Starting phenix.real_space_refine on Mon Mar 11 13:01:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdo_34676/03_2024/8hdo_34676_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdo_34676/03_2024/8hdo_34676.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdo_34676/03_2024/8hdo_34676_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdo_34676/03_2024/8hdo_34676_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdo_34676/03_2024/8hdo_34676_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdo_34676/03_2024/8hdo_34676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdo_34676/03_2024/8hdo_34676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdo_34676/03_2024/8hdo_34676_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdo_34676/03_2024/8hdo_34676_neut_updated.pdb" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5314 2.51 5 N 1410 2.21 5 O 1498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "R GLU 4": "OE1" <-> "OE2" Residue "R ASP 7": "OD1" <-> "OD2" Residue "R ASP 74": "OD1" <-> "OD2" Residue "R PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 174": "OE1" <-> "OE2" Residue "R PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8277 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1952 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2562 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 432 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2358 Unusual residues: {'CLR': 7, 'I5D': 1} Classifications: {'peptide': 276, 'undetermined': 8} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 264, None: 8} Not linked: pdbres="LEU R 309 " pdbres="CLR R 401 " Not linked: pdbres="CLR R 401 " pdbres="CLR R 402 " Not linked: pdbres="CLR R 402 " pdbres="CLR R 403 " Not linked: pdbres="CLR R 403 " pdbres="CLR R 404 " Not linked: pdbres="CLR R 404 " pdbres="CLR R 405 " ... (remaining 3 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 4.88, per 1000 atoms: 0.59 Number of scatterers: 8277 At special positions: 0 Unit cell: (90.4, 77.6, 129.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1498 8.00 N 1410 7.00 C 5314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 171 " distance=2.03 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: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 11 sheets defined 38.9% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.757A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 185 through 203 removed outlier: 3.665A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.806A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 22 removed outlier: 3.570A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'N' and resid 109 through 111 No H-bonds generated for 'chain 'N' and resid 109 through 111' Processing helix chain 'R' and resid 5 through 34 removed outlier: 3.777A pdb=" N LEU R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL R 28 " --> pdb=" O GLY R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 58 removed outlier: 4.471A pdb=" N PHE R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 68 Processing helix chain 'R' and resid 75 through 108 removed outlier: 3.921A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 116 removed outlier: 4.754A pdb=" N LYS R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER R 115 " --> pdb=" O LEU R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 137 Processing helix chain 'R' and resid 139 through 142 No H-bonds generated for 'chain 'R' and resid 139 through 142' Processing helix chain 'R' and resid 173 through 176 No H-bonds generated for 'chain 'R' and resid 173 through 176' Processing helix chain 'R' and resid 179 through 183 Processing helix chain 'R' and resid 187 through 190 No H-bonds generated for 'chain 'R' and resid 187 through 190' Processing helix chain 'R' and resid 192 through 214 Processing helix chain 'R' and resid 225 through 258 removed outlier: 4.279A pdb=" N ILE R 239 " --> pdb=" O SER R 235 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE R 242 " --> pdb=" O MET R 238 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 271 through 290 removed outlier: 3.723A pdb=" N ASN R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER R 283 " --> pdb=" O SER R 279 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 295 through 308 Processing sheet with id= A, first strand: chain 'A' and resid 212 through 215 removed outlier: 3.862A pdb=" N TYR A 212 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASN A 80 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU A 43 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS A 82 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU A 45 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE A 84 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N GLY A 47 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL A 86 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.947A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.067A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.822A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.615A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.567A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.662A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 336 through 339 Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.800A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 Processing sheet with id= K, first strand: chain 'N' and resid 93 through 98 removed outlier: 3.748A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1059 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: 2.19 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1316 1.27 - 1.41: 2117 1.41 - 1.55: 4945 1.55 - 1.69: 4 1.69 - 1.83: 77 Bond restraints: 8459 Sorted by residual: bond pdb=" C17 I5D R 408 " pdb=" C4' I5D R 408 " ideal model delta sigma weight residual 1.391 1.539 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C11 I5D R 408 " pdb=" C16 I5D R 408 " ideal model delta sigma weight residual 1.391 1.537 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" C10 I5D R 408 " pdb=" C5' I5D R 408 " ideal model delta sigma weight residual 1.391 1.536 -0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" C10 I5D R 408 " pdb=" C11 I5D R 408 " ideal model delta sigma weight residual 1.391 1.326 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C4' I5D R 408 " pdb=" C5' I5D R 408 " ideal model delta sigma weight residual 1.390 1.326 0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 8454 not shown) Histogram of bond angle deviations from ideal: 59.88 - 83.81: 3 83.81 - 107.75: 291 107.75 - 131.69: 11198 131.69 - 155.63: 18 155.63 - 179.56: 2 Bond angle restraints: 11512 Sorted by residual: angle pdb=" C GLN R 260 " pdb=" N PRO R 261 " pdb=" CA PRO R 261 " ideal model delta sigma weight residual 119.84 114.73 5.11 1.25e+00 6.40e-01 1.67e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 122.61 127.59 -4.98 1.56e+00 4.11e-01 1.02e+01 angle pdb=" N VAL R 256 " pdb=" CA VAL R 256 " pdb=" C VAL R 256 " ideal model delta sigma weight residual 113.07 109.44 3.63 1.36e+00 5.41e-01 7.14e+00 angle pdb=" N9 I5D R 408 " pdb=" C8 I5D R 408 " pdb=" NAA I5D R 408 " ideal model delta sigma weight residual 112.13 120.05 -7.92 3.00e+00 1.11e-01 6.96e+00 angle pdb=" C GLN R 260 " pdb=" N PRO R 261 " pdb=" CD PRO R 261 " ideal model delta sigma weight residual 125.00 135.82 -10.82 4.10e+00 5.95e-02 6.96e+00 ... (remaining 11507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.13: 5121 29.13 - 58.26: 209 58.26 - 87.39: 18 87.39 - 116.52: 1 116.52 - 145.65: 1 Dihedral angle restraints: 5350 sinusoidal: 2355 harmonic: 2995 Sorted by residual: dihedral pdb=" N1 I5D R 408 " pdb=" C5 I5D R 408 " pdb=" C6 I5D R 408 " pdb=" S1 I5D R 408 " ideal model delta sinusoidal sigma weight residual 172.38 26.73 145.65 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CB GLU G 58 " pdb=" CG GLU G 58 " pdb=" CD GLU G 58 " pdb=" OE1 GLU G 58 " ideal model delta sinusoidal sigma weight residual 0.00 -87.65 87.65 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASP N 73 " pdb=" CB ASP N 73 " pdb=" CG ASP N 73 " pdb=" OD1 ASP N 73 " ideal model delta sinusoidal sigma weight residual -30.00 -84.90 54.90 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 5347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1054 0.047 - 0.094: 198 0.094 - 0.141: 64 0.141 - 0.188: 6 0.188 - 0.235: 7 Chirality restraints: 1329 Sorted by residual: chirality pdb=" C13 CLR R 404 " pdb=" C12 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C17 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C13 CLR R 403 " pdb=" C12 CLR R 403 " pdb=" C14 CLR R 403 " pdb=" C17 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.71 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1326 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 248 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO R 249 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 249 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 249 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 192 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO R 193 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 193 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 193 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C THR B 87 " -0.024 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.008 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 113 2.64 - 3.20: 7286 3.20 - 3.77: 13207 3.77 - 4.33: 18341 4.33 - 4.90: 30023 Nonbonded interactions: 68970 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.069 2.440 nonbonded pdb=" CD1 LEU R 96 " pdb=" OH TYR R 290 " model vdw 2.134 3.460 nonbonded pdb=" O VAL R 253 " pdb=" OG1 THR R 257 " model vdw 2.244 2.440 nonbonded pdb=" O ILE R 136 " pdb=" OH TYR R 181 " model vdw 2.262 2.440 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.274 2.440 ... (remaining 68965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 7.260 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.490 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 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 0.148 8459 Z= 0.269 Angle : 0.612 10.818 11512 Z= 0.315 Chirality : 0.044 0.235 1329 Planarity : 0.003 0.039 1424 Dihedral : 14.133 145.646 3407 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.12 % Allowed : 22.47 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.24), residues: 1008 helix: -0.07 (0.24), residues: 392 sheet: -0.88 (0.31), residues: 217 loop : -1.56 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.002 0.000 HIS B 142 PHE 0.008 0.001 PHE B 199 TYR 0.008 0.001 TYR N 95 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 0.970 Fit side-chains REVERT: G 21 MET cc_start: 0.7485 (mpt) cc_final: 0.7200 (mpt) REVERT: N 77 ASN cc_start: 0.7797 (m-40) cc_final: 0.7547 (m-40) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 1.1274 time to fit residues: 212.6277 Evaluate side-chains 95 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 0.0770 chunk 42 optimal weight: 0.1980 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 0.1980 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 59 GLN A 82 HIS A 89 GLN A 214 HIS A 239 HIS A 242 GLN B 44 GLN B 75 GLN B 155 ASN B 293 ASN B 340 ASN G 18 GLN N 13 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 251 HIS R 273 ASN R 286 ASN R 294 ASN R 302 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8459 Z= 0.137 Angle : 0.463 6.654 11512 Z= 0.234 Chirality : 0.039 0.130 1329 Planarity : 0.003 0.036 1424 Dihedral : 7.697 115.712 1580 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.46 % Allowed : 26.84 % Favored : 69.70 % 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: -0.01 (0.26), residues: 1008 helix: 1.25 (0.26), residues: 401 sheet: -0.56 (0.30), residues: 236 loop : -0.91 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 247 HIS 0.007 0.001 HIS R 302 PHE 0.009 0.001 PHE B 199 TYR 0.013 0.001 TYR R 299 ARG 0.007 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 1.107 Fit side-chains REVERT: B 259 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8095 (pt0) REVERT: G 21 MET cc_start: 0.7371 (mpt) cc_final: 0.6942 (mmm) REVERT: N 77 ASN cc_start: 0.7801 (m-40) cc_final: 0.7588 (m-40) REVERT: N 80 TYR cc_start: 0.7804 (m-80) cc_final: 0.7541 (m-80) REVERT: N 85 SER cc_start: 0.6962 (OUTLIER) cc_final: 0.6730 (p) outliers start: 30 outliers final: 13 residues processed: 126 average time/residue: 1.0554 time to fit residues: 142.7707 Evaluate side-chains 109 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 340 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 254 ASN R 302 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8459 Z= 0.196 Angle : 0.497 6.323 11512 Z= 0.253 Chirality : 0.040 0.152 1329 Planarity : 0.004 0.040 1424 Dihedral : 7.260 115.465 1580 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.57 % Allowed : 27.19 % Favored : 69.24 % 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: 0.24 (0.26), residues: 1008 helix: 1.38 (0.26), residues: 413 sheet: -0.43 (0.32), residues: 218 loop : -0.75 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 247 HIS 0.006 0.002 HIS B 142 PHE 0.013 0.001 PHE B 292 TYR 0.020 0.001 TYR R 202 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 0.934 Fit side-chains REVERT: B 308 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8256 (mt) REVERT: G 14 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6482 (ttmt) REVERT: G 21 MET cc_start: 0.7380 (mpt) cc_final: 0.7076 (mpt) REVERT: N 60 TYR cc_start: 0.8862 (m-80) cc_final: 0.8480 (m-80) REVERT: N 77 ASN cc_start: 0.7965 (m-40) cc_final: 0.7699 (m-40) REVERT: N 80 TYR cc_start: 0.7923 (m-80) cc_final: 0.7620 (m-80) REVERT: N 117 TYR cc_start: 0.7979 (m-80) cc_final: 0.7735 (m-80) outliers start: 31 outliers final: 16 residues processed: 130 average time/residue: 1.0702 time to fit residues: 149.5860 Evaluate side-chains 113 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 89 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 131 ASN B 75 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 302 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8459 Z= 0.223 Angle : 0.507 11.193 11512 Z= 0.256 Chirality : 0.041 0.141 1329 Planarity : 0.004 0.040 1424 Dihedral : 7.273 116.079 1580 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.49 % Allowed : 27.07 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1008 helix: 1.50 (0.26), residues: 414 sheet: -0.29 (0.32), residues: 222 loop : -0.51 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS R 302 PHE 0.013 0.001 PHE B 292 TYR 0.017 0.001 TYR R 202 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 104 time to evaluate : 0.876 Fit side-chains REVERT: A 208 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7112 (mtm-85) REVERT: B 304 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7321 (mtp180) REVERT: G 14 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6479 (ttmt) REVERT: G 21 MET cc_start: 0.7329 (mpt) cc_final: 0.7065 (mpt) REVERT: N 103 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7778 (p90) outliers start: 39 outliers final: 22 residues processed: 131 average time/residue: 1.1080 time to fit residues: 156.1845 Evaluate side-chains 126 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 141 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8459 Z= 0.253 Angle : 0.522 10.076 11512 Z= 0.265 Chirality : 0.041 0.160 1329 Planarity : 0.004 0.042 1424 Dihedral : 7.381 120.305 1580 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.18 % Allowed : 26.38 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1008 helix: 1.46 (0.26), residues: 415 sheet: -0.35 (0.32), residues: 222 loop : -0.37 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 247 HIS 0.005 0.001 HIS A 239 PHE 0.015 0.001 PHE B 292 TYR 0.020 0.001 TYR R 202 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 103 time to evaluate : 0.840 Fit side-chains REVERT: A 208 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7207 (mtm-85) REVERT: G 14 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6505 (ttmt) REVERT: G 21 MET cc_start: 0.7314 (mpt) cc_final: 0.7042 (mpt) outliers start: 45 outliers final: 26 residues processed: 130 average time/residue: 1.0143 time to fit residues: 141.9437 Evaluate side-chains 123 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 141 PHE Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 6.9990 chunk 19 optimal weight: 0.0970 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.0270 chunk 94 optimal weight: 0.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8459 Z= 0.139 Angle : 0.464 8.389 11512 Z= 0.235 Chirality : 0.039 0.146 1329 Planarity : 0.003 0.039 1424 Dihedral : 7.101 118.136 1580 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.15 % Allowed : 27.65 % Favored : 68.20 % 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: 0.89 (0.27), residues: 1008 helix: 1.81 (0.26), residues: 406 sheet: -0.18 (0.31), residues: 232 loop : -0.15 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS B 142 PHE 0.009 0.001 PHE B 151 TYR 0.013 0.001 TYR R 202 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 0.896 Fit side-chains REVERT: A 136 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8750 (t) REVERT: A 208 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7129 (mtm-85) REVERT: G 21 MET cc_start: 0.7328 (mpt) cc_final: 0.7054 (mpt) REVERT: N 77 ASN cc_start: 0.8041 (m-40) cc_final: 0.7823 (m-40) REVERT: N 80 TYR cc_start: 0.7979 (m-80) cc_final: 0.7623 (m-80) outliers start: 36 outliers final: 24 residues processed: 128 average time/residue: 1.0179 time to fit residues: 140.3324 Evaluate side-chains 122 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 141 PHE Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8459 Z= 0.161 Angle : 0.478 9.591 11512 Z= 0.241 Chirality : 0.039 0.162 1329 Planarity : 0.003 0.038 1424 Dihedral : 7.128 134.629 1580 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.15 % Allowed : 27.53 % Favored : 68.32 % 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: 0.91 (0.27), residues: 1008 helix: 1.85 (0.26), residues: 408 sheet: -0.14 (0.32), residues: 226 loop : -0.20 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 96 HIS 0.004 0.001 HIS B 142 PHE 0.010 0.001 PHE B 151 TYR 0.014 0.001 TYR R 202 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 0.926 Fit side-chains REVERT: A 136 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8779 (t) REVERT: A 208 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7141 (mtm-85) REVERT: G 14 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6557 (ttmt) REVERT: G 21 MET cc_start: 0.7330 (mpt) cc_final: 0.7059 (mpt) REVERT: G 50 LEU cc_start: 0.8104 (mm) cc_final: 0.7840 (mp) REVERT: N 80 TYR cc_start: 0.7974 (m-80) cc_final: 0.7645 (m-80) outliers start: 36 outliers final: 23 residues processed: 123 average time/residue: 1.0198 time to fit residues: 134.9968 Evaluate side-chains 124 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 141 PHE Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 6 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8459 Z= 0.251 Angle : 0.537 10.496 11512 Z= 0.270 Chirality : 0.041 0.181 1329 Planarity : 0.003 0.039 1424 Dihedral : 7.368 135.395 1580 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.61 % Allowed : 27.07 % Favored : 68.32 % 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: 0.85 (0.27), residues: 1008 helix: 1.77 (0.26), residues: 408 sheet: -0.23 (0.32), residues: 212 loop : -0.18 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 239 PHE 0.014 0.001 PHE B 292 TYR 0.018 0.001 TYR R 202 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 103 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7204 (mtm-85) REVERT: G 14 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6532 (ttmt) REVERT: G 21 MET cc_start: 0.7302 (mpt) cc_final: 0.7060 (mpt) outliers start: 40 outliers final: 28 residues processed: 129 average time/residue: 1.0858 time to fit residues: 151.2261 Evaluate side-chains 127 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 97 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 141 PHE Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 54 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8459 Z= 0.153 Angle : 0.487 9.232 11512 Z= 0.247 Chirality : 0.039 0.156 1329 Planarity : 0.003 0.039 1424 Dihedral : 7.212 135.027 1580 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.57 % Allowed : 28.11 % Favored : 68.32 % 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: 0.90 (0.27), residues: 1008 helix: 1.88 (0.26), residues: 408 sheet: -0.18 (0.32), residues: 220 loop : -0.25 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS B 142 PHE 0.010 0.001 PHE B 151 TYR 0.012 0.001 TYR R 202 ARG 0.008 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 0.975 Fit side-chains REVERT: A 136 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8755 (t) REVERT: A 208 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7161 (mtm-85) REVERT: G 14 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6571 (ttmt) REVERT: G 21 MET cc_start: 0.7305 (mpt) cc_final: 0.7068 (mpt) REVERT: N 80 TYR cc_start: 0.8019 (m-80) cc_final: 0.7762 (m-80) outliers start: 31 outliers final: 22 residues processed: 122 average time/residue: 1.0506 time to fit residues: 137.7825 Evaluate side-chains 123 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 141 PHE Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8459 Z= 0.303 Angle : 0.574 11.103 11512 Z= 0.289 Chirality : 0.042 0.183 1329 Planarity : 0.004 0.041 1424 Dihedral : 7.671 139.459 1580 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.92 % Allowed : 27.65 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 1008 helix: 1.71 (0.26), residues: 408 sheet: -0.29 (0.33), residues: 215 loop : -0.21 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.017 0.002 PHE B 292 TYR 0.019 0.002 TYR R 202 ARG 0.007 0.000 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7602 (mmmm) REVERT: A 208 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7225 (mtm-85) REVERT: G 14 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6587 (ttmt) REVERT: G 21 MET cc_start: 0.7334 (mpt) cc_final: 0.7104 (mpt) REVERT: N 106 ASP cc_start: 0.7723 (p0) cc_final: 0.7417 (p0) outliers start: 34 outliers final: 22 residues processed: 120 average time/residue: 1.1273 time to fit residues: 144.8767 Evaluate side-chains 121 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 141 PHE Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.142976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106166 restraints weight = 9724.348| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.16 r_work: 0.3268 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 8459 Z= 0.286 Angle : 0.930 59.176 11512 Z= 0.540 Chirality : 0.043 0.368 1329 Planarity : 0.004 0.041 1424 Dihedral : 7.667 139.420 1580 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.00 % Allowed : 28.92 % Favored : 68.09 % Cbeta Deviations : 0.10 % 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: 0.75 (0.27), residues: 1008 helix: 1.68 (0.26), residues: 408 sheet: -0.24 (0.33), residues: 214 loop : -0.24 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.016 0.001 PHE B 292 TYR 0.018 0.001 TYR R 202 ARG 0.006 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3347.78 seconds wall clock time: 60 minutes 23.38 seconds (3623.38 seconds total)