 337 ARG 0.001 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 1.432 Fit side-chains REVERT: C 401 GLU cc_start: 0.6599 (tp30) cc_final: 0.6355 (mm-30) outliers start: 33 outliers final: 25 residues processed: 117 average time/residue: 1.4264 time to fit residues: 181.4414 Evaluate side-chains 124 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.3980 chunk 87 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 chunk 13 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN C 88 ASN C 130 GLN C 407 GLN D 407 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 12340 Z= 0.109 Angle : 0.424 5.498 16680 Z= 0.210 Chirality : 0.038 0.132 1788 Planarity : 0.003 0.027 2152 Dihedral : 9.007 92.741 1860 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.91 % Allowed : 13.62 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.22), residues: 1532 helix: 2.63 (0.17), residues: 812 sheet: -0.05 (0.36), residues: 180 loop : 0.53 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 191 HIS 0.001 0.000 HIS D 415 PHE 0.004 0.001 PHE C 381 TYR 0.014 0.001 TYR B 337 ARG 0.001 0.000 ARG C 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 1.405 Fit side-chains REVERT: A 325 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5956 (mt-10) REVERT: B 325 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5954 (mt-10) REVERT: C 401 GLU cc_start: 0.6575 (tp30) cc_final: 0.6356 (mm-30) outliers start: 23 outliers final: 8 residues processed: 118 average time/residue: 1.4475 time to fit residues: 185.1027 Evaluate side-chains 109 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 82 optimal weight: 0.0060 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12340 Z= 0.152 Angle : 0.436 5.599 16680 Z= 0.216 Chirality : 0.039 0.133 1788 Planarity : 0.003 0.026 2152 Dihedral : 8.914 92.936 1860 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.08 % Allowed : 13.70 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.21), residues: 1532 helix: 2.62 (0.17), residues: 812 sheet: -0.06 (0.36), residues: 180 loop : 0.53 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 191 HIS 0.001 0.000 HIS A 415 PHE 0.006 0.001 PHE A 381 TYR 0.016 0.001 TYR C 337 ARG 0.001 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 1.307 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 113 average time/residue: 1.4303 time to fit residues: 175.0474 Evaluate side-chains 108 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 128 optimal weight: 6.9990 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 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12340 Z= 0.162 Angle : 0.453 5.587 16680 Z= 0.225 Chirality : 0.040 0.182 1788 Planarity : 0.003 0.027 2152 Dihedral : 8.860 92.408 1860 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.74 % Allowed : 13.70 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.21), residues: 1532 helix: 2.56 (0.17), residues: 812 sheet: -0.06 (0.36), residues: 180 loop : 0.44 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 191 HIS 0.001 0.000 HIS D 415 PHE 0.005 0.001 PHE A 381 TYR 0.016 0.001 TYR C 337 ARG 0.001 0.000 ARG C 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.434 Fit side-chains REVERT: C 325 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.6009 (mt-10) outliers start: 21 outliers final: 11 residues processed: 109 average time/residue: 1.5850 time to fit residues: 185.9524 Evaluate side-chains 104 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 0.0040 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.077567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.063703 restraints weight = 20549.610| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.31 r_work: 0.2564 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12340 Z= 0.165 Angle : 0.450 5.600 16680 Z= 0.224 Chirality : 0.039 0.177 1788 Planarity : 0.003 0.027 2152 Dihedral : 8.778 91.644 1860 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.24 % Allowed : 13.21 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.21), residues: 1532 helix: 2.56 (0.17), residues: 812 sheet: -0.08 (0.36), residues: 180 loop : 0.52 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 191 HIS 0.001 0.000 HIS D 415 PHE 0.006 0.001 PHE B 381 TYR 0.017 0.001 TYR D 337 ARG 0.001 0.000 ARG C 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4045.92 seconds wall clock time: 73 minutes 50.27 seconds (4430.27 seconds total)