Starting phenix.real_space_refine on Sat Dec 28 17:00:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efb_28077/12_2024/8efb_28077.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efb_28077/12_2024/8efb_28077.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/cci-nas-00/data/ceres_data/8efb_28077/12_2024/8efb_28077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efb_28077/12_2024/8efb_28077.map" model { file = "/net/cci-nas-00/data/ceres_data/8efb_28077/12_2024/8efb_28077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efb_28077/12_2024/8efb_28077.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= 0.007 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 73 5.16 5 C 5701 2.51 5 N 1508 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 16 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: 8947 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2290 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 273} Chain: "A" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1826 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 436 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1792 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'WH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.46, per 1000 atoms: 0.61 Number of scatterers: 8947 At special positions: 0 Unit cell: (125.28, 113.4, 108, 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 73 16.00 O 1665 8.00 N 1508 7.00 C 5701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 39.2% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'R' and resid 69 through 98 Processing helix chain 'R' and resid 103 through 133 Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.911A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 3.569A pdb=" N ALA R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 264 removed outlier: 4.758A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 340 Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 removed outlier: 3.515A pdb=" N PHE R 352 " --> pdb=" O CYS R 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 213 removed outlier: 4.210A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.605A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.553A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.045A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.948A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.888A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.230A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.151A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.729A pdb=" N MET A 198 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.817A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.805A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.994A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.681A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.707A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.025A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.878A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.660A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.660A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 149 removed outlier: 7.062A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1404 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: 2.69 Time building geometry restraints manager: 2.58 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: 2721 1.34 - 1.46: 2195 1.46 - 1.59: 4114 1.59 - 1.71: 0 1.71 - 1.83: 107 Bond restraints: 9137 Sorted by residual: bond pdb=" C22 WH2 R 500 " pdb=" O02 WH2 R 500 " ideal model delta sigma weight residual 1.428 1.557 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C ALA E 40 " pdb=" N PRO E 41 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.18e+00 bond pdb=" C PHE B 235 " pdb=" N PRO B 236 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.19e-02 7.06e+03 6.75e+00 bond pdb=" C LEU R 123 " pdb=" N PRO R 124 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.36e-02 5.41e+03 5.40e+00 bond pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.23e-02 6.61e+03 4.81e+00 ... (remaining 9132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 11785 1.93 - 3.86: 517 3.86 - 5.79: 53 5.79 - 7.72: 19 7.72 - 9.65: 4 Bond angle restraints: 12378 Sorted by residual: angle pdb=" CA ARG E 219 " pdb=" CB ARG E 219 " pdb=" CG ARG E 219 " ideal model delta sigma weight residual 114.10 123.25 -9.15 2.00e+00 2.50e-01 2.09e+01 angle pdb=" C ALA R 104 " pdb=" N THR R 105 " pdb=" CA THR R 105 " ideal model delta sigma weight residual 120.38 126.28 -5.90 1.37e+00 5.33e-01 1.85e+01 angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 125.66 133.36 -7.70 1.85e+00 2.92e-01 1.73e+01 angle pdb=" CA PHE R 206 " pdb=" CB PHE R 206 " pdb=" CG PHE R 206 " ideal model delta sigma weight residual 113.80 117.91 -4.11 1.00e+00 1.00e+00 1.69e+01 angle pdb=" N PHE R 206 " pdb=" CA PHE R 206 " pdb=" CB PHE R 206 " ideal model delta sigma weight residual 110.16 115.12 -4.96 1.48e+00 4.57e-01 1.12e+01 ... (remaining 12373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.23: 5004 11.23 - 22.47: 365 22.47 - 33.70: 58 33.70 - 44.94: 17 44.94 - 56.17: 5 Dihedral angle restraints: 5449 sinusoidal: 2147 harmonic: 3302 Sorted by residual: 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 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" N PHE R 206 " pdb=" C PHE R 206 " pdb=" CA PHE R 206 " pdb=" CB PHE R 206 " ideal model delta harmonic sigma weight residual 122.80 131.76 -8.96 0 2.50e+00 1.60e-01 1.29e+01 ... (remaining 5446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1052 0.057 - 0.114: 272 0.114 - 0.171: 67 0.171 - 0.228: 13 0.228 - 0.285: 2 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA PHE R 206 " pdb=" N PHE R 206 " pdb=" C PHE R 206 " pdb=" CB PHE R 206 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE R 140 " pdb=" CA ILE R 140 " pdb=" CG1 ILE R 140 " pdb=" CG2 ILE R 140 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB THR E 91 " pdb=" CA THR E 91 " pdb=" OG1 THR E 91 " pdb=" CG2 THR E 91 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1403 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 206 " 0.025 2.00e-02 2.50e+03 2.05e-02 7.32e+00 pdb=" CG PHE R 206 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE R 206 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 206 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE R 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 206 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE R 206 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 158 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C TRP R 158 " -0.046 2.00e-02 2.50e+03 pdb=" O TRP R 158 " 0.017 2.00e-02 2.50e+03 pdb=" N THR R 159 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 197 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C SER R 197 " 0.044 2.00e-02 2.50e+03 pdb=" O SER R 197 " -0.017 2.00e-02 2.50e+03 pdb=" N SER R 198 " -0.015 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1318 2.78 - 3.31: 8464 3.31 - 3.84: 14836 3.84 - 4.37: 16974 4.37 - 4.90: 30493 Nonbonded interactions: 72085 Sorted by model distance: nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.247 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.257 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.294 3.040 nonbonded pdb=" O ARG R 260 " pdb=" OG SER R 263 " model vdw 2.331 3.040 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.349 3.120 ... (remaining 72080 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: 0.250 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 9137 Z= 0.345 Angle : 0.908 9.648 12378 Z= 0.538 Chirality : 0.056 0.285 1406 Planarity : 0.007 0.049 1554 Dihedral : 8.311 56.169 3313 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.18 (0.24), residues: 1122 helix: 2.62 (0.24), residues: 413 sheet: 0.17 (0.29), residues: 283 loop : -0.63 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 111 HIS 0.009 0.002 HIS B 54 PHE 0.042 0.003 PHE R 206 TYR 0.037 0.003 TYR R 151 ARG 0.006 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 132 MET cc_start: 0.6703 (mmm) cc_final: 0.6449 (mmt) REVERT: R 223 PHE cc_start: 0.6558 (m-80) cc_final: 0.6263 (m-10) REVERT: R 268 SER cc_start: 0.6932 (m) cc_final: 0.6722 (p) REVERT: A 28 GLU cc_start: 0.6333 (mt-10) cc_final: 0.5904 (mp0) REVERT: A 207 GLU cc_start: 0.6510 (tt0) cc_final: 0.6137 (tt0) REVERT: A 298 GLU cc_start: 0.6951 (tt0) cc_final: 0.6327 (mt-10) REVERT: A 337 ASP cc_start: 0.7986 (m-30) cc_final: 0.7674 (m-30) REVERT: B 36 ASN cc_start: 0.7609 (m-40) cc_final: 0.7333 (p0) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.2548 time to fit residues: 91.8763 Evaluate side-chains 160 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 0.1980 chunk 100 optimal weight: 8.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 173 HIS R 334 ASN A 244 HIS A 322 HIS B 35 ASN B 91 HIS B 266 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9137 Z= 0.357 Angle : 0.648 10.795 12378 Z= 0.346 Chirality : 0.046 0.156 1406 Planarity : 0.005 0.057 1554 Dihedral : 4.650 38.292 1271 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.16 % Allowed : 7.86 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.38 (0.24), residues: 1122 helix: 2.82 (0.24), residues: 404 sheet: 0.22 (0.29), residues: 288 loop : -0.43 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 111 HIS 0.008 0.002 HIS B 62 PHE 0.028 0.002 PHE R 206 TYR 0.021 0.002 TYR R 108 ARG 0.005 0.001 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: R 97 ARG cc_start: 0.6506 (mmp-170) cc_final: 0.5921 (ttm-80) REVERT: R 123 LEU cc_start: 0.8398 (tp) cc_final: 0.8148 (tp) REVERT: R 132 MET cc_start: 0.7085 (mmm) cc_final: 0.6734 (mmt) REVERT: R 223 PHE cc_start: 0.6540 (m-80) cc_final: 0.6161 (m-10) REVERT: R 257 MET cc_start: 0.8333 (ttp) cc_final: 0.8048 (ttt) REVERT: A 308 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: A 313 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7497 (ttm170) REVERT: B 32 GLN cc_start: 0.8146 (mt0) cc_final: 0.7577 (mp10) REVERT: B 43 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8058 (mt) REVERT: B 59 TYR cc_start: 0.8708 (m-80) cc_final: 0.8367 (m-80) REVERT: B 98 SER cc_start: 0.8508 (m) cc_final: 0.8264 (t) REVERT: E 187 GLN cc_start: 0.8477 (pt0) cc_final: 0.8184 (pt0) outliers start: 31 outliers final: 22 residues processed: 202 average time/residue: 0.2368 time to fit residues: 64.1310 Evaluate side-chains 185 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain R residue 333 LEU Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 225 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 333 GLN B 88 ASN B 295 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9137 Z= 0.180 Angle : 0.519 9.921 12378 Z= 0.279 Chirality : 0.041 0.171 1406 Planarity : 0.004 0.047 1554 Dihedral : 4.199 32.818 1271 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.55 % Allowed : 12.24 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.37 (0.24), residues: 1122 helix: 2.76 (0.24), residues: 409 sheet: 0.10 (0.29), residues: 275 loop : -0.31 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.022 0.001 PHE R 223 TYR 0.017 0.001 TYR R 151 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 132 MET cc_start: 0.6982 (mmm) cc_final: 0.6647 (mmt) REVERT: R 205 MET cc_start: 0.6447 (OUTLIER) cc_final: 0.6112 (tpp) REVERT: R 257 MET cc_start: 0.8305 (ttp) cc_final: 0.8034 (ttt) REVERT: A 244 HIS cc_start: 0.7710 (m90) cc_final: 0.7449 (m90) REVERT: A 298 GLU cc_start: 0.7087 (tt0) cc_final: 0.6566 (mt-10) REVERT: A 308 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: B 43 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7958 (mt) REVERT: B 59 TYR cc_start: 0.8641 (m-80) cc_final: 0.8245 (m-80) REVERT: E 187 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8280 (pt0) outliers start: 25 outliers final: 16 residues processed: 170 average time/residue: 0.2246 time to fit residues: 51.8560 Evaluate side-chains 160 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain R residue 333 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 152 ASN A 213 HIS B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9137 Z= 0.306 Angle : 0.564 9.986 12378 Z= 0.300 Chirality : 0.043 0.196 1406 Planarity : 0.004 0.048 1554 Dihedral : 4.402 28.941 1271 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.78 % Allowed : 12.14 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.24), residues: 1122 helix: 2.42 (0.24), residues: 414 sheet: -0.18 (0.29), residues: 280 loop : -0.24 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.002 HIS B 54 PHE 0.016 0.002 PHE R 206 TYR 0.014 0.002 TYR B 264 ARG 0.006 0.001 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: R 132 MET cc_start: 0.7008 (mmm) cc_final: 0.6625 (mmt) REVERT: R 213 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.6093 (ptp-170) REVERT: A 9 ASP cc_start: 0.7723 (m-30) cc_final: 0.7304 (t0) REVERT: A 244 HIS cc_start: 0.7844 (m90) cc_final: 0.7529 (m90) REVERT: A 308 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: B 59 TYR cc_start: 0.8799 (m-80) cc_final: 0.8472 (m-80) REVERT: B 61 MET cc_start: 0.8552 (ppp) cc_final: 0.8311 (ppp) REVERT: B 217 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7151 (ptm) REVERT: B 292 PHE cc_start: 0.8895 (m-10) cc_final: 0.8303 (m-80) REVERT: E 203 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7647 (mtm180) outliers start: 37 outliers final: 27 residues processed: 181 average time/residue: 0.2461 time to fit residues: 59.4764 Evaluate side-chains 178 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain R residue 333 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 225 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN E 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9137 Z= 0.219 Angle : 0.518 10.944 12378 Z= 0.275 Chirality : 0.042 0.219 1406 Planarity : 0.004 0.047 1554 Dihedral : 4.219 27.309 1271 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.27 % Allowed : 13.67 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.09 (0.25), residues: 1122 helix: 2.37 (0.25), residues: 417 sheet: -0.14 (0.29), residues: 285 loop : -0.26 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 321 PHE 0.013 0.001 PHE R 206 TYR 0.018 0.002 TYR B 264 ARG 0.004 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.029 Fit side-chains REVERT: R 132 MET cc_start: 0.6999 (mmm) cc_final: 0.6607 (mmt) REVERT: R 213 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5936 (ptp-170) REVERT: A 9 ASP cc_start: 0.7684 (m-30) cc_final: 0.7253 (t0) REVERT: A 231 ASP cc_start: 0.6803 (t70) cc_final: 0.6490 (t0) REVERT: A 244 HIS cc_start: 0.7854 (m90) cc_final: 0.7494 (m90) REVERT: A 273 LEU cc_start: 0.7964 (mt) cc_final: 0.7714 (tt) REVERT: A 308 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: B 43 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8070 (mt) REVERT: B 59 TYR cc_start: 0.8689 (m-80) cc_final: 0.8390 (m-80) REVERT: B 292 PHE cc_start: 0.8748 (m-10) cc_final: 0.8150 (m-80) REVERT: E 203 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7667 (mtm180) outliers start: 32 outliers final: 22 residues processed: 176 average time/residue: 0.2364 time to fit residues: 56.3495 Evaluate side-chains 169 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 0.0040 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 GLN A 255 ASN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9137 Z= 0.227 Angle : 0.524 10.838 12378 Z= 0.278 Chirality : 0.042 0.224 1406 Planarity : 0.004 0.047 1554 Dihedral : 4.202 26.430 1271 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.27 % Allowed : 13.88 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.06 (0.25), residues: 1122 helix: 2.35 (0.25), residues: 416 sheet: -0.18 (0.30), residues: 284 loop : -0.26 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.011 0.001 PHE R 206 TYR 0.022 0.002 TYR R 229 ARG 0.004 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: R 132 MET cc_start: 0.6966 (mmm) cc_final: 0.6566 (mmt) REVERT: R 213 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.5916 (ptp-170) REVERT: A 9 ASP cc_start: 0.7688 (m-30) cc_final: 0.7262 (t0) REVERT: A 231 ASP cc_start: 0.6899 (t70) cc_final: 0.6576 (t0) REVERT: A 244 HIS cc_start: 0.7807 (m90) cc_final: 0.7433 (m90) REVERT: A 308 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: B 59 TYR cc_start: 0.8636 (m-80) cc_final: 0.8338 (m-80) REVERT: B 292 PHE cc_start: 0.8760 (m-10) cc_final: 0.8179 (m-80) REVERT: E 203 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7686 (mtm180) outliers start: 32 outliers final: 27 residues processed: 175 average time/residue: 0.2351 time to fit residues: 55.2034 Evaluate side-chains 171 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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: 0.7694 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9137 Z= 0.148 Angle : 0.497 11.039 12378 Z= 0.262 Chirality : 0.041 0.217 1406 Planarity : 0.004 0.046 1554 Dihedral : 4.018 25.739 1271 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.65 % Allowed : 15.41 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.17 (0.25), residues: 1122 helix: 2.40 (0.25), residues: 419 sheet: -0.11 (0.30), residues: 282 loop : -0.18 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.010 0.001 PHE B 199 TYR 0.017 0.001 TYR R 229 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.074 Fit side-chains REVERT: R 132 MET cc_start: 0.6862 (mmm) cc_final: 0.6486 (mmt) REVERT: R 206 PHE cc_start: 0.6698 (p90) cc_final: 0.5010 (m-80) REVERT: R 213 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.5818 (ptp-170) REVERT: A 231 ASP cc_start: 0.6818 (t70) cc_final: 0.6515 (t0) REVERT: A 244 HIS cc_start: 0.7775 (m90) cc_final: 0.7395 (m90) REVERT: A 308 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: B 43 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8096 (mt) REVERT: B 59 TYR cc_start: 0.8523 (m-80) cc_final: 0.8279 (m-80) outliers start: 26 outliers final: 20 residues processed: 172 average time/residue: 0.2223 time to fit residues: 52.2808 Evaluate side-chains 170 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9137 Z= 0.242 Angle : 0.530 11.504 12378 Z= 0.281 Chirality : 0.042 0.220 1406 Planarity : 0.004 0.047 1554 Dihedral : 4.170 23.915 1271 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.86 % Allowed : 15.31 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.15 (0.25), residues: 1122 helix: 2.51 (0.25), residues: 411 sheet: -0.13 (0.30), residues: 282 loop : -0.28 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.012 0.001 PHE R 206 TYR 0.018 0.002 TYR B 264 ARG 0.005 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: R 132 MET cc_start: 0.6960 (mmm) cc_final: 0.6560 (mmt) REVERT: R 206 PHE cc_start: 0.6737 (p90) cc_final: 0.5010 (m-80) REVERT: R 213 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.6058 (ptp-170) REVERT: A 9 ASP cc_start: 0.7689 (m-30) cc_final: 0.7261 (t0) REVERT: A 231 ASP cc_start: 0.6961 (t70) cc_final: 0.6676 (t0) REVERT: A 308 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: B 59 TYR cc_start: 0.8590 (m-80) cc_final: 0.8316 (m-80) REVERT: B 292 PHE cc_start: 0.8754 (m-10) cc_final: 0.8121 (m-80) outliers start: 28 outliers final: 23 residues processed: 166 average time/residue: 0.2342 time to fit residues: 53.1830 Evaluate side-chains 168 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9137 Z= 0.162 Angle : 0.502 11.673 12378 Z= 0.265 Chirality : 0.041 0.231 1406 Planarity : 0.004 0.045 1554 Dihedral : 4.035 23.331 1271 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.45 % Allowed : 16.12 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.17 (0.25), residues: 1122 helix: 2.48 (0.25), residues: 413 sheet: -0.15 (0.30), residues: 282 loop : -0.21 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS R 321 PHE 0.010 0.001 PHE B 151 TYR 0.017 0.001 TYR B 264 ARG 0.004 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: R 132 MET cc_start: 0.6945 (mmm) cc_final: 0.6569 (mmt) REVERT: R 206 PHE cc_start: 0.6712 (p90) cc_final: 0.5049 (m-80) REVERT: R 213 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.5898 (ptp-170) REVERT: A 231 ASP cc_start: 0.6905 (t70) cc_final: 0.6636 (t0) REVERT: A 244 HIS cc_start: 0.7890 (m90) cc_final: 0.7422 (m90) REVERT: A 308 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: B 59 TYR cc_start: 0.8493 (m-80) cc_final: 0.8241 (m-80) REVERT: B 292 PHE cc_start: 0.8638 (m-10) cc_final: 0.8052 (m-80) REVERT: E 87 ARG cc_start: 0.8052 (ptp-170) cc_final: 0.7600 (mpp80) outliers start: 24 outliers final: 21 residues processed: 161 average time/residue: 0.2334 time to fit residues: 52.0407 Evaluate side-chains 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.0570 chunk 101 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9137 Z= 0.168 Angle : 0.506 11.898 12378 Z= 0.267 Chirality : 0.041 0.229 1406 Planarity : 0.004 0.045 1554 Dihedral : 3.992 22.546 1271 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.35 % Allowed : 16.12 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.20 (0.25), residues: 1122 helix: 2.50 (0.25), residues: 413 sheet: -0.14 (0.30), residues: 282 loop : -0.18 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 321 PHE 0.010 0.001 PHE B 199 TYR 0.017 0.001 TYR R 93 ARG 0.005 0.000 ARG E 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: R 132 MET cc_start: 0.6978 (mmm) cc_final: 0.6623 (mmt) REVERT: R 206 PHE cc_start: 0.6647 (p90) cc_final: 0.4942 (m-80) REVERT: R 213 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5889 (ptp-170) REVERT: A 231 ASP cc_start: 0.6863 (t70) cc_final: 0.6606 (t0) REVERT: A 244 HIS cc_start: 0.7913 (m90) cc_final: 0.7449 (m90) REVERT: A 308 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: B 59 TYR cc_start: 0.8502 (m-80) cc_final: 0.8251 (m-80) REVERT: B 234 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8078 (t80) REVERT: B 292 PHE cc_start: 0.8623 (m-10) cc_final: 0.8038 (m-80) REVERT: E 87 ARG cc_start: 0.8051 (ptp-170) cc_final: 0.7604 (mpp80) outliers start: 23 outliers final: 19 residues processed: 159 average time/residue: 0.2244 time to fit residues: 48.9223 Evaluate side-chains 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.0030 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118721 restraints weight = 9991.953| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.87 r_work: 0.3034 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9137 Z= 0.141 Angle : 0.496 12.001 12378 Z= 0.260 Chirality : 0.041 0.209 1406 Planarity : 0.004 0.045 1554 Dihedral : 3.894 22.153 1271 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.24 % Allowed : 16.63 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1122 helix: 2.57 (0.25), residues: 413 sheet: 0.01 (0.30), residues: 277 loop : -0.15 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 321 PHE 0.011 0.001 PHE B 151 TYR 0.015 0.001 TYR R 151 ARG 0.005 0.000 ARG E 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.30 seconds wall clock time: 41 minutes 58.80 seconds (2518.80 seconds total)