Starting phenix.real_space_refine on Fri Oct 11 18:11:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xos_38539/10_2024/8xos_38539.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xos_38539/10_2024/8xos_38539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xos_38539/10_2024/8xos_38539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xos_38539/10_2024/8xos_38539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xos_38539/10_2024/8xos_38539.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xos_38539/10_2024/8xos_38539.cif" } resolution = 3.2 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= 0.004 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 1946 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 65 5.16 5 C 5713 2.51 5 N 1476 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 8919 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2577 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} 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: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2335 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 2 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.50, per 1000 atoms: 0.62 Number of scatterers: 8919 At special positions: 0 Unit cell: (116.739, 94.248, 117.81, 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 65 16.00 O 1665 8.00 N 1476 7.00 C 5713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 175 " - pdb=" SG CYS R 254 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 38.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.511A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 207 through 218 removed outlier: 4.707A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.434A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.504A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 89 through 98 Processing helix chain 'R' and resid 103 through 127 Proline residue: R 118 - end of helix Processing helix chain 'R' and resid 135 through 154 removed outlier: 3.553A pdb=" N VAL R 154 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 164 removed outlier: 3.872A pdb=" N LYS R 158 " --> pdb=" O VAL R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 206 Processing helix chain 'R' and resid 206 through 214 removed outlier: 3.618A pdb=" N LEU R 211 " --> pdb=" O PRO R 207 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER R 212 " --> pdb=" O MET R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 234 removed outlier: 3.653A pdb=" N VAL R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 240 Processing helix chain 'R' and resid 260 through 266 Processing helix chain 'R' and resid 266 through 279 Processing helix chain 'R' and resid 279 through 298 Processing helix chain 'R' and resid 308 through 325 Processing helix chain 'R' and resid 326 through 337 Processing helix chain 'R' and resid 342 through 361 removed outlier: 4.407A pdb=" N GLU R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA R 348 " --> pdb=" O SER R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 372 Proline residue: R 368 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 9.071A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.531A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.578A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.916A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.543A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.427A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.686A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.772A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.513A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.513A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.152A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 87 through 88 446 hydrogen bonds defined for protein. 1224 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: 2.70 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2817 1.34 - 1.46: 2032 1.46 - 1.58: 4174 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 9114 Sorted by residual: bond pdb=" CD2 HIS E 232 " pdb=" NE2 HIS E 232 " ideal model delta sigma weight residual 1.374 1.397 -0.023 1.10e-02 8.26e+03 4.40e+00 bond pdb=" N SER A 6 " pdb=" CA SER A 6 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.27e-02 6.20e+03 3.62e+00 bond pdb=" C13 CLR R 601 " pdb=" C17 CLR R 601 " ideal model delta sigma weight residual 1.550 1.513 0.037 2.00e-02 2.50e+03 3.48e+00 bond pdb=" C13 CLR R 602 " pdb=" C17 CLR R 602 " ideal model delta sigma weight residual 1.550 1.514 0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" CE1 HIS E 232 " pdb=" NE2 HIS E 232 " ideal model delta sigma weight residual 1.321 1.339 -0.018 1.00e-02 1.00e+04 3.22e+00 ... (remaining 9109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 11435 1.58 - 3.16: 786 3.16 - 4.73: 111 4.73 - 6.31: 18 6.31 - 7.89: 10 Bond angle restraints: 12360 Sorted by residual: angle pdb=" CB HIS E 35 " pdb=" CG HIS E 35 " pdb=" CD2 HIS E 35 " ideal model delta sigma weight residual 131.20 125.42 5.78 1.30e+00 5.92e-01 1.98e+01 angle pdb=" CB HIS E 167 " pdb=" CG HIS E 167 " pdb=" CD2 HIS E 167 " ideal model delta sigma weight residual 131.20 125.62 5.58 1.30e+00 5.92e-01 1.84e+01 angle pdb=" CB HIS E 232 " pdb=" CG HIS E 232 " pdb=" CD2 HIS E 232 " ideal model delta sigma weight residual 131.20 126.66 4.54 1.30e+00 5.92e-01 1.22e+01 angle pdb=" ND1 HIS E 167 " pdb=" CG HIS E 167 " pdb=" CD2 HIS E 167 " ideal model delta sigma weight residual 106.10 109.54 -3.44 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CB ARG B 314 " pdb=" CG ARG B 314 " pdb=" CD ARG B 314 " ideal model delta sigma weight residual 111.30 103.41 7.89 2.30e+00 1.89e-01 1.18e+01 ... (remaining 12355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5080 17.74 - 35.49: 324 35.49 - 53.23: 55 53.23 - 70.97: 18 70.97 - 88.72: 5 Dihedral angle restraints: 5482 sinusoidal: 2174 harmonic: 3308 Sorted by residual: dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ALA E 92 " pdb=" C ALA E 92 " pdb=" N MET E 93 " pdb=" CA MET E 93 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 5479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1129 0.068 - 0.135: 257 0.135 - 0.202: 24 0.202 - 0.270: 3 0.270 - 0.337: 2 Chirality restraints: 1415 Sorted by residual: chirality pdb=" C13 CLR R 601 " pdb=" C12 CLR R 601 " pdb=" C14 CLR R 601 " pdb=" C17 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C13 CLR R 602 " pdb=" C12 CLR R 602 " pdb=" C14 CLR R 602 " pdb=" C17 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.62 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1412 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 59 " -0.081 2.00e-02 2.50e+03 4.15e-02 3.44e+01 pdb=" CG TYR E 59 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 59 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR E 59 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR E 59 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR E 59 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 59 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 101 " 0.059 2.00e-02 2.50e+03 3.09e-02 1.91e+01 pdb=" CG TYR E 101 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR E 101 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 101 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR E 101 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR E 101 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 101 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 101 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 191 " -0.090 9.50e-02 1.11e+02 5.24e-02 1.50e+01 pdb=" NE ARG E 191 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG E 191 " -0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG E 191 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG E 191 " 0.018 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 970 2.74 - 3.28: 9488 3.28 - 3.82: 14879 3.82 - 4.36: 18335 4.36 - 4.90: 31266 Nonbonded interactions: 74938 Sorted by model distance: nonbonded pdb=" CE1 PHE B 253 " pdb=" CG GLU B 260 " model vdw 2.197 3.740 nonbonded pdb=" CD2 TYR E 50 " pdb=" OH TYR E 235 " model vdw 2.236 3.340 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 230 " pdb=" OG SER A 281 " model vdw 2.255 3.040 nonbonded pdb=" O GLY R 165 " pdb=" OG SER R 166 " model vdw 2.289 3.040 ... (remaining 74933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.920 Find NCS groups from input model: 0.120 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.008 0.060 9114 Z= 0.527 Angle : 0.900 7.888 12360 Z= 0.523 Chirality : 0.057 0.337 1415 Planarity : 0.007 0.052 1540 Dihedral : 12.894 88.719 3345 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.72 % Allowed : 4.42 % Favored : 94.86 % 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: -0.80 (0.24), residues: 1116 helix: -0.52 (0.25), residues: 377 sheet: 0.32 (0.30), residues: 269 loop : -0.91 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP E 47 HIS 0.011 0.002 HIS R 143 PHE 0.040 0.003 PHE E 177 TYR 0.081 0.007 TYR E 59 ARG 0.065 0.009 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 200 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8393 (t70) cc_final: 0.8127 (t0) REVERT: A 204 GLN cc_start: 0.9165 (pp30) cc_final: 0.8878 (pp30) REVERT: B 12 GLU cc_start: 0.9425 (tp30) cc_final: 0.9176 (tp30) REVERT: B 17 GLN cc_start: 0.9594 (tm-30) cc_final: 0.9271 (tm-30) REVERT: B 32 GLN cc_start: 0.8902 (mt0) cc_final: 0.8662 (mt0) REVERT: B 220 GLN cc_start: 0.9068 (mt0) cc_final: 0.8776 (mt0) REVERT: C 58 GLU cc_start: 0.8248 (tp30) cc_final: 0.8010 (tp30) REVERT: E 73 ASP cc_start: 0.8323 (t0) cc_final: 0.8009 (t70) REVERT: E 120 SER cc_start: 0.8709 (t) cc_final: 0.8503 (p) REVERT: E 230 MET cc_start: 0.9003 (tmm) cc_final: 0.8432 (ttt) REVERT: R 167 ASP cc_start: 0.8660 (t0) cc_final: 0.8457 (t70) REVERT: R 193 MET cc_start: 0.8832 (mtm) cc_final: 0.8614 (mtt) REVERT: R 347 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8106 (mm-30) REVERT: R 367 ASP cc_start: 0.8635 (m-30) cc_final: 0.8434 (m-30) outliers start: 7 outliers final: 3 residues processed: 206 average time/residue: 0.2916 time to fit residues: 76.5074 Evaluate side-chains 130 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain R residue 215 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.0670 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN B 62 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN B 295 ASN B 340 ASN C 24 ASN R 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9114 Z= 0.216 Angle : 0.647 7.162 12360 Z= 0.345 Chirality : 0.044 0.207 1415 Planarity : 0.005 0.050 1540 Dihedral : 6.910 54.350 1359 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.36 % Allowed : 9.15 % Favored : 88.49 % 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: 0.44 (0.25), residues: 1116 helix: 1.21 (0.26), residues: 370 sheet: 0.30 (0.29), residues: 284 loop : -0.37 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.005 0.001 HIS R 143 PHE 0.022 0.001 PHE A 196 TYR 0.029 0.002 TYR E 235 ARG 0.006 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.071 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 20 ASP cc_start: 0.8309 (t70) cc_final: 0.8051 (t0) REVERT: A 204 GLN cc_start: 0.9199 (pp30) cc_final: 0.8729 (pp30) REVERT: A 243 MET cc_start: 0.8601 (tpp) cc_final: 0.7506 (tpp) REVERT: B 10 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8801 (mp0) REVERT: B 215 GLU cc_start: 0.8855 (mp0) cc_final: 0.8352 (mp0) REVERT: C 58 GLU cc_start: 0.8165 (tp30) cc_final: 0.7943 (tp30) REVERT: E 223 ASP cc_start: 0.9160 (m-30) cc_final: 0.8851 (m-30) REVERT: E 246 GLU cc_start: 0.7008 (pm20) cc_final: 0.6760 (pm20) REVERT: R 135 LYS cc_start: 0.8257 (mtpt) cc_final: 0.8040 (mmmt) REVERT: R 167 ASP cc_start: 0.8642 (t0) cc_final: 0.8360 (t70) REVERT: R 193 MET cc_start: 0.8744 (mtm) cc_final: 0.8531 (mtt) REVERT: R 347 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8078 (mm-30) outliers start: 23 outliers final: 9 residues processed: 153 average time/residue: 0.2390 time to fit residues: 48.8588 Evaluate side-chains 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain R residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 0.0570 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 239 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9114 Z= 0.248 Angle : 0.619 7.063 12360 Z= 0.328 Chirality : 0.043 0.204 1415 Planarity : 0.004 0.051 1540 Dihedral : 6.098 53.459 1356 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.75 % Allowed : 11.41 % Favored : 86.84 % 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: 0.64 (0.25), residues: 1116 helix: 1.42 (0.27), residues: 370 sheet: 0.49 (0.30), residues: 280 loop : -0.35 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS B 225 PHE 0.029 0.001 PHE E 68 TYR 0.024 0.002 TYR E 235 ARG 0.004 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.069 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: A 20 ASP cc_start: 0.8343 (t70) cc_final: 0.8076 (t0) REVERT: A 204 GLN cc_start: 0.9183 (pp30) cc_final: 0.8692 (pp30) REVERT: A 243 MET cc_start: 0.8381 (tpp) cc_final: 0.7584 (tpp) REVERT: C 17 GLU cc_start: 0.9507 (mm-30) cc_final: 0.9301 (tm-30) REVERT: C 20 LYS cc_start: 0.9492 (pptt) cc_final: 0.9208 (pptt) REVERT: C 22 GLU cc_start: 0.8141 (tp30) cc_final: 0.7915 (tt0) REVERT: C 30 VAL cc_start: 0.8634 (t) cc_final: 0.8250 (p) REVERT: C 58 GLU cc_start: 0.8132 (tp30) cc_final: 0.7876 (tp30) REVERT: E 73 ASP cc_start: 0.8146 (t0) cc_final: 0.7815 (t70) REVERT: E 220 GLU cc_start: 0.8479 (mp0) cc_final: 0.8001 (mp0) REVERT: E 223 ASP cc_start: 0.9213 (m-30) cc_final: 0.8405 (m-30) REVERT: E 230 MET cc_start: 0.8715 (tmm) cc_final: 0.8445 (ttm) REVERT: E 244 LYS cc_start: 0.8686 (tptp) cc_final: 0.8451 (tptt) REVERT: R 167 ASP cc_start: 0.8608 (t0) cc_final: 0.8327 (t70) REVERT: R 193 MET cc_start: 0.8779 (mtm) cc_final: 0.8565 (mtt) REVERT: R 347 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8035 (mm-30) outliers start: 17 outliers final: 12 residues processed: 148 average time/residue: 0.2292 time to fit residues: 46.3421 Evaluate side-chains 136 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9114 Z= 0.307 Angle : 0.627 7.084 12360 Z= 0.330 Chirality : 0.044 0.231 1415 Planarity : 0.004 0.054 1540 Dihedral : 5.855 52.324 1356 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.57 % Allowed : 12.64 % Favored : 84.79 % 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: 0.70 (0.26), residues: 1116 helix: 1.52 (0.27), residues: 370 sheet: 0.56 (0.31), residues: 278 loop : -0.38 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.006 0.001 HIS B 225 PHE 0.016 0.001 PHE A 196 TYR 0.026 0.002 TYR E 235 ARG 0.004 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.065 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: A 20 ASP cc_start: 0.8381 (t70) cc_final: 0.8087 (t0) REVERT: A 204 GLN cc_start: 0.9212 (pp30) cc_final: 0.8690 (pp30) REVERT: B 32 GLN cc_start: 0.8753 (mt0) cc_final: 0.8508 (mt0) REVERT: C 17 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9157 (tm-30) REVERT: C 22 GLU cc_start: 0.8129 (tp30) cc_final: 0.7761 (tt0) REVERT: C 58 GLU cc_start: 0.8181 (tp30) cc_final: 0.7905 (tp30) REVERT: E 73 ASP cc_start: 0.8106 (t0) cc_final: 0.7372 (t70) REVERT: E 76 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8814 (mtmm) REVERT: E 220 GLU cc_start: 0.8480 (mp0) cc_final: 0.8269 (mp0) REVERT: E 230 MET cc_start: 0.8710 (tmm) cc_final: 0.8394 (ttt) REVERT: E 244 LYS cc_start: 0.8668 (tptp) cc_final: 0.8418 (tptp) REVERT: E 246 GLU cc_start: 0.7201 (pm20) cc_final: 0.6847 (pm20) REVERT: R 167 ASP cc_start: 0.8617 (t0) cc_final: 0.8332 (t70) REVERT: R 193 MET cc_start: 0.8792 (mtm) cc_final: 0.8553 (mtt) REVERT: R 347 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8009 (mm-30) outliers start: 25 outliers final: 16 residues processed: 143 average time/residue: 0.2323 time to fit residues: 45.5927 Evaluate side-chains 134 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9114 Z= 0.276 Angle : 0.620 8.941 12360 Z= 0.324 Chirality : 0.044 0.302 1415 Planarity : 0.004 0.053 1540 Dihedral : 5.622 51.127 1356 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.47 % Allowed : 13.36 % Favored : 84.17 % 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: 0.64 (0.26), residues: 1116 helix: 1.45 (0.27), residues: 377 sheet: 0.44 (0.31), residues: 280 loop : -0.37 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 100 HIS 0.005 0.001 HIS B 225 PHE 0.036 0.001 PHE E 68 TYR 0.024 0.002 TYR E 235 ARG 0.003 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8410 (t70) cc_final: 0.8112 (t0) REVERT: A 22 ASN cc_start: 0.8981 (m-40) cc_final: 0.8732 (t0) REVERT: A 287 TYR cc_start: 0.8931 (m-80) cc_final: 0.8717 (m-80) REVERT: A 306 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8638 (mm-40) REVERT: B 10 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8612 (mp0) REVERT: B 32 GLN cc_start: 0.8725 (mt0) cc_final: 0.8496 (mt0) REVERT: C 58 GLU cc_start: 0.8237 (tp30) cc_final: 0.7970 (tp30) REVERT: E 73 ASP cc_start: 0.8066 (t0) cc_final: 0.7311 (t70) REVERT: E 76 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8879 (mtmm) REVERT: E 230 MET cc_start: 0.8708 (tmm) cc_final: 0.8362 (ttt) REVERT: R 167 ASP cc_start: 0.8655 (t0) cc_final: 0.8380 (t70) REVERT: R 193 MET cc_start: 0.8771 (mtm) cc_final: 0.8537 (mtt) REVERT: R 347 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7947 (mm-30) outliers start: 24 outliers final: 17 residues processed: 142 average time/residue: 0.2318 time to fit residues: 45.1486 Evaluate side-chains 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 199 ASP Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9114 Z= 0.379 Angle : 0.674 10.357 12360 Z= 0.351 Chirality : 0.046 0.322 1415 Planarity : 0.004 0.057 1540 Dihedral : 5.737 52.694 1356 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.57 % Allowed : 13.98 % Favored : 83.45 % 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: 0.56 (0.26), residues: 1116 helix: 1.44 (0.27), residues: 371 sheet: 0.33 (0.31), residues: 280 loop : -0.40 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.005 0.001 HIS B 225 PHE 0.028 0.002 PHE E 68 TYR 0.029 0.002 TYR E 235 ARG 0.005 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8473 (t70) cc_final: 0.8144 (t0) REVERT: A 22 ASN cc_start: 0.8994 (m-40) cc_final: 0.8763 (t0) REVERT: B 14 LEU cc_start: 0.9129 (mm) cc_final: 0.8893 (mt) REVERT: B 32 GLN cc_start: 0.8801 (mt0) cc_final: 0.8544 (mt0) REVERT: C 58 GLU cc_start: 0.8275 (tp30) cc_final: 0.7988 (tp30) REVERT: E 73 ASP cc_start: 0.8128 (t0) cc_final: 0.7800 (t70) REVERT: E 230 MET cc_start: 0.8697 (tmm) cc_final: 0.8374 (ttt) REVERT: E 244 LYS cc_start: 0.8686 (tptp) cc_final: 0.8415 (tptt) REVERT: R 167 ASP cc_start: 0.8624 (t0) cc_final: 0.8346 (t70) REVERT: R 193 MET cc_start: 0.8786 (mtm) cc_final: 0.8558 (mtt) REVERT: R 258 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8438 (mp) REVERT: R 347 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7961 (mm-30) outliers start: 25 outliers final: 19 residues processed: 138 average time/residue: 0.2379 time to fit residues: 44.6880 Evaluate side-chains 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 324 ILE Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 360 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9114 Z= 0.181 Angle : 0.618 11.298 12360 Z= 0.319 Chirality : 0.042 0.338 1415 Planarity : 0.004 0.054 1540 Dihedral : 5.311 49.680 1356 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.16 % Allowed : 14.90 % Favored : 82.94 % 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: 0.64 (0.26), residues: 1116 helix: 1.49 (0.27), residues: 377 sheet: 0.43 (0.31), residues: 277 loop : -0.40 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 332 HIS 0.003 0.001 HIS B 225 PHE 0.018 0.001 PHE E 68 TYR 0.019 0.001 TYR E 235 ARG 0.002 0.000 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8373 (t70) cc_final: 0.8101 (t0) REVERT: B 14 LEU cc_start: 0.9110 (mm) cc_final: 0.8887 (mt) REVERT: B 32 GLN cc_start: 0.8767 (mt0) cc_final: 0.8538 (mt0) REVERT: C 58 GLU cc_start: 0.8220 (tp30) cc_final: 0.7985 (tp30) REVERT: E 73 ASP cc_start: 0.8248 (t0) cc_final: 0.7649 (t70) REVERT: E 76 LYS cc_start: 0.9079 (mtmm) cc_final: 0.8795 (mtmm) REVERT: E 153 GLU cc_start: 0.8515 (pt0) cc_final: 0.8288 (pm20) REVERT: E 230 MET cc_start: 0.8682 (tmm) cc_final: 0.8284 (ttt) REVERT: R 258 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8118 (mp) REVERT: R 347 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7933 (mm-30) outliers start: 21 outliers final: 13 residues processed: 145 average time/residue: 0.2395 time to fit residues: 46.8315 Evaluate side-chains 132 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN E 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9114 Z= 0.195 Angle : 0.634 12.193 12360 Z= 0.326 Chirality : 0.042 0.352 1415 Planarity : 0.004 0.051 1540 Dihedral : 5.144 47.683 1356 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.95 % Allowed : 15.31 % Favored : 82.73 % 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: 0.65 (0.26), residues: 1116 helix: 1.54 (0.27), residues: 378 sheet: 0.41 (0.31), residues: 279 loop : -0.41 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.003 0.000 HIS B 225 PHE 0.016 0.001 PHE E 68 TYR 0.024 0.001 TYR E 235 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8384 (t70) cc_final: 0.8114 (t0) REVERT: B 14 LEU cc_start: 0.9123 (mm) cc_final: 0.8895 (mt) REVERT: C 58 GLU cc_start: 0.8227 (tp30) cc_final: 0.7990 (tp30) REVERT: E 73 ASP cc_start: 0.8286 (t0) cc_final: 0.7554 (t70) REVERT: E 76 LYS cc_start: 0.9078 (mtmm) cc_final: 0.8788 (mtmm) REVERT: E 153 GLU cc_start: 0.8545 (pt0) cc_final: 0.8292 (pm20) REVERT: E 230 MET cc_start: 0.8623 (tmm) cc_final: 0.8287 (ttt) REVERT: R 158 LYS cc_start: 0.9528 (mttm) cc_final: 0.9316 (mttt) REVERT: R 167 ASP cc_start: 0.8415 (t0) cc_final: 0.7979 (t70) REVERT: R 258 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8230 (mp) REVERT: R 347 GLU cc_start: 0.8585 (mm-30) cc_final: 0.7936 (mm-30) outliers start: 19 outliers final: 14 residues processed: 143 average time/residue: 0.2275 time to fit residues: 44.7229 Evaluate side-chains 135 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.2980 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9114 Z= 0.196 Angle : 0.629 12.617 12360 Z= 0.323 Chirality : 0.042 0.364 1415 Planarity : 0.004 0.053 1540 Dihedral : 5.071 46.877 1356 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.54 % Allowed : 16.24 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1116 helix: 1.48 (0.27), residues: 384 sheet: 0.34 (0.30), residues: 282 loop : -0.43 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.003 0.000 HIS B 225 PHE 0.022 0.001 PHE E 68 TYR 0.021 0.001 TYR E 235 ARG 0.003 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8391 (t70) cc_final: 0.8112 (t0) REVERT: A 22 ASN cc_start: 0.8994 (m-40) cc_final: 0.8785 (t0) REVERT: B 14 LEU cc_start: 0.9126 (mm) cc_final: 0.8899 (mt) REVERT: C 58 GLU cc_start: 0.8257 (tp30) cc_final: 0.8027 (tp30) REVERT: E 73 ASP cc_start: 0.8296 (t0) cc_final: 0.7525 (t70) REVERT: E 76 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8831 (mtmm) REVERT: E 153 GLU cc_start: 0.8503 (pt0) cc_final: 0.8197 (pm20) REVERT: E 223 ASP cc_start: 0.8713 (m-30) cc_final: 0.8132 (m-30) REVERT: E 230 MET cc_start: 0.8616 (tmm) cc_final: 0.8324 (ttt) REVERT: R 158 LYS cc_start: 0.9527 (mttm) cc_final: 0.9320 (mttt) REVERT: R 167 ASP cc_start: 0.8411 (t0) cc_final: 0.8025 (t70) REVERT: R 258 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8239 (mp) REVERT: R 347 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7932 (mm-30) outliers start: 15 outliers final: 13 residues processed: 139 average time/residue: 0.2331 time to fit residues: 44.2760 Evaluate side-chains 135 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9114 Z= 0.215 Angle : 0.640 12.173 12360 Z= 0.328 Chirality : 0.043 0.361 1415 Planarity : 0.004 0.054 1540 Dihedral : 5.083 46.711 1356 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.64 % Allowed : 15.83 % Favored : 82.53 % 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: 0.64 (0.26), residues: 1116 helix: 1.54 (0.27), residues: 384 sheet: 0.37 (0.31), residues: 282 loop : -0.44 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 PHE 0.017 0.001 PHE E 68 TYR 0.021 0.001 TYR E 235 ARG 0.005 0.000 ARG E 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8409 (t70) cc_final: 0.8116 (t0) REVERT: A 22 ASN cc_start: 0.8998 (m-40) cc_final: 0.8794 (t0) REVERT: B 14 LEU cc_start: 0.9148 (mm) cc_final: 0.8925 (mt) REVERT: C 58 GLU cc_start: 0.8270 (tp30) cc_final: 0.8036 (tp30) REVERT: E 73 ASP cc_start: 0.8263 (t0) cc_final: 0.7468 (t70) REVERT: E 76 LYS cc_start: 0.9074 (mtmm) cc_final: 0.8824 (mtmm) REVERT: E 153 GLU cc_start: 0.8514 (pt0) cc_final: 0.8184 (pm20) REVERT: E 223 ASP cc_start: 0.8641 (m-30) cc_final: 0.8441 (m-30) REVERT: R 158 LYS cc_start: 0.9526 (mttm) cc_final: 0.9320 (mttt) REVERT: R 167 ASP cc_start: 0.8423 (t0) cc_final: 0.8033 (t70) REVERT: R 258 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8371 (mp) REVERT: R 347 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8040 (mm-30) outliers start: 16 outliers final: 14 residues processed: 135 average time/residue: 0.2352 time to fit residues: 43.2914 Evaluate side-chains 136 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 199 ASP Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 0.0060 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.058770 restraints weight = 21375.395| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.31 r_work: 0.2741 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9114 Z= 0.254 Angle : 0.651 12.731 12360 Z= 0.335 Chirality : 0.043 0.351 1415 Planarity : 0.004 0.052 1540 Dihedral : 5.212 47.131 1356 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.64 % Allowed : 15.83 % Favored : 82.53 % 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: 0.66 (0.26), residues: 1116 helix: 1.54 (0.27), residues: 385 sheet: 0.32 (0.31), residues: 286 loop : -0.38 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 211 HIS 0.004 0.001 HIS B 225 PHE 0.014 0.001 PHE A 196 TYR 0.027 0.001 TYR E 235 ARG 0.003 0.000 ARG E 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.22 seconds wall clock time: 38 minutes 23.78 seconds (2303.78 seconds total)