Starting phenix.real_space_refine on Sat Apr 6 19:10:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j19_35914/04_2024/8j19_35914_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j19_35914/04_2024/8j19_35914.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j19_35914/04_2024/8j19_35914_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j19_35914/04_2024/8j19_35914_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j19_35914/04_2024/8j19_35914_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j19_35914/04_2024/8j19_35914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j19_35914/04_2024/8j19_35914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j19_35914/04_2024/8j19_35914_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j19_35914/04_2024/8j19_35914_neut_updated.pdb" } resolution = 3.23 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= 0.001 sd= 0.038 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 59 5.16 5 C 5619 2.51 5 N 1509 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 313": "OE1" <-> "OE2" Residue "R PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8801 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2232 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "S" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'SWO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.21, per 1000 atoms: 0.59 Number of scatterers: 8801 At special positions: 0 Unit cell: (96.408, 117.832, 124.424, 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 59 16.00 O 1614 8.00 N 1509 7.00 C 5619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 166 " distance=2.12 Simple disulfide: pdb=" SG CYS R 93 " - pdb=" SG CYS R 168 " distance=1.66 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " 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: 3.67 Conformation dependent library (CDL) restraints added in 1.8 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 35.6% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'R' and resid 15 through 18 removed outlier: 4.094A pdb=" N GLY R 18 " --> pdb=" O SER R 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 15 through 18' Processing helix chain 'R' and resid 20 through 47 Processing helix chain 'R' and resid 49 through 51 No H-bonds generated for 'chain 'R' and resid 49 through 51' Processing helix chain 'R' and resid 56 through 83 removed outlier: 4.730A pdb=" N GLN R 74 " --> pdb=" O CYS R 70 " (cutoff:3.500A) Proline residue: R 75 - end of helix Processing helix chain 'R' and resid 90 through 123 removed outlier: 3.873A pdb=" N VAL R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU R 98 " --> pdb=" O ARG R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 131 Proline residue: R 129 - end of helix No H-bonds generated for 'chain 'R' and resid 125 through 131' Processing helix chain 'R' and resid 134 through 158 removed outlier: 4.658A pdb=" N VAL R 138 " --> pdb=" O ALA R 134 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) Proline residue: R 154 - end of helix Proline residue: R 157 - end of helix Processing helix chain 'R' and resid 176 through 215 removed outlier: 3.851A pdb=" N PHE R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU R 212 " --> pdb=" O ALA R 208 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN R 214 " --> pdb=" O GLN R 210 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR R 215 " --> pdb=" O ALA R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 341 Proline residue: R 334 - end of helix Processing helix chain 'R' and resid 349 through 371 removed outlier: 3.651A pdb=" N MET R 353 " --> pdb=" O ARG R 349 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY R 363 " --> pdb=" O THR R 359 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS R 364 " --> pdb=" O TRP R 360 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 375 through 384 removed outlier: 3.696A pdb=" N GLN R 379 " --> pdb=" O ARG R 375 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA R 380 " --> pdb=" O GLN R 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.734A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.331A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 removed outlier: 3.920A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.559A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.569A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing sheet with id= A, first strand: chain 'R' and resid 159 through 162 removed outlier: 3.944A pdb=" N THR R 167 " --> pdb=" O VAL R 162 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.665A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 196 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.785A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.764A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.976A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.963A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.702A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.458A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.670A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 115 through 117 removed outlier: 5.779A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.419A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= N, first strand: chain 'S' and resid 225 through 231 removed outlier: 6.160A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1164 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: 2.71 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1409 1.32 - 1.44: 2494 1.44 - 1.57: 4997 1.57 - 1.69: 2 1.69 - 1.81: 82 Bond restraints: 8984 Sorted by residual: bond pdb=" C ILE R 185 " pdb=" N TYR R 186 " ideal model delta sigma weight residual 1.334 1.434 -0.100 1.49e-02 4.50e+03 4.52e+01 bond pdb=" C03 SWO R 401 " pdb=" N04 SWO R 401 " ideal model delta sigma weight residual 1.363 1.240 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C03 SWO R 401 " pdb=" C07 SWO R 401 " ideal model delta sigma weight residual 1.598 1.481 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C12 SWO R 401 " pdb=" C13 SWO R 401 " ideal model delta sigma weight residual 1.581 1.466 0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" CA TRP R 156 " pdb=" C TRP R 156 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.00e-02 1.00e+04 2.51e+01 ... (remaining 8979 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.91: 188 106.91 - 113.68: 4998 113.68 - 120.45: 3392 120.45 - 127.22: 3507 127.22 - 133.99: 89 Bond angle restraints: 12174 Sorted by residual: angle pdb=" N GLY R 315 " pdb=" CA GLY R 315 " pdb=" C GLY R 315 " ideal model delta sigma weight residual 114.37 102.26 12.11 1.26e+00 6.30e-01 9.24e+01 angle pdb=" O ILE R 185 " pdb=" C ILE R 185 " pdb=" N TYR R 186 " ideal model delta sigma weight residual 121.87 112.94 8.93 1.01e+00 9.80e-01 7.82e+01 angle pdb=" N ILE R 340 " pdb=" CA ILE R 340 " pdb=" C ILE R 340 " ideal model delta sigma weight residual 111.56 105.89 5.67 8.60e-01 1.35e+00 4.35e+01 angle pdb=" CA ILE R 185 " pdb=" C ILE R 185 " pdb=" N TYR R 186 " ideal model delta sigma weight residual 117.53 123.82 -6.29 1.19e+00 7.06e-01 2.79e+01 angle pdb=" N VAL S 5 " pdb=" CA VAL S 5 " pdb=" C VAL S 5 " ideal model delta sigma weight residual 109.17 101.82 7.35 1.54e+00 4.22e-01 2.28e+01 ... (remaining 12169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4677 17.72 - 35.44: 480 35.44 - 53.16: 118 53.16 - 70.88: 28 70.88 - 88.60: 13 Dihedral angle restraints: 5316 sinusoidal: 2047 harmonic: 3269 Sorted by residual: dihedral pdb=" CB CYS R 93 " pdb=" SG CYS R 93 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual 93.00 19.08 73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" C ILE R 333 " pdb=" N ILE R 333 " pdb=" CA ILE R 333 " pdb=" CB ILE R 333 " ideal model delta harmonic sigma weight residual -122.00 -133.36 11.36 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N ILE R 333 " pdb=" C ILE R 333 " pdb=" CA ILE R 333 " pdb=" CB ILE R 333 " ideal model delta harmonic sigma weight residual 123.40 132.76 -9.36 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 5313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1207 0.058 - 0.117: 156 0.117 - 0.175: 22 0.175 - 0.233: 4 0.233 - 0.291: 2 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA VAL S 5 " pdb=" N VAL S 5 " pdb=" C VAL S 5 " pdb=" CB VAL S 5 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ILE R 333 " pdb=" N ILE R 333 " pdb=" C ILE R 333 " pdb=" CB ILE R 333 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE R 340 " pdb=" N ILE R 340 " pdb=" C ILE R 340 " pdb=" CB ILE R 340 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.94e-01 ... (remaining 1388 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 185 " -0.030 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C ILE R 185 " 0.092 2.00e-02 2.50e+03 pdb=" O ILE R 185 " -0.033 2.00e-02 2.50e+03 pdb=" N TYR R 186 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 SWO R 401 " -0.003 2.00e-02 2.50e+03 2.26e-02 1.15e+01 pdb=" C02 SWO R 401 " 0.017 2.00e-02 2.50e+03 pdb=" C03 SWO R 401 " -0.033 2.00e-02 2.50e+03 pdb=" C05 SWO R 401 " 0.007 2.00e-02 2.50e+03 pdb=" C06 SWO R 401 " -0.001 2.00e-02 2.50e+03 pdb=" C07 SWO R 401 " -0.012 2.00e-02 2.50e+03 pdb=" N04 SWO R 401 " 0.050 2.00e-02 2.50e+03 pdb=" O16 SWO R 401 " -0.003 2.00e-02 2.50e+03 pdb=" O17 SWO R 401 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 175 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLY R 175 " -0.055 2.00e-02 2.50e+03 pdb=" O GLY R 175 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG R 176 " 0.018 2.00e-02 2.50e+03 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1362 2.76 - 3.29: 8615 3.29 - 3.83: 14372 3.83 - 4.36: 17189 4.36 - 4.90: 30896 Nonbonded interactions: 72434 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.274 2.440 nonbonded pdb=" O ALA R 31 " pdb=" OG1 THR R 35 " model vdw 2.275 2.440 nonbonded pdb=" ND1 HIS S 167 " pdb=" OD1 ASN S 169 " model vdw 2.289 2.520 nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.290 2.440 ... (remaining 72429 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: 0.770 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: 3.990 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.880 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.005 0.123 8984 Z= 0.311 Angle : 0.632 12.792 12174 Z= 0.377 Chirality : 0.043 0.291 1391 Planarity : 0.005 0.078 1533 Dihedral : 15.955 88.596 3201 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.74 % Allowed : 17.11 % Favored : 82.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1111 helix: 2.32 (0.28), residues: 368 sheet: -0.11 (0.32), residues: 292 loop : -0.30 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 156 HIS 0.002 0.001 HIS A 322 PHE 0.009 0.001 PHE S 80 TYR 0.009 0.001 TYR S 190 ARG 0.010 0.000 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 0.988 Fit side-chains REVERT: R 88 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6562 (p) REVERT: R 313 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: R 316 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7876 (tptt) REVERT: R 349 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.5572 (mtp180) REVERT: A 255 ASN cc_start: 0.8380 (m-40) cc_final: 0.8161 (m110) REVERT: B 323 ASP cc_start: 0.8538 (p0) cc_final: 0.8317 (p0) REVERT: S 179 GLN cc_start: 0.8824 (tt0) cc_final: 0.8621 (tt0) outliers start: 7 outliers final: 0 residues processed: 119 average time/residue: 0.2602 time to fit residues: 41.8870 Evaluate side-chains 109 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 313 GLU Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 349 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 352 HIS A 269 ASN B 75 GLN B 142 HIS B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8984 Z= 0.232 Angle : 0.556 8.913 12174 Z= 0.286 Chirality : 0.042 0.143 1391 Planarity : 0.004 0.045 1533 Dihedral : 6.095 88.923 1244 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.17 % Allowed : 16.26 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1111 helix: 2.27 (0.27), residues: 368 sheet: -0.09 (0.31), residues: 285 loop : -0.25 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE S 68 TYR 0.016 0.001 TYR B 59 ARG 0.004 0.000 ARG R 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 1.033 Fit side-chains REVERT: R 316 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7490 (ttmt) REVERT: S 113 GLN cc_start: 0.8359 (tp40) cc_final: 0.8041 (mm-40) REVERT: S 179 GLN cc_start: 0.8597 (tt0) cc_final: 0.8367 (tt0) REVERT: S 204 SER cc_start: 0.8944 (t) cc_final: 0.8599 (p) outliers start: 30 outliers final: 13 residues processed: 131 average time/residue: 0.2243 time to fit residues: 40.7838 Evaluate side-chains 117 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain G residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN S 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8984 Z= 0.147 Angle : 0.499 9.157 12174 Z= 0.255 Chirality : 0.040 0.147 1391 Planarity : 0.003 0.039 1533 Dihedral : 5.045 73.213 1236 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.53 % Allowed : 17.53 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.95 (0.26), residues: 1111 helix: 2.29 (0.27), residues: 373 sheet: -0.21 (0.31), residues: 278 loop : -0.12 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 PHE 0.010 0.001 PHE S 68 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG R 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.918 Fit side-chains REVERT: R 84 LEU cc_start: 0.6899 (mp) cc_final: 0.6469 (mt) REVERT: R 316 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7483 (ttmt) REVERT: A 8 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: S 204 SER cc_start: 0.8965 (t) cc_final: 0.8621 (p) outliers start: 24 outliers final: 11 residues processed: 128 average time/residue: 0.2060 time to fit residues: 37.2951 Evaluate side-chains 116 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain G residue 9 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8984 Z= 0.288 Angle : 0.559 9.772 12174 Z= 0.288 Chirality : 0.042 0.136 1391 Planarity : 0.004 0.038 1533 Dihedral : 5.152 59.870 1236 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.48 % Allowed : 18.69 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.62 (0.26), residues: 1111 helix: 2.02 (0.27), residues: 369 sheet: -0.47 (0.30), residues: 291 loop : -0.23 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 322 PHE 0.017 0.002 PHE B 235 TYR 0.017 0.001 TYR B 59 ARG 0.005 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.016 Fit side-chains REVERT: R 316 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7580 (ttmt) REVERT: R 326 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7218 (mt) REVERT: A 8 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: A 348 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8112 (mp) REVERT: S 160 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7580 (mtm110) REVERT: S 204 SER cc_start: 0.8946 (t) cc_final: 0.8580 (p) outliers start: 33 outliers final: 20 residues processed: 130 average time/residue: 0.2192 time to fit residues: 39.7542 Evaluate side-chains 124 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 0.0050 chunk 90 optimal weight: 0.0170 chunk 73 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8984 Z= 0.128 Angle : 0.489 10.317 12174 Z= 0.247 Chirality : 0.039 0.133 1391 Planarity : 0.003 0.036 1533 Dihedral : 4.771 58.501 1236 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.06 % Allowed : 19.11 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.77 (0.26), residues: 1111 helix: 2.18 (0.28), residues: 370 sheet: -0.44 (0.30), residues: 296 loop : -0.13 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 225 PHE 0.011 0.001 PHE R 335 TYR 0.009 0.001 TYR R 186 ARG 0.003 0.000 ARG R 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.028 Fit side-chains REVERT: R 66 ASP cc_start: 0.5994 (m-30) cc_final: 0.5742 (m-30) REVERT: R 316 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7552 (ttmt) REVERT: R 326 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7227 (mt) REVERT: A 8 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: S 160 ARG cc_start: 0.7857 (mtm110) cc_final: 0.7592 (mtm110) REVERT: S 204 SER cc_start: 0.8945 (t) cc_final: 0.8542 (p) outliers start: 29 outliers final: 21 residues processed: 140 average time/residue: 0.2123 time to fit residues: 42.1655 Evaluate side-chains 133 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8984 Z= 0.263 Angle : 0.545 10.601 12174 Z= 0.278 Chirality : 0.042 0.134 1391 Planarity : 0.004 0.036 1533 Dihedral : 5.007 59.483 1236 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.12 % Allowed : 19.43 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.58 (0.26), residues: 1111 helix: 2.05 (0.28), residues: 368 sheet: -0.55 (0.29), residues: 298 loop : -0.25 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 PHE 0.016 0.002 PHE B 235 TYR 0.014 0.001 TYR B 59 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 107 time to evaluate : 1.039 Fit side-chains REVERT: R 316 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7635 (ttmt) REVERT: R 326 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7231 (mt) REVERT: A 8 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: A 348 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8076 (mp) REVERT: S 204 SER cc_start: 0.8958 (t) cc_final: 0.8509 (p) outliers start: 39 outliers final: 23 residues processed: 138 average time/residue: 0.2174 time to fit residues: 41.4204 Evaluate side-chains 131 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.0070 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8984 Z= 0.133 Angle : 0.485 9.995 12174 Z= 0.244 Chirality : 0.039 0.132 1391 Planarity : 0.003 0.036 1533 Dihedral : 4.721 59.651 1236 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.27 % Allowed : 20.59 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.70 (0.26), residues: 1111 helix: 2.14 (0.28), residues: 370 sheet: -0.46 (0.30), residues: 283 loop : -0.22 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 PHE 0.011 0.001 PHE R 335 TYR 0.009 0.001 TYR R 186 ARG 0.007 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 1.064 Fit side-chains REVERT: R 316 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7588 (ttmt) REVERT: R 326 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7204 (mt) REVERT: A 8 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: A 348 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8085 (mp) REVERT: S 204 SER cc_start: 0.8986 (t) cc_final: 0.8544 (p) outliers start: 31 outliers final: 23 residues processed: 132 average time/residue: 0.2102 time to fit residues: 38.7440 Evaluate side-chains 134 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8984 Z= 0.139 Angle : 0.485 11.405 12174 Z= 0.243 Chirality : 0.039 0.133 1391 Planarity : 0.003 0.035 1533 Dihedral : 4.635 57.558 1236 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.38 % Allowed : 21.01 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.79 (0.26), residues: 1111 helix: 2.20 (0.28), residues: 370 sheet: -0.41 (0.31), residues: 275 loop : -0.17 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 PHE 0.011 0.001 PHE R 335 TYR 0.008 0.001 TYR S 190 ARG 0.007 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 1.037 Fit side-chains REVERT: R 66 ASP cc_start: 0.5808 (m-30) cc_final: 0.5475 (m-30) REVERT: R 316 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7614 (ttmt) REVERT: R 326 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7188 (mt) REVERT: A 8 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7316 (pt0) REVERT: A 18 MET cc_start: 0.8289 (ttm) cc_final: 0.8038 (mtp) REVERT: A 348 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8038 (mp) REVERT: S 204 SER cc_start: 0.8981 (t) cc_final: 0.8533 (p) outliers start: 32 outliers final: 23 residues processed: 131 average time/residue: 0.2119 time to fit residues: 38.7545 Evaluate side-chains 129 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8984 Z= 0.179 Angle : 0.508 11.166 12174 Z= 0.253 Chirality : 0.040 0.133 1391 Planarity : 0.003 0.035 1533 Dihedral : 4.708 56.624 1236 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.17 % Allowed : 20.91 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.72 (0.26), residues: 1111 helix: 2.15 (0.28), residues: 370 sheet: -0.44 (0.30), residues: 289 loop : -0.19 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE R 335 TYR 0.010 0.001 TYR S 190 ARG 0.007 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 0.980 Fit side-chains REVERT: R 316 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7591 (ttmt) REVERT: R 326 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7194 (mt) REVERT: A 8 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: A 348 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8051 (mp) REVERT: S 204 SER cc_start: 0.8966 (t) cc_final: 0.8513 (p) outliers start: 30 outliers final: 23 residues processed: 125 average time/residue: 0.2098 time to fit residues: 36.7727 Evaluate side-chains 125 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8984 Z= 0.157 Angle : 0.502 11.119 12174 Z= 0.250 Chirality : 0.039 0.132 1391 Planarity : 0.003 0.035 1533 Dihedral : 4.680 56.583 1236 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.17 % Allowed : 20.80 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1111 helix: 2.19 (0.28), residues: 369 sheet: -0.41 (0.30), residues: 288 loop : -0.21 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 PHE 0.010 0.001 PHE R 335 TYR 0.009 0.001 TYR S 190 ARG 0.007 0.000 ARG S 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 0.953 Fit side-chains REVERT: R 316 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7581 (ttmt) REVERT: R 326 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7203 (mt) REVERT: A 8 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: A 348 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8047 (mp) REVERT: S 11 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8274 (tt) REVERT: S 204 SER cc_start: 0.8959 (t) cc_final: 0.8507 (p) outliers start: 30 outliers final: 24 residues processed: 121 average time/residue: 0.2109 time to fit residues: 35.6527 Evaluate side-chains 128 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.0050 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 0.0270 overall best weight: 0.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.184480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144645 restraints weight = 9739.227| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.03 r_work: 0.3520 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8984 Z= 0.127 Angle : 0.487 11.360 12174 Z= 0.240 Chirality : 0.039 0.133 1391 Planarity : 0.003 0.035 1533 Dihedral : 4.585 59.777 1236 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.06 % Allowed : 20.91 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.86 (0.26), residues: 1111 helix: 2.25 (0.28), residues: 370 sheet: -0.34 (0.31), residues: 269 loop : -0.15 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 PHE 0.010 0.001 PHE R 335 TYR 0.010 0.001 TYR A 302 ARG 0.007 0.000 ARG S 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2314.02 seconds wall clock time: 42 minutes 49.49 seconds (2569.49 seconds total)