Starting phenix.real_space_refine on Sat Dec 28 18:48:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwk_37891/12_2024/8wwk_37891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwk_37891/12_2024/8wwk_37891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwk_37891/12_2024/8wwk_37891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwk_37891/12_2024/8wwk_37891.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwk_37891/12_2024/8wwk_37891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwk_37891/12_2024/8wwk_37891.cif" } resolution = 2.61 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= 0.087 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 68 5.16 5 C 5712 2.51 5 N 1519 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8967 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2242 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 139 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.42, per 1000 atoms: 0.60 Number of scatterers: 8967 At special positions: 0 Unit cell: (88.81, 117.7, 120.91, 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 68 16.00 O 1668 8.00 N 1519 7.00 C 5712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 38.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.572A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.289A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.920A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.663A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.085A 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 310 removed outlier: 4.317A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 108 through 138 removed outlier: 3.573A pdb=" N MET R 112 " --> pdb=" O ILE R 108 " (cutoff:3.500A) Proline residue: R 113 - end of helix removed outlier: 3.819A pdb=" N SER R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 164 Processing helix chain 'R' and resid 164 through 174 removed outlier: 5.108A pdb=" N GLN R 171 " --> pdb=" O PHE R 167 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU R 172 " --> pdb=" O MET R 168 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY R 174 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 216 removed outlier: 3.892A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.725A pdb=" N LYS R 222 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 Processing helix chain 'R' and resid 244 through 250 Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.824A pdb=" N LEU R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 302 Processing helix chain 'R' and resid 313 through 348 Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.027A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.317A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.804A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.558A 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: 3.570A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.797A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.170A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.602A 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: 6.873A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.095A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.759A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.234A 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: 6.796A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.479A 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: 4.164A 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 141 removed outlier: 3.545A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.505A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.141A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 251 through 255 Processing sheet with id=AB7, first strand: chain 'L' and resid 8 through 9 485 hydrogen bonds defined for protein. 1329 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: 2.95 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2888 1.34 - 1.46: 2186 1.46 - 1.58: 3985 1.58 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 9158 Sorted by residual: bond pdb=" N GLY B 116 " pdb=" CA GLY B 116 " ideal model delta sigma weight residual 1.458 1.447 0.010 9.20e-03 1.18e+04 1.30e+00 bond pdb=" C LEU A 39 " pdb=" N GLY A 40 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.70e-01 bond pdb=" C GLY B 116 " pdb=" O GLY B 116 " ideal model delta sigma weight residual 1.239 1.234 0.005 8.50e-03 1.38e+04 3.64e-01 bond pdb=" C MET R 165 " pdb=" N PRO R 166 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.28e-02 6.10e+03 3.18e-01 bond pdb=" CB PHE B 292 " pdb=" CG PHE B 292 " ideal model delta sigma weight residual 1.502 1.515 -0.013 2.30e-02 1.89e+03 3.12e-01 ... (remaining 9153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 12233 1.17 - 2.33: 148 2.33 - 3.50: 34 3.50 - 4.67: 7 4.67 - 5.84: 5 Bond angle restraints: 12427 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.88e+00 angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 109.34 112.83 -3.49 2.08e+00 2.31e-01 2.82e+00 angle pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " pdb=" CG LEU B 190 " ideal model delta sigma weight residual 116.30 122.14 -5.84 3.50e+00 8.16e-02 2.78e+00 angle pdb=" N GLY B 116 " pdb=" CA GLY B 116 " pdb=" C GLY B 116 " ideal model delta sigma weight residual 111.16 114.03 -2.87 1.76e+00 3.23e-01 2.65e+00 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 124.82 127.34 -2.52 1.78e+00 3.16e-01 2.01e+00 ... (remaining 12422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 5228 16.13 - 32.25: 166 32.25 - 48.38: 28 48.38 - 64.50: 6 64.50 - 80.63: 1 Dihedral angle restraints: 5429 sinusoidal: 2063 harmonic: 3366 Sorted by residual: dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LYS R 139 " pdb=" C LYS R 139 " pdb=" N LEU R 140 " pdb=" CA LEU R 140 " ideal model delta harmonic sigma weight residual 180.00 164.93 15.07 0 5.00e+00 4.00e-02 9.08e+00 dihedral pdb=" N LYS A 312 " pdb=" CA LYS A 312 " pdb=" CB LYS A 312 " pdb=" CG LYS A 312 " ideal model delta sinusoidal sigma weight residual 180.00 -127.96 -52.04 3 1.50e+01 4.44e-03 9.08e+00 ... (remaining 5426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 875 0.026 - 0.051: 316 0.051 - 0.077: 136 0.077 - 0.102: 63 0.102 - 0.128: 36 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1423 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO B 236 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO E 107 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.22e+00 pdb=" N PRO B 194 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.016 5.00e-02 4.00e+02 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 782 2.74 - 3.28: 8784 3.28 - 3.82: 15448 3.82 - 4.36: 19349 4.36 - 4.90: 32640 Nonbonded interactions: 77003 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASN A 269 " pdb=" OG1 THR A 324 " model vdw 2.242 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.283 3.040 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.291 3.040 ... (remaining 76998 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: 0.790 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.030 Find NCS groups from input model: 0.080 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.002 0.017 9158 Z= 0.100 Angle : 0.392 5.837 12427 Z= 0.207 Chirality : 0.039 0.128 1426 Planarity : 0.003 0.050 1570 Dihedral : 8.406 80.627 3245 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.72 % Allowed : 2.58 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1144 helix: 1.16 (0.25), residues: 394 sheet: 0.97 (0.30), residues: 288 loop : 0.36 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.002 0.001 HIS B 62 PHE 0.009 0.001 PHE B 199 TYR 0.010 0.001 TYR E 190 ARG 0.001 0.000 ARG R 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 1.019 Fit side-chains REVERT: A 8 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8499 (mt-10) REVERT: A 10 LYS cc_start: 0.8813 (mttt) cc_final: 0.8530 (mtmp) REVERT: A 29 LYS cc_start: 0.8064 (tttt) cc_final: 0.7657 (ttpp) REVERT: B 25 CYS cc_start: 0.7906 (p) cc_final: 0.6766 (m) REVERT: B 130 GLU cc_start: 0.8313 (mp0) cc_final: 0.8105 (mp0) REVERT: C 21 MET cc_start: 0.7082 (mmm) cc_final: 0.6469 (tmt) REVERT: C 47 GLU cc_start: 0.7999 (pt0) cc_final: 0.7741 (mp0) REVERT: E 43 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8073 (mtmt) REVERT: E 77 ASN cc_start: 0.8277 (m-40) cc_final: 0.7925 (m-40) REVERT: E 223 ASP cc_start: 0.8634 (m-30) cc_final: 0.8395 (m-30) REVERT: R 142 TRP cc_start: 0.6869 (m-90) cc_final: 0.5954 (m100) REVERT: R 252 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6406 (mpp-170) outliers start: 7 outliers final: 5 residues processed: 190 average time/residue: 1.3186 time to fit residues: 266.6137 Evaluate side-chains 147 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 220 GLN B 259 GLN R 194 ASN R 281 GLN R 345 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9158 Z= 0.195 Angle : 0.527 5.653 12427 Z= 0.286 Chirality : 0.042 0.137 1426 Planarity : 0.004 0.054 1570 Dihedral : 5.106 55.884 1267 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.79 % Allowed : 7.84 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1144 helix: 2.26 (0.25), residues: 394 sheet: 0.59 (0.29), residues: 279 loop : 0.20 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.013 0.002 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.006 0.001 ARG R 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.967 Fit side-chains REVERT: A 8 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8493 (mt-10) REVERT: A 28 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: A 29 LYS cc_start: 0.7930 (tttt) cc_final: 0.7616 (ttpp) REVERT: A 33 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: B 130 GLU cc_start: 0.8403 (mp0) cc_final: 0.8018 (mp0) REVERT: B 170 ASP cc_start: 0.8775 (t70) cc_final: 0.8558 (t70) REVERT: B 217 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8124 (pmm) REVERT: E 3 GLN cc_start: 0.8148 (tt0) cc_final: 0.7914 (tt0) REVERT: E 43 LYS cc_start: 0.8529 (mmtm) cc_final: 0.8052 (mtmt) REVERT: E 77 ASN cc_start: 0.8314 (m-40) cc_final: 0.7884 (m-40) REVERT: R 142 TRP cc_start: 0.6947 (m-90) cc_final: 0.5990 (m100) REVERT: R 165 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7842 (ttt) REVERT: R 187 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7280 (mm) REVERT: R 235 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7802 (mp) REVERT: R 252 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6259 (mpp-170) REVERT: R 356 LEU cc_start: 0.8259 (mm) cc_final: 0.8039 (mm) outliers start: 27 outliers final: 10 residues processed: 161 average time/residue: 1.4320 time to fit residues: 244.3060 Evaluate side-chains 162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 322 HIS B 156 GLN B 259 GLN E 82 GLN R 345 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9158 Z= 0.233 Angle : 0.528 6.204 12427 Z= 0.286 Chirality : 0.043 0.164 1426 Planarity : 0.004 0.057 1570 Dihedral : 5.314 58.415 1267 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.10 % Allowed : 9.60 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1144 helix: 2.47 (0.25), residues: 393 sheet: 0.36 (0.29), residues: 276 loop : 0.06 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.015 0.002 PHE B 151 TYR 0.013 0.002 TYR R 341 ARG 0.005 0.001 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7079 (mt-10) REVERT: A 29 LYS cc_start: 0.7915 (tttt) cc_final: 0.7595 (ttpp) REVERT: A 33 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: B 217 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8216 (pmm) REVERT: E 43 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8057 (mtmt) REVERT: E 77 ASN cc_start: 0.8410 (m-40) cc_final: 0.8001 (m-40) REVERT: E 234 GLU cc_start: 0.8694 (pt0) cc_final: 0.8410 (pt0) REVERT: R 142 TRP cc_start: 0.6925 (m-90) cc_final: 0.6010 (m100) REVERT: R 250 TYR cc_start: 0.8255 (m-80) cc_final: 0.8017 (m-10) REVERT: R 252 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6898 (mpt90) REVERT: R 356 LEU cc_start: 0.8185 (mm) cc_final: 0.7979 (mm) outliers start: 30 outliers final: 16 residues processed: 158 average time/residue: 1.4055 time to fit residues: 235.2745 Evaluate side-chains 161 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 322 HIS B 156 GLN E 82 GLN R 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9158 Z= 0.216 Angle : 0.513 5.947 12427 Z= 0.277 Chirality : 0.042 0.155 1426 Planarity : 0.004 0.058 1570 Dihedral : 5.342 59.604 1267 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.51 % Allowed : 10.01 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1144 helix: 2.55 (0.25), residues: 393 sheet: 0.23 (0.29), residues: 281 loop : 0.04 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR R 341 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8492 (mt-10) REVERT: A 28 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: A 29 LYS cc_start: 0.7898 (tttt) cc_final: 0.7605 (ttpp) REVERT: A 33 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: B 217 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8363 (pp-130) REVERT: C 58 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: E 43 LYS cc_start: 0.8516 (mmtm) cc_final: 0.8055 (mtmt) REVERT: E 77 ASN cc_start: 0.8408 (m-40) cc_final: 0.7972 (m-40) REVERT: E 234 GLU cc_start: 0.8701 (pt0) cc_final: 0.8418 (pt0) REVERT: R 142 TRP cc_start: 0.6968 (m-90) cc_final: 0.5905 (m100) REVERT: R 250 TYR cc_start: 0.8207 (m-80) cc_final: 0.7949 (m-10) REVERT: R 356 LEU cc_start: 0.8151 (mm) cc_final: 0.7950 (mm) outliers start: 34 outliers final: 20 residues processed: 160 average time/residue: 1.4280 time to fit residues: 242.2984 Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 156 GLN R 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9158 Z= 0.234 Angle : 0.522 6.259 12427 Z= 0.282 Chirality : 0.043 0.160 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.016 43.468 1263 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.41 % Allowed : 10.84 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1144 helix: 2.54 (0.25), residues: 394 sheet: 0.16 (0.29), residues: 285 loop : 0.01 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.015 0.002 PHE B 151 TYR 0.013 0.002 TYR R 341 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: A 29 LYS cc_start: 0.7927 (tttt) cc_final: 0.7633 (ttpp) REVERT: A 33 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: A 270 LYS cc_start: 0.8468 (mttt) cc_final: 0.8018 (mttp) REVERT: B 42 ARG cc_start: 0.7012 (tpt170) cc_final: 0.6387 (tpt170) REVERT: B 217 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8166 (pmm) REVERT: C 58 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: E 43 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8000 (mtmt) REVERT: E 77 ASN cc_start: 0.8438 (m-40) cc_final: 0.7990 (m-40) REVERT: E 234 GLU cc_start: 0.8716 (pt0) cc_final: 0.8454 (pt0) REVERT: R 142 TRP cc_start: 0.6967 (m-90) cc_final: 0.5888 (m100) REVERT: R 165 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7638 (ttt) REVERT: R 250 TYR cc_start: 0.8233 (m-80) cc_final: 0.7992 (m-10) outliers start: 33 outliers final: 21 residues processed: 157 average time/residue: 1.4993 time to fit residues: 248.4862 Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 156 GLN E 82 GLN R 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9158 Z= 0.222 Angle : 0.520 6.104 12427 Z= 0.280 Chirality : 0.043 0.176 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.005 43.610 1263 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.51 % Allowed : 11.25 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1144 helix: 2.59 (0.25), residues: 394 sheet: 0.15 (0.29), residues: 284 loop : -0.01 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.015 0.001 PHE B 151 TYR 0.013 0.002 TYR R 341 ARG 0.006 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.930 Fit side-chains REVERT: A 28 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7079 (mt-10) REVERT: A 29 LYS cc_start: 0.7907 (tttt) cc_final: 0.7626 (ttpp) REVERT: A 33 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: A 270 LYS cc_start: 0.8480 (mttt) cc_final: 0.8028 (mttp) REVERT: B 42 ARG cc_start: 0.7010 (tpt170) cc_final: 0.6389 (tpt170) REVERT: B 217 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8355 (pp-130) REVERT: C 58 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: E 43 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8055 (mtmt) REVERT: E 77 ASN cc_start: 0.8432 (m-40) cc_final: 0.7995 (m-40) REVERT: E 234 GLU cc_start: 0.8720 (pt0) cc_final: 0.8468 (pt0) REVERT: R 142 TRP cc_start: 0.6976 (m-90) cc_final: 0.5907 (m100) REVERT: R 165 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7646 (ttt) REVERT: R 250 TYR cc_start: 0.8230 (m-80) cc_final: 0.7989 (m-10) outliers start: 34 outliers final: 20 residues processed: 158 average time/residue: 1.4756 time to fit residues: 246.4612 Evaluate side-chains 163 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 156 GLN R 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9158 Z= 0.255 Angle : 0.541 6.532 12427 Z= 0.290 Chirality : 0.043 0.196 1426 Planarity : 0.004 0.061 1570 Dihedral : 5.078 43.815 1263 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.61 % Allowed : 10.84 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1144 helix: 2.56 (0.25), residues: 396 sheet: 0.18 (0.28), residues: 296 loop : -0.09 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.015 0.002 PHE B 151 TYR 0.014 0.002 TYR R 341 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.058 Fit side-chains REVERT: A 28 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: A 29 LYS cc_start: 0.7910 (tttt) cc_final: 0.7631 (ttpp) REVERT: A 33 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: A 270 LYS cc_start: 0.8484 (mttt) cc_final: 0.8021 (mttp) REVERT: B 42 ARG cc_start: 0.7034 (tpt170) cc_final: 0.6418 (tpt170) REVERT: B 217 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8346 (pp-130) REVERT: C 58 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: E 43 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8030 (mtmt) REVERT: E 77 ASN cc_start: 0.8440 (m-40) cc_final: 0.8000 (m-40) REVERT: E 234 GLU cc_start: 0.8715 (pt0) cc_final: 0.8452 (pt0) REVERT: R 142 TRP cc_start: 0.6955 (m-90) cc_final: 0.5861 (m100) REVERT: R 165 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7668 (ttt) REVERT: R 250 TYR cc_start: 0.8228 (m-80) cc_final: 0.7994 (m-10) outliers start: 35 outliers final: 20 residues processed: 159 average time/residue: 1.4926 time to fit residues: 250.4072 Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.0470 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 156 GLN R 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9158 Z= 0.171 Angle : 0.494 5.768 12427 Z= 0.266 Chirality : 0.042 0.193 1426 Planarity : 0.004 0.061 1570 Dihedral : 4.878 43.952 1262 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.20 % Allowed : 10.94 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1144 helix: 2.72 (0.25), residues: 394 sheet: 0.19 (0.29), residues: 277 loop : 0.01 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.006 0.001 HIS A 188 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR E 190 ARG 0.008 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.344 Fit side-chains REVERT: A 28 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: A 29 LYS cc_start: 0.7889 (tttt) cc_final: 0.7604 (ttpp) REVERT: A 32 ARG cc_start: 0.7818 (mtt90) cc_final: 0.7589 (mtt90) REVERT: A 33 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: A 243 MET cc_start: 0.8682 (tpp) cc_final: 0.8413 (ttm) REVERT: A 270 LYS cc_start: 0.8496 (mttt) cc_final: 0.8127 (mttp) REVERT: B 217 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8328 (pp-130) REVERT: E 43 LYS cc_start: 0.8527 (mmtm) cc_final: 0.7975 (mtpt) REVERT: E 77 ASN cc_start: 0.8394 (m-40) cc_final: 0.7987 (m-40) REVERT: E 234 GLU cc_start: 0.8712 (pt0) cc_final: 0.8449 (pt0) REVERT: R 142 TRP cc_start: 0.6960 (m-90) cc_final: 0.5876 (m100) REVERT: R 184 MET cc_start: 0.7144 (tpt) cc_final: 0.6865 (tpt) outliers start: 31 outliers final: 20 residues processed: 160 average time/residue: 1.4323 time to fit residues: 242.6932 Evaluate side-chains 162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 156 GLN R 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9158 Z= 0.232 Angle : 0.541 6.989 12427 Z= 0.288 Chirality : 0.043 0.185 1426 Planarity : 0.004 0.060 1570 Dihedral : 4.998 43.550 1262 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.20 % Allowed : 11.15 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1144 helix: 2.64 (0.25), residues: 396 sheet: 0.07 (0.29), residues: 285 loop : -0.02 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.003 0.001 HIS A 188 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.002 TYR R 341 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.066 Fit side-chains REVERT: A 28 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6984 (mt-10) REVERT: A 29 LYS cc_start: 0.7901 (tttt) cc_final: 0.7607 (ttpp) REVERT: A 33 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: A 270 LYS cc_start: 0.8496 (mttt) cc_final: 0.8130 (mttp) REVERT: B 217 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8311 (pp-130) REVERT: E 43 LYS cc_start: 0.8525 (mmtm) cc_final: 0.7971 (mtpt) REVERT: E 77 ASN cc_start: 0.8427 (m-40) cc_final: 0.7993 (m-40) REVERT: E 234 GLU cc_start: 0.8722 (pt0) cc_final: 0.8451 (pt0) REVERT: R 142 TRP cc_start: 0.6952 (m-90) cc_final: 0.5861 (m100) outliers start: 31 outliers final: 23 residues processed: 159 average time/residue: 1.4603 time to fit residues: 245.5618 Evaluate side-chains 166 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 156 GLN R 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9158 Z= 0.273 Angle : 0.576 10.425 12427 Z= 0.305 Chirality : 0.044 0.207 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.133 43.959 1262 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.89 % Allowed : 11.87 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1144 helix: 2.55 (0.25), residues: 394 sheet: 0.07 (0.28), residues: 296 loop : -0.07 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.014 0.002 PHE B 151 TYR 0.014 0.002 TYR R 341 ARG 0.009 0.001 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 2.244 Fit side-chains REVERT: A 28 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: A 29 LYS cc_start: 0.7896 (tttt) cc_final: 0.7617 (ttpp) REVERT: A 33 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: A 270 LYS cc_start: 0.8490 (mttt) cc_final: 0.8122 (mttp) REVERT: B 42 ARG cc_start: 0.7021 (tpt170) cc_final: 0.6407 (tpt170) REVERT: E 43 LYS cc_start: 0.8526 (mmtm) cc_final: 0.7962 (mtpt) REVERT: E 77 ASN cc_start: 0.8441 (m-40) cc_final: 0.8005 (m-40) REVERT: E 234 GLU cc_start: 0.8716 (pt0) cc_final: 0.8486 (pt0) REVERT: R 142 TRP cc_start: 0.6946 (m-90) cc_final: 0.5833 (m100) outliers start: 28 outliers final: 22 residues processed: 154 average time/residue: 1.5920 time to fit residues: 258.4837 Evaluate side-chains 162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 156 GLN R 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.168174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131101 restraints weight = 8662.975| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.69 r_work: 0.3055 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9158 Z= 0.182 Angle : 0.513 8.166 12427 Z= 0.274 Chirality : 0.042 0.137 1426 Planarity : 0.004 0.060 1570 Dihedral : 4.938 44.021 1262 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.79 % Allowed : 12.18 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1144 helix: 2.71 (0.25), residues: 396 sheet: 0.07 (0.29), residues: 278 loop : -0.01 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.009 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4176.86 seconds wall clock time: 75 minutes 32.76 seconds (4532.76 seconds total)