Starting phenix.real_space_refine on Fri Feb 16 18:51:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni3_9376/02_2024/6ni3_9376_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni3_9376/02_2024/6ni3_9376.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni3_9376/02_2024/6ni3_9376_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni3_9376/02_2024/6ni3_9376_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni3_9376/02_2024/6ni3_9376_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni3_9376/02_2024/6ni3_9376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni3_9376/02_2024/6ni3_9376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni3_9376/02_2024/6ni3_9376_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni3_9376/02_2024/6ni3_9376_updated.pdb" } resolution = 3.8 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8114 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5164 2.51 5 N 1399 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8136 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1912 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2587 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2202 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'P0G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.77, per 1000 atoms: 0.59 Number of scatterers: 8136 At special positions: 0 Unit cell: (101.92, 122.72, 101.92, 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 1518 8.00 N 1399 7.00 C 5164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 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: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1962 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 10 sheets defined 40.1% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.578A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.788A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.000A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.581A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.605A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 22 removed outlier: 3.977A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 47 removed outlier: 5.581A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 60 removed outlier: 3.928A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 84 removed outlier: 3.502A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 96 Processing helix chain 'R' and resid 103 through 136 Processing helix chain 'R' and resid 138 through 144 removed outlier: 4.030A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 171 removed outlier: 4.971A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 180 through 186 Processing helix chain 'R' and resid 197 through 207 removed outlier: 3.592A pdb=" N ALA R 202 " --> pdb=" O ALA R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 236 Processing helix chain 'R' and resid 266 through 298 removed outlier: 4.119A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.711A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 326 removed outlier: 3.695A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 339 removed outlier: 3.563A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) 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 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.295A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.949A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.564A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.779A 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: 7.027A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.754A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.807A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 306 through 308 removed outlier: 3.957A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 7.025A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 4.058A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.501A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1119 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: 2.49 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1883 1.33 - 1.45: 2038 1.45 - 1.58: 4300 1.58 - 1.70: 2 1.70 - 1.83: 76 Bond restraints: 8299 Sorted by residual: bond pdb=" CB TRP R 313 " pdb=" CG TRP R 313 " ideal model delta sigma weight residual 1.498 1.408 0.090 3.10e-02 1.04e+03 8.46e+00 bond pdb=" CAO P0G R1601 " pdb=" CAV P0G R1601 " ideal model delta sigma weight residual 1.550 1.600 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C VAL R 210 " pdb=" N PRO R 211 " ideal model delta sigma weight residual 1.334 1.371 -0.037 1.51e-02 4.39e+03 6.06e+00 bond pdb=" CB TRP B 169 " pdb=" CG TRP B 169 " ideal model delta sigma weight residual 1.498 1.426 0.072 3.10e-02 1.04e+03 5.37e+00 bond pdb=" CB TRP N 47 " pdb=" CG TRP N 47 " ideal model delta sigma weight residual 1.498 1.427 0.071 3.10e-02 1.04e+03 5.30e+00 ... (remaining 8294 not shown) Histogram of bond angle deviations from ideal: 93.90 - 104.20: 83 104.20 - 114.51: 4922 114.51 - 124.81: 6085 124.81 - 135.12: 169 135.12 - 145.42: 1 Bond angle restraints: 11260 Sorted by residual: angle pdb=" CAO P0G R1601 " pdb=" CAV P0G R1601 " pdb=" CAT P0G R1601 " ideal model delta sigma weight residual 79.91 133.20 -53.29 3.00e+00 1.11e-01 3.16e+02 angle pdb=" CAJ P0G R1601 " pdb=" CAV P0G R1601 " pdb=" CAO P0G R1601 " ideal model delta sigma weight residual 139.47 108.09 31.38 3.00e+00 1.11e-01 1.09e+02 angle pdb=" CAA P0G R1601 " pdb=" CAT P0G R1601 " pdb=" CAV P0G R1601 " ideal model delta sigma weight residual 116.05 145.42 -29.37 3.00e+00 1.11e-01 9.59e+01 angle pdb=" CB ARG R 221 " pdb=" CG ARG R 221 " pdb=" CD ARG R 221 " ideal model delta sigma weight residual 111.30 101.01 10.29 2.30e+00 1.89e-01 2.00e+01 angle pdb=" C THR N 113 " pdb=" N THR N 114 " pdb=" CA THR N 114 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 ... (remaining 11255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 4642 16.41 - 32.82: 218 32.82 - 49.23: 44 49.23 - 65.64: 9 65.64 - 82.05: 4 Dihedral angle restraints: 4917 sinusoidal: 1886 harmonic: 3031 Sorted by residual: dihedral pdb=" CA THR A 364 " pdb=" C THR A 364 " pdb=" N CYS A 365 " pdb=" CA CYS A 365 " ideal model delta harmonic sigma weight residual 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA PHE A 363 " pdb=" C PHE A 363 " pdb=" N THR A 364 " pdb=" CA THR A 364 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA THR N 113 " pdb=" C THR N 113 " pdb=" N THR N 114 " pdb=" CA THR N 114 " ideal model delta harmonic sigma weight residual -180.00 -155.98 -24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 4914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1099 0.095 - 0.191: 165 0.191 - 0.286: 14 0.286 - 0.381: 0 0.381 - 0.477: 2 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CB ILE N 70 " pdb=" CA ILE N 70 " pdb=" CG1 ILE N 70 " pdb=" CG2 ILE N 70 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CB ILE B 232 " pdb=" CA ILE B 232 " pdb=" CG1 ILE B 232 " pdb=" CG2 ILE B 232 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB ILE B 58 " pdb=" CA ILE B 58 " pdb=" CG1 ILE B 58 " pdb=" CG2 ILE B 58 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1277 not shown) Planarity restraints: 1436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 294 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C ILE R 294 " 0.064 2.00e-02 2.50e+03 pdb=" O ILE R 294 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL R 295 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 325 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ILE R 325 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE R 325 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR R 326 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 44 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C VAL R 44 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL R 44 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU R 45 " 0.016 2.00e-02 2.50e+03 ... (remaining 1433 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1808 2.79 - 3.31: 7643 3.31 - 3.84: 13411 3.84 - 4.37: 14889 4.37 - 4.90: 26038 Nonbonded interactions: 63789 Sorted by model distance: nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR A 40 " model vdw 2.258 2.440 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.300 2.440 nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 98 " model vdw 2.310 2.520 nonbonded pdb=" OG1 THR B 128 " pdb=" O GLY B 131 " model vdw 2.325 2.440 nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.338 2.520 ... (remaining 63784 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 group one per residue 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.000 Extract box with map and model: 3.920 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.510 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 0.010 0.126 8299 Z= 0.658 Angle : 1.374 53.293 11260 Z= 0.718 Chirality : 0.069 0.477 1280 Planarity : 0.008 0.063 1436 Dihedral : 10.674 82.046 2946 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.23 % Allowed : 5.09 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.22), residues: 1025 helix: -2.10 (0.19), residues: 413 sheet: -1.40 (0.30), residues: 230 loop : -1.68 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.006 TRP B 211 HIS 0.010 0.003 HIS A 362 PHE 0.045 0.005 PHE B 234 TYR 0.042 0.005 TYR R 316 ARG 0.010 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 249 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5346 (t80) cc_final: 0.4601 (t80) REVERT: B 18 ILE cc_start: 0.8840 (mt) cc_final: 0.8518 (tp) REVERT: R 36 MET cc_start: 0.7182 (mmm) cc_final: 0.6305 (mtp) REVERT: R 40 MET cc_start: 0.7157 (mtt) cc_final: 0.6766 (mmt) REVERT: R 124 LEU cc_start: 0.8672 (mt) cc_final: 0.8453 (tp) REVERT: R 273 LYS cc_start: 0.8113 (tttt) cc_final: 0.7804 (tttp) REVERT: N 90 ASP cc_start: 0.7148 (m-30) cc_final: 0.6887 (m-30) REVERT: N 125 THR cc_start: 0.8320 (m) cc_final: 0.7543 (p) outliers start: 2 outliers final: 1 residues processed: 250 average time/residue: 0.2718 time to fit residues: 85.0817 Evaluate side-chains 136 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 292 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN B 88 ASN B 239 ASN B 266 HIS G 24 ASN R 65 GLN R 69 ASN R 172 HIS R 337 GLN N 1 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8299 Z= 0.242 Angle : 0.725 19.148 11260 Z= 0.359 Chirality : 0.044 0.165 1280 Planarity : 0.004 0.057 1436 Dihedral : 6.028 59.845 1137 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.05 % Allowed : 11.46 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1025 helix: 0.60 (0.25), residues: 419 sheet: -0.96 (0.31), residues: 213 loop : -1.17 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.005 0.001 HIS B 311 PHE 0.021 0.002 PHE B 253 TYR 0.020 0.002 TYR A 37 ARG 0.009 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.8693 (m-80) cc_final: 0.8444 (m-10) REVERT: B 9 GLN cc_start: 0.8979 (tt0) cc_final: 0.8768 (mt0) REVERT: B 169 TRP cc_start: 0.5811 (m100) cc_final: 0.5135 (m100) REVERT: G 14 LYS cc_start: 0.9235 (pttp) cc_final: 0.8764 (pptt) REVERT: G 38 MET cc_start: 0.7760 (tmm) cc_final: 0.7505 (tmm) REVERT: R 36 MET cc_start: 0.7002 (mmm) cc_final: 0.6156 (mtp) REVERT: R 273 LYS cc_start: 0.8009 (tttt) cc_final: 0.7765 (tttp) REVERT: N 96 CYS cc_start: 0.4946 (p) cc_final: 0.4503 (p) REVERT: N 120 GLN cc_start: 0.8425 (mp10) cc_final: 0.7904 (pm20) outliers start: 35 outliers final: 23 residues processed: 186 average time/residue: 0.2412 time to fit residues: 59.0993 Evaluate side-chains 149 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain R residue 49 PHE Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 0.4980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 75 GLN B 176 GLN R 65 GLN R 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8299 Z= 0.319 Angle : 0.740 19.303 11260 Z= 0.365 Chirality : 0.044 0.150 1280 Planarity : 0.004 0.057 1436 Dihedral : 5.843 53.067 1137 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.98 % Allowed : 14.70 % Favored : 80.32 % 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: -0.28 (0.26), residues: 1025 helix: 1.12 (0.25), residues: 421 sheet: -1.05 (0.31), residues: 218 loop : -1.03 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.006 0.001 HIS B 311 PHE 0.021 0.002 PHE B 253 TYR 0.018 0.002 TYR A 37 ARG 0.007 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 135 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.8075 (tpp80) cc_final: 0.7863 (tpp80) REVERT: A 360 TYR cc_start: 0.8849 (m-80) cc_final: 0.8508 (m-10) REVERT: B 9 GLN cc_start: 0.8954 (tt0) cc_final: 0.8742 (mt0) REVERT: B 169 TRP cc_start: 0.6125 (m100) cc_final: 0.5338 (m100) REVERT: G 14 LYS cc_start: 0.9276 (pttp) cc_final: 0.8834 (pptt) REVERT: G 38 MET cc_start: 0.7844 (tmm) cc_final: 0.7591 (tmm) REVERT: G 48 ASP cc_start: 0.7809 (t0) cc_final: 0.7477 (t0) REVERT: G 51 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7811 (mt) REVERT: R 36 MET cc_start: 0.6354 (mmm) cc_final: 0.5985 (mtp) REVERT: R 40 MET cc_start: 0.7943 (mmm) cc_final: 0.7728 (mmm) REVERT: R 131 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7718 (mtt180) REVERT: R 273 LYS cc_start: 0.8054 (tttt) cc_final: 0.7822 (tttp) REVERT: N 78 THR cc_start: 0.6801 (OUTLIER) cc_final: 0.6524 (m) REVERT: N 79 LEU cc_start: 0.8289 (tp) cc_final: 0.8030 (mp) outliers start: 43 outliers final: 31 residues processed: 164 average time/residue: 0.2137 time to fit residues: 46.9022 Evaluate side-chains 158 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 0.0070 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8299 Z= 0.158 Angle : 0.644 18.909 11260 Z= 0.309 Chirality : 0.041 0.158 1280 Planarity : 0.003 0.053 1436 Dihedral : 5.397 55.876 1137 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.89 % Allowed : 17.01 % Favored : 80.09 % 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: 0.17 (0.26), residues: 1025 helix: 1.52 (0.26), residues: 418 sheet: -0.83 (0.31), residues: 219 loop : -0.78 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.033 0.001 PHE R 208 TYR 0.017 0.001 TYR A 37 ARG 0.005 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8651 (p0) cc_final: 0.7920 (p0) REVERT: A 333 ARG cc_start: 0.7924 (tpp80) cc_final: 0.7702 (tpp80) REVERT: B 169 TRP cc_start: 0.5809 (m100) cc_final: 0.5364 (m100) REVERT: G 14 LYS cc_start: 0.9272 (pttp) cc_final: 0.8823 (pptt) REVERT: G 38 MET cc_start: 0.7911 (tmm) cc_final: 0.7652 (tmm) REVERT: G 48 ASP cc_start: 0.7753 (t0) cc_final: 0.7385 (t0) REVERT: R 36 MET cc_start: 0.6182 (mmm) cc_final: 0.5972 (ttt) REVERT: R 40 MET cc_start: 0.7933 (mmm) cc_final: 0.7548 (mmm) REVERT: R 188 GLU cc_start: 0.7410 (pm20) cc_final: 0.6868 (tt0) REVERT: R 204 SER cc_start: 0.8307 (m) cc_final: 0.7503 (t) REVERT: R 273 LYS cc_start: 0.8042 (tttt) cc_final: 0.7787 (ttpt) REVERT: R 312 ASN cc_start: 0.8032 (t160) cc_final: 0.7593 (t0) REVERT: N 78 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6499 (m) REVERT: N 120 GLN cc_start: 0.8306 (mp10) cc_final: 0.7882 (pm20) outliers start: 25 outliers final: 17 residues processed: 159 average time/residue: 0.2193 time to fit residues: 46.2715 Evaluate side-chains 143 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8299 Z= 0.314 Angle : 0.730 19.103 11260 Z= 0.359 Chirality : 0.044 0.148 1280 Planarity : 0.004 0.054 1436 Dihedral : 5.579 45.453 1137 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.32 % Allowed : 17.01 % Favored : 77.66 % 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: 0.02 (0.26), residues: 1025 helix: 1.36 (0.25), residues: 416 sheet: -0.91 (0.31), residues: 217 loop : -0.80 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.005 0.001 HIS B 311 PHE 0.021 0.002 PHE B 253 TYR 0.031 0.002 TYR A 253 ARG 0.007 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 137 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.6195 (m100) cc_final: 0.5636 (m100) REVERT: G 38 MET cc_start: 0.7967 (tmm) cc_final: 0.7681 (tmm) REVERT: R 40 MET cc_start: 0.8041 (mmm) cc_final: 0.7629 (mmm) REVERT: R 79 ASP cc_start: 0.8669 (m-30) cc_final: 0.8422 (t0) REVERT: R 273 LYS cc_start: 0.8046 (tttt) cc_final: 0.7819 (ttpt) REVERT: R 312 ASN cc_start: 0.8145 (t160) cc_final: 0.7757 (t0) REVERT: N 34 MET cc_start: 0.7523 (mmm) cc_final: 0.7248 (mtp) REVERT: N 78 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6653 (m) REVERT: N 79 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7746 (mp) outliers start: 46 outliers final: 32 residues processed: 166 average time/residue: 0.2110 time to fit residues: 46.9431 Evaluate side-chains 161 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 109 TRP Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.0770 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN R 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8299 Z= 0.158 Angle : 0.660 18.824 11260 Z= 0.313 Chirality : 0.041 0.162 1280 Planarity : 0.003 0.052 1436 Dihedral : 5.241 54.684 1137 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.01 % Allowed : 20.02 % Favored : 76.97 % 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: 0.40 (0.26), residues: 1025 helix: 1.72 (0.26), residues: 413 sheet: -0.66 (0.33), residues: 201 loop : -0.69 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS B 311 PHE 0.015 0.001 PHE B 253 TYR 0.019 0.001 TYR A 253 ARG 0.006 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8278 (t) REVERT: B 169 TRP cc_start: 0.5991 (m100) cc_final: 0.5506 (m100) REVERT: B 228 ASP cc_start: 0.7389 (m-30) cc_final: 0.7104 (m-30) REVERT: G 38 MET cc_start: 0.7932 (tmm) cc_final: 0.7678 (tmm) REVERT: R 40 MET cc_start: 0.7959 (mmm) cc_final: 0.7601 (mmm) REVERT: R 79 ASP cc_start: 0.8620 (m-30) cc_final: 0.8328 (t0) REVERT: R 188 GLU cc_start: 0.7343 (pm20) cc_final: 0.6710 (tt0) REVERT: R 204 SER cc_start: 0.8345 (m) cc_final: 0.7570 (t) REVERT: R 312 ASN cc_start: 0.8063 (t160) cc_final: 0.7570 (t0) REVERT: N 34 MET cc_start: 0.7300 (mmm) cc_final: 0.7008 (mtp) REVERT: N 78 THR cc_start: 0.6803 (OUTLIER) cc_final: 0.6528 (m) REVERT: N 80 TYR cc_start: 0.7166 (m-80) cc_final: 0.6776 (m-80) REVERT: N 120 GLN cc_start: 0.8359 (mp10) cc_final: 0.7975 (pm20) outliers start: 26 outliers final: 17 residues processed: 158 average time/residue: 0.2212 time to fit residues: 46.3275 Evaluate side-chains 142 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN N 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8299 Z= 0.203 Angle : 0.689 18.911 11260 Z= 0.329 Chirality : 0.042 0.171 1280 Planarity : 0.003 0.052 1436 Dihedral : 5.052 50.425 1136 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.24 % Allowed : 21.18 % Favored : 75.58 % 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: 0.43 (0.26), residues: 1025 helix: 1.68 (0.26), residues: 413 sheet: -0.55 (0.33), residues: 205 loop : -0.65 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS R 93 PHE 0.016 0.001 PHE B 253 TYR 0.018 0.002 TYR A 253 ARG 0.007 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASN cc_start: 0.8620 (m-40) cc_final: 0.8350 (m-40) REVERT: B 34 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8301 (t) REVERT: B 169 TRP cc_start: 0.5993 (m100) cc_final: 0.5485 (m100) REVERT: B 228 ASP cc_start: 0.7545 (m-30) cc_final: 0.7257 (m-30) REVERT: G 38 MET cc_start: 0.7994 (tmm) cc_final: 0.7719 (tmm) REVERT: R 40 MET cc_start: 0.7986 (mmm) cc_final: 0.6818 (mmm) REVERT: R 312 ASN cc_start: 0.8115 (t160) cc_final: 0.7720 (t0) REVERT: N 80 TYR cc_start: 0.7098 (m-80) cc_final: 0.6701 (m-80) outliers start: 28 outliers final: 24 residues processed: 152 average time/residue: 0.2071 time to fit residues: 42.5220 Evaluate side-chains 152 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 0.0470 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 0.1980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8299 Z= 0.157 Angle : 0.675 18.772 11260 Z= 0.316 Chirality : 0.041 0.168 1280 Planarity : 0.003 0.051 1436 Dihedral : 4.896 56.779 1136 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.24 % Allowed : 21.88 % Favored : 74.88 % 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: 0.54 (0.27), residues: 1025 helix: 1.74 (0.26), residues: 413 sheet: -0.40 (0.34), residues: 206 loop : -0.61 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 297 HIS 0.002 0.001 HIS B 311 PHE 0.014 0.001 PHE B 253 TYR 0.016 0.001 TYR A 360 ARG 0.008 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASN cc_start: 0.8531 (m-40) cc_final: 0.8209 (m-40) REVERT: B 15 LYS cc_start: 0.8886 (ttpp) cc_final: 0.8499 (tttt) REVERT: B 34 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8401 (t) REVERT: B 169 TRP cc_start: 0.5899 (m100) cc_final: 0.5297 (m100) REVERT: B 228 ASP cc_start: 0.7457 (m-30) cc_final: 0.7130 (m-30) REVERT: G 38 MET cc_start: 0.7928 (tmm) cc_final: 0.7662 (tmm) REVERT: R 40 MET cc_start: 0.7954 (mmm) cc_final: 0.6800 (mmm) REVERT: R 51 ASN cc_start: 0.6067 (m-40) cc_final: 0.5733 (m110) REVERT: R 204 SER cc_start: 0.8335 (m) cc_final: 0.7559 (t) REVERT: R 312 ASN cc_start: 0.8173 (t160) cc_final: 0.7783 (t0) REVERT: N 80 TYR cc_start: 0.6957 (m-80) cc_final: 0.6659 (m-80) REVERT: N 120 GLN cc_start: 0.8263 (mp10) cc_final: 0.7984 (pm20) outliers start: 28 outliers final: 25 residues processed: 155 average time/residue: 0.2055 time to fit residues: 43.1962 Evaluate side-chains 151 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 overall best weight: 2.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 ASN R 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8299 Z= 0.301 Angle : 0.748 18.899 11260 Z= 0.363 Chirality : 0.043 0.171 1280 Planarity : 0.004 0.053 1436 Dihedral : 5.207 47.205 1136 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.47 % Allowed : 22.34 % Favored : 74.19 % 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: 0.30 (0.27), residues: 1025 helix: 1.49 (0.26), residues: 418 sheet: -0.58 (0.33), residues: 224 loop : -0.68 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 297 HIS 0.005 0.001 HIS B 311 PHE 0.019 0.002 PHE B 253 TYR 0.037 0.002 TYR A 391 ARG 0.007 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8592 (tttt) REVERT: B 34 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8307 (t) REVERT: B 169 TRP cc_start: 0.6129 (m100) cc_final: 0.5520 (m100) REVERT: G 14 LYS cc_start: 0.9172 (pttp) cc_final: 0.8875 (ptmm) REVERT: R 70 TYR cc_start: 0.7835 (m-80) cc_final: 0.7526 (m-10) REVERT: R 79 ASP cc_start: 0.7827 (t0) cc_final: 0.6891 (t0) outliers start: 30 outliers final: 25 residues processed: 147 average time/residue: 0.2113 time to fit residues: 41.8847 Evaluate side-chains 146 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN R 322 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8299 Z= 0.184 Angle : 0.711 18.696 11260 Z= 0.335 Chirality : 0.042 0.176 1280 Planarity : 0.004 0.051 1436 Dihedral : 4.974 55.313 1136 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.12 % Allowed : 22.80 % Favored : 74.07 % 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: 0.51 (0.27), residues: 1025 helix: 1.65 (0.26), residues: 417 sheet: -0.38 (0.34), residues: 210 loop : -0.59 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 47 HIS 0.003 0.001 HIS B 311 PHE 0.015 0.001 PHE B 253 TYR 0.018 0.001 TYR A 360 ARG 0.009 0.000 ARG B 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8918 (ttpp) cc_final: 0.8598 (tttt) REVERT: B 34 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8281 (t) REVERT: B 169 TRP cc_start: 0.5938 (m100) cc_final: 0.5383 (m100) REVERT: B 228 ASP cc_start: 0.7555 (m-30) cc_final: 0.7257 (m-30) REVERT: R 79 ASP cc_start: 0.7529 (t0) cc_final: 0.6656 (t70) REVERT: R 80 LEU cc_start: 0.8514 (tt) cc_final: 0.8082 (tp) REVERT: N 120 GLN cc_start: 0.8297 (mp10) cc_final: 0.7964 (pm20) outliers start: 27 outliers final: 24 residues processed: 143 average time/residue: 0.2106 time to fit residues: 41.0289 Evaluate side-chains 145 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN R 322 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.103179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087262 restraints weight = 21972.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.089618 restraints weight = 12538.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.091241 restraints weight = 8572.089| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8299 Z= 0.183 Angle : 0.697 18.630 11260 Z= 0.328 Chirality : 0.041 0.171 1280 Planarity : 0.004 0.051 1436 Dihedral : 4.887 55.531 1136 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.01 % Allowed : 22.69 % Favored : 74.31 % 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: 0.63 (0.27), residues: 1025 helix: 1.75 (0.26), residues: 411 sheet: -0.31 (0.34), residues: 207 loop : -0.50 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 47 HIS 0.002 0.001 HIS B 311 PHE 0.015 0.001 PHE B 253 TYR 0.029 0.002 TYR A 253 ARG 0.008 0.000 ARG B 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1867.35 seconds wall clock time: 34 minutes 42.49 seconds (2082.49 seconds total)