Starting phenix.real_space_refine on Fri Jul 3 08:15:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7td1_25820/07_2026/7td1_25820_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7td1_25820/07_2026/7td1_25820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7td1_25820/07_2026/7td1_25820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7td1_25820/07_2026/7td1_25820.map" model { file = "/net/cci-nas-00/data/ceres_data/7td1_25820/07_2026/7td1_25820_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7td1_25820/07_2026/7td1_25820_trim.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 1.082 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 59 5.16 5 C 4407 2.51 5 N 1164 2.21 5 O 1268 1.98 5 H 6593 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13492 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4580 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 7, 'TRANS': 285} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 4849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 4849 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 3355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3355 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 679 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'NKP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.83, per 1000 atoms: 0.21 Number of scatterers: 13492 At special positions: 0 Unit cell: (96.824, 96.824, 124.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 59 16.00 P 1 15.00 O 1268 8.00 N 1164 7.00 C 4407 6.00 H 6593 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 190 " distance=2.04 Simple disulfide: pdb=" SG CYS R 188 " - pdb=" SG CYS R 195 " distance=2.18 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 287 " 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: 1.03 Conformation dependent library (CDL) restraints added in 501.2 milliseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1718 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 45.9% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 29 through 37 removed outlier: 3.663A pdb=" N PHE R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER R 37 " --> pdb=" O PHE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 77 Processing helix chain 'R' and resid 82 through 106 Processing helix chain 'R' and resid 109 through 116 Processing helix chain 'R' and resid 117 through 152 removed outlier: 3.706A pdb=" N ILE R 128 " --> pdb=" O ARG R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 181 Processing helix chain 'R' and resid 203 through 241 removed outlier: 4.726A pdb=" N ARG R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N MET R 239 " --> pdb=" O ARG R 235 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG R 241 " --> pdb=" O MET R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 284 removed outlier: 3.501A pdb=" N SER R 255 " --> pdb=" O ASP R 251 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.668A pdb=" N LEU R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU R 278 " --> pdb=" O GLY R 274 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU R 279 " --> pdb=" O LEU R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 291 removed outlier: 3.608A pdb=" N ALA R 291 " --> pdb=" O ASP R 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 288 through 291' Processing helix chain 'R' and resid 292 through 311 removed outlier: 3.852A pdb=" N SER R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.272A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.030A 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: 3.502A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.513A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.554A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.543A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.635A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.631A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.193A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.806A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.967A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.172A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.588A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.749A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.472A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 268 " --> pdb=" O HIS A 322 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1065 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: 3.19 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6568 1.04 - 1.23: 143 1.23 - 1.43: 2856 1.43 - 1.63: 3974 1.63 - 1.82: 88 Bond restraints: 13629 Sorted by residual: bond pdb=" OAD NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.696 1.509 0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.683 1.510 0.173 2.00e-02 2.50e+03 7.48e+01 bond pdb=" C ASN A 331 " pdb=" O ASN A 331 " ideal model delta sigma weight residual 1.236 1.156 0.080 1.26e-02 6.30e+03 4.07e+01 bond pdb=" CAH NKP R 401 " pdb=" OBC NKP R 401 " ideal model delta sigma weight residual 1.468 1.400 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" N THR A 329 " pdb=" CA THR A 329 " ideal model delta sigma weight residual 1.462 1.505 -0.043 1.46e-02 4.69e+03 8.61e+00 ... (remaining 13624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.26: 24462 11.26 - 22.53: 2 22.53 - 33.79: 0 33.79 - 45.06: 0 45.06 - 56.32: 1 Bond angle restraints: 24465 Sorted by residual: angle pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAD NKP R 401 " ideal model delta sigma weight residual 53.21 109.53 -56.32 3.00e+00 1.11e-01 3.52e+02 angle pdb=" OAA NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAB NKP R 401 " ideal model delta sigma weight residual 128.27 109.65 18.62 3.00e+00 1.11e-01 3.85e+01 angle pdb=" CA ASP A 328 " pdb=" C ASP A 328 " pdb=" O ASP A 328 " ideal model delta sigma weight residual 119.97 115.18 4.79 1.15e+00 7.56e-01 1.73e+01 angle pdb=" OAA NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAD NKP R 401 " ideal model delta sigma weight residual 121.86 109.59 12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" CA ASN A 331 " pdb=" C ASN A 331 " pdb=" O ASN A 331 " ideal model delta sigma weight residual 119.97 115.47 4.50 1.15e+00 7.56e-01 1.53e+01 ... (remaining 24460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6076 17.88 - 35.77: 311 35.77 - 53.65: 77 53.65 - 71.53: 24 71.53 - 89.42: 5 Dihedral angle restraints: 6493 sinusoidal: 3343 harmonic: 3150 Sorted by residual: dihedral pdb=" CB CYS R 24 " pdb=" SG CYS R 24 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 35.61 57.39 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB MET R 239 " pdb=" CG MET R 239 " pdb=" SD MET R 239 " pdb=" CE MET R 239 " ideal model delta sinusoidal sigma weight residual 180.00 121.69 58.31 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA ASP A 272 " pdb=" CB ASP A 272 " pdb=" CG ASP A 272 " pdb=" OD1 ASP A 272 " ideal model delta sinusoidal sigma weight residual -30.00 -82.18 52.18 1 2.00e+01 2.50e-03 9.28e+00 ... (remaining 6490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1032 0.068 - 0.137: 88 0.137 - 0.205: 1 0.205 - 0.274: 0 0.274 - 0.342: 1 Chirality restraints: 1122 Sorted by residual: chirality pdb=" CAH NKP R 401 " pdb=" CAG NKP R 401 " pdb=" CAI NKP R 401 " pdb=" OBC NKP R 401 " both_signs ideal model delta sigma weight residual False -2.84 -2.50 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA LYS A 330 " pdb=" N LYS A 330 " pdb=" C LYS A 330 " pdb=" CB LYS A 330 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1119 not shown) Planarity restraints: 2085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.151 2.00e-02 2.50e+03 1.64e-01 4.05e+02 pdb=" CG ASN A 331 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.144 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.024 2.00e-02 2.50e+03 pdb="HD21 ASN A 331 " -0.250 2.00e-02 2.50e+03 pdb="HD22 ASN A 331 " 0.236 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 331 " -0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C ASN A 331 " 0.058 2.00e-02 2.50e+03 pdb=" O ASN A 331 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 332 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 331 " -0.017 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" N VAL A 332 " 0.055 2.00e-02 2.50e+03 pdb=" CA VAL A 332 " -0.015 2.00e-02 2.50e+03 pdb=" H VAL A 332 " -0.023 2.00e-02 2.50e+03 ... (remaining 2082 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 705 2.21 - 2.81: 27745 2.81 - 3.40: 35493 3.40 - 4.00: 47107 4.00 - 4.60: 73773 Nonbonded interactions: 184823 Sorted by model distance: nonbonded pdb=" O ASN B 340 " pdb="HD22 ASN G 59 " model vdw 1.612 2.450 nonbonded pdb=" O ILE B 58 " pdb=" HG SER B 316 " model vdw 1.653 2.450 nonbonded pdb=" O LYS B 57 " pdb=" HG SER B 74 " model vdw 1.668 2.450 nonbonded pdb=" O ASP B 333 " pdb=" HG SER B 334 " model vdw 1.678 2.450 nonbonded pdb=" O ASP B 170 " pdb=" H GLY B 174 " model vdw 1.708 2.450 ... (remaining 184818 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=0.00 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: 0.170 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: 0.090 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.480 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 0.187 7039 Z= 0.243 Angle : 0.796 56.323 9568 Z= 0.349 Chirality : 0.038 0.342 1122 Planarity : 0.002 0.034 1204 Dihedral : 12.331 89.418 2424 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.28 % Allowed : 4.81 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.27), residues: 892 helix: 1.18 (0.26), residues: 383 sheet: -1.55 (0.34), residues: 190 loop : -1.46 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 152 TYR 0.009 0.001 TYR R 231 PHE 0.007 0.001 PHE A 189 TRP 0.005 0.001 TRP R 121 HIS 0.002 0.000 HIS R 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.23 ( 7036) covalent geometry : angle 0.79351 / 0.35 ( 9562) SS BOND : bond 0.08574 / 4.08 ( 3) SS BOND : angle 2.59631 / 1.35 ( 6) hydrogen bonds : bond 0.12636 / 8.41 ( 371) hydrogen bonds : angle 4.59672 / 3.38 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 152 ARG cc_start: 0.7191 (ptp90) cc_final: 0.6875 (ptt180) REVERT: R 209 PHE cc_start: 0.7263 (t80) cc_final: 0.7041 (t80) REVERT: B 259 GLN cc_start: 0.7803 (pt0) cc_final: 0.7275 (pt0) REVERT: B 268 ASN cc_start: 0.7425 (t0) cc_final: 0.7134 (t0) REVERT: B 269 ILE cc_start: 0.8480 (mt) cc_final: 0.8242 (mt) REVERT: B 340 ASN cc_start: 0.6060 (t0) cc_final: 0.5846 (t0) REVERT: A 310 LEU cc_start: 0.8419 (mt) cc_final: 0.8176 (mt) outliers start: 2 outliers final: 2 residues processed: 185 average time/residue: 0.1925 time to fit residues: 45.3778 Evaluate side-chains 155 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain B residue 70 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN A 306 GLN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.157801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127355 restraints weight = 23658.374| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.34 r_work: 0.3270 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 7039 Z= 0.112 Angle : 0.437 4.549 9568 Z= 0.238 Chirality : 0.038 0.140 1122 Planarity : 0.003 0.040 1204 Dihedral : 6.915 70.769 998 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.71 % Allowed : 9.90 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.28), residues: 892 helix: 2.06 (0.26), residues: 390 sheet: -1.10 (0.35), residues: 190 loop : -1.05 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 235 TYR 0.018 0.001 TYR R 231 PHE 0.010 0.001 PHE A 196 TRP 0.005 0.001 TRP R 121 HIS 0.004 0.001 HIS R 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 7036) covalent geometry : angle 0.43367 / 0.24 ( 9562) SS BOND : bond 0.00408 / 0.21 ( 3) SS BOND : angle 2.03787 / 1.18 ( 6) hydrogen bonds : bond 0.03804 / 2.53 ( 371) hydrogen bonds : angle 3.98669 / 2.83 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 MET cc_start: 0.7212 (tpp) cc_final: 0.6974 (tpp) REVERT: R 152 ARG cc_start: 0.7385 (ptp90) cc_final: 0.6850 (ptt180) REVERT: B 201 SER cc_start: 0.9148 (m) cc_final: 0.8801 (p) REVERT: B 259 GLN cc_start: 0.7953 (pt0) cc_final: 0.7157 (pt0) REVERT: B 340 ASN cc_start: 0.6627 (t0) cc_final: 0.6237 (t0) REVERT: A 349 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8370 (mttt) outliers start: 5 outliers final: 3 residues processed: 156 average time/residue: 0.1802 time to fit residues: 36.0500 Evaluate side-chains 152 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 16 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 40 HIS A 269 ASN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120853 restraints weight = 24043.489| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.43 r_work: 0.3170 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7039 Z= 0.182 Angle : 0.485 6.926 9568 Z= 0.265 Chirality : 0.039 0.134 1122 Planarity : 0.004 0.050 1204 Dihedral : 6.888 80.886 995 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.27 % Allowed : 11.32 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.28), residues: 892 helix: 2.21 (0.26), residues: 392 sheet: -0.73 (0.37), residues: 183 loop : -1.06 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 235 TYR 0.020 0.001 TYR R 231 PHE 0.013 0.001 PHE A 196 TRP 0.007 0.001 TRP R 121 HIS 0.010 0.001 HIS R 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 7036) covalent geometry : angle 0.47873 / 0.26 ( 9562) SS BOND : bond 0.00266 / 0.14 ( 3) SS BOND : angle 3.22501 / 1.86 ( 6) hydrogen bonds : bond 0.04067 / 2.74 ( 371) hydrogen bonds : angle 4.06361 / 2.88 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 PHE cc_start: 0.8452 (t80) cc_final: 0.8166 (t80) REVERT: R 152 ARG cc_start: 0.7456 (ptp90) cc_final: 0.6835 (ptt180) REVERT: B 83 ASP cc_start: 0.8450 (t0) cc_final: 0.7905 (t0) REVERT: B 201 SER cc_start: 0.9171 (m) cc_final: 0.8856 (p) REVERT: B 340 ASN cc_start: 0.7147 (t0) cc_final: 0.6761 (t0) REVERT: A 349 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8307 (mttt) outliers start: 9 outliers final: 8 residues processed: 173 average time/residue: 0.1772 time to fit residues: 39.7932 Evaluate side-chains 168 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 HIS Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.148649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117601 restraints weight = 23967.160| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.35 r_work: 0.3141 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7039 Z= 0.174 Angle : 0.481 7.107 9568 Z= 0.265 Chirality : 0.038 0.135 1122 Planarity : 0.003 0.041 1204 Dihedral : 6.503 85.506 995 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.56 % Allowed : 12.45 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.29), residues: 892 helix: 2.36 (0.26), residues: 392 sheet: -0.68 (0.38), residues: 182 loop : -1.05 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 115 TYR 0.015 0.001 TYR R 231 PHE 0.010 0.001 PHE A 196 TRP 0.007 0.001 TRP B 82 HIS 0.020 0.002 HIS R 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 7036) covalent geometry : angle 0.47792 / 0.26 ( 9562) SS BOND : bond 0.00371 / 0.20 ( 3) SS BOND : angle 2.35220 / 1.34 ( 6) hydrogen bonds : bond 0.04004 / 2.68 ( 371) hydrogen bonds : angle 4.06266 / 2.88 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 PHE cc_start: 0.8481 (t80) cc_final: 0.8179 (t80) REVERT: R 152 ARG cc_start: 0.7530 (ptp90) cc_final: 0.6889 (ptt180) REVERT: R 235 ARG cc_start: 0.7091 (ttm170) cc_final: 0.6884 (ttm170) REVERT: B 83 ASP cc_start: 0.8445 (t0) cc_final: 0.7932 (t0) REVERT: B 201 SER cc_start: 0.9183 (m) cc_final: 0.8902 (p) REVERT: B 340 ASN cc_start: 0.7374 (t0) cc_final: 0.7034 (t0) REVERT: A 349 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8364 (mttt) outliers start: 11 outliers final: 8 residues processed: 184 average time/residue: 0.1683 time to fit residues: 40.5892 Evaluate side-chains 179 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 16 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.147843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116794 restraints weight = 24391.279| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.37 r_work: 0.3156 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7039 Z= 0.173 Angle : 0.474 5.419 9568 Z= 0.260 Chirality : 0.039 0.138 1122 Planarity : 0.004 0.050 1204 Dihedral : 6.168 83.422 995 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.98 % Allowed : 13.15 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.29), residues: 892 helix: 2.40 (0.26), residues: 393 sheet: -0.68 (0.38), residues: 184 loop : -1.04 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 115 TYR 0.011 0.001 TYR R 231 PHE 0.010 0.001 PHE A 196 TRP 0.007 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 7036) covalent geometry : angle 0.47003 / 0.26 ( 9562) SS BOND : bond 0.01140 / 0.60 ( 3) SS BOND : angle 2.58648 / 1.49 ( 6) hydrogen bonds : bond 0.04091 / 2.73 ( 371) hydrogen bonds : angle 4.08201 / 2.90 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 152 ARG cc_start: 0.7580 (ptp90) cc_final: 0.6899 (ptt180) REVERT: B 83 ASP cc_start: 0.8455 (t0) cc_final: 0.7985 (t0) REVERT: B 201 SER cc_start: 0.9183 (m) cc_final: 0.8950 (p) REVERT: B 340 ASN cc_start: 0.7430 (t0) cc_final: 0.7140 (t0) REVERT: A 216 GLU cc_start: 0.8546 (tt0) cc_final: 0.8234 (tt0) REVERT: A 252 SER cc_start: 0.8779 (m) cc_final: 0.8495 (m) outliers start: 14 outliers final: 11 residues processed: 179 average time/residue: 0.1605 time to fit residues: 37.8304 Evaluate side-chains 179 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.150434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120032 restraints weight = 24250.670| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.34 r_work: 0.3162 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7039 Z= 0.101 Angle : 0.437 4.691 9568 Z= 0.236 Chirality : 0.038 0.136 1122 Planarity : 0.004 0.052 1204 Dihedral : 5.316 63.390 995 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.27 % Allowed : 14.00 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.29), residues: 892 helix: 2.70 (0.26), residues: 393 sheet: -0.54 (0.38), residues: 184 loop : -0.96 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 115 TYR 0.025 0.001 TYR A 302 PHE 0.014 0.001 PHE A 354 TRP 0.005 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 7036) covalent geometry : angle 0.43420 / 0.23 ( 9562) SS BOND : bond 0.00393 / 0.21 ( 3) SS BOND : angle 2.06034 / 1.21 ( 6) hydrogen bonds : bond 0.03507 / 2.35 ( 371) hydrogen bonds : angle 3.88842 / 2.75 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 152 ARG cc_start: 0.7476 (ptp90) cc_final: 0.6877 (ptt180) REVERT: B 83 ASP cc_start: 0.8418 (t0) cc_final: 0.7926 (t0) REVERT: B 201 SER cc_start: 0.9173 (m) cc_final: 0.8925 (p) REVERT: B 340 ASN cc_start: 0.7316 (t0) cc_final: 0.6999 (t0) REVERT: A 252 SER cc_start: 0.8753 (m) cc_final: 0.8487 (m) outliers start: 9 outliers final: 9 residues processed: 173 average time/residue: 0.1653 time to fit residues: 37.6597 Evaluate side-chains 179 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 40.0000 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.147589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117064 restraints weight = 24314.566| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.33 r_work: 0.3109 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7039 Z= 0.197 Angle : 0.494 5.615 9568 Z= 0.271 Chirality : 0.039 0.138 1122 Planarity : 0.004 0.054 1204 Dihedral : 5.466 53.539 995 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.56 % Allowed : 14.00 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.29), residues: 892 helix: 2.53 (0.26), residues: 393 sheet: -0.58 (0.38), residues: 184 loop : -1.10 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 115 TYR 0.023 0.001 TYR A 302 PHE 0.010 0.001 PHE A 196 TRP 0.009 0.001 TRP R 121 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 ( 7036) covalent geometry : angle 0.48991 / 0.27 ( 9562) SS BOND : bond 0.00095 / 0.05 ( 3) SS BOND : angle 2.45502 / 1.43 ( 6) hydrogen bonds : bond 0.04195 / 2.81 ( 371) hydrogen bonds : angle 4.11392 / 2.92 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 152 ARG cc_start: 0.7523 (ptp90) cc_final: 0.6821 (ptt180) REVERT: B 83 ASP cc_start: 0.8396 (t0) cc_final: 0.7946 (t0) REVERT: B 201 SER cc_start: 0.9173 (m) cc_final: 0.8953 (p) REVERT: B 259 GLN cc_start: 0.8141 (pt0) cc_final: 0.7129 (pt0) REVERT: A 252 SER cc_start: 0.8749 (m) cc_final: 0.8472 (m) outliers start: 11 outliers final: 11 residues processed: 171 average time/residue: 0.1815 time to fit residues: 40.0093 Evaluate side-chains 174 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 8 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.146576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115875 restraints weight = 24147.223| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.32 r_work: 0.3111 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7039 Z= 0.153 Angle : 0.461 4.693 9568 Z= 0.252 Chirality : 0.038 0.136 1122 Planarity : 0.004 0.057 1204 Dihedral : 5.262 49.316 995 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.56 % Allowed : 14.57 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.29), residues: 892 helix: 2.62 (0.26), residues: 393 sheet: -0.57 (0.38), residues: 184 loop : -1.06 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 115 TYR 0.024 0.001 TYR A 302 PHE 0.008 0.001 PHE A 196 TRP 0.007 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 7036) covalent geometry : angle 0.45991 / 0.25 ( 9562) SS BOND : bond 0.00120 / 0.06 ( 3) SS BOND : angle 1.47206 / 0.87 ( 6) hydrogen bonds : bond 0.03929 / 2.63 ( 371) hydrogen bonds : angle 4.04798 / 2.87 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 152 ARG cc_start: 0.7429 (ptp90) cc_final: 0.6771 (ptt180) REVERT: B 83 ASP cc_start: 0.8380 (t0) cc_final: 0.7929 (t0) REVERT: B 201 SER cc_start: 0.9176 (m) cc_final: 0.8952 (p) REVERT: B 259 GLN cc_start: 0.8054 (pt0) cc_final: 0.7086 (pt0) REVERT: A 252 SER cc_start: 0.8741 (m) cc_final: 0.8471 (m) REVERT: A 306 GLN cc_start: 0.8110 (mm110) cc_final: 0.7672 (mt0) outliers start: 11 outliers final: 10 residues processed: 178 average time/residue: 0.1826 time to fit residues: 42.6684 Evaluate side-chains 178 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116267 restraints weight = 24402.595| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.41 r_work: 0.3104 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7039 Z= 0.156 Angle : 0.467 5.020 9568 Z= 0.256 Chirality : 0.039 0.137 1122 Planarity : 0.004 0.060 1204 Dihedral : 5.286 46.304 995 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.56 % Allowed : 14.99 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.29), residues: 892 helix: 2.65 (0.26), residues: 393 sheet: -0.60 (0.38), residues: 184 loop : -1.06 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 115 TYR 0.023 0.001 TYR A 302 PHE 0.009 0.001 PHE A 196 TRP 0.007 0.001 TRP R 121 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 7036) covalent geometry : angle 0.46389 / 0.25 ( 9562) SS BOND : bond 0.00129 / 0.07 ( 3) SS BOND : angle 2.23447 / 1.30 ( 6) hydrogen bonds : bond 0.03925 / 2.63 ( 371) hydrogen bonds : angle 4.03479 / 2.86 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 152 ARG cc_start: 0.7395 (ptp90) cc_final: 0.6722 (ptt180) REVERT: B 83 ASP cc_start: 0.8352 (t0) cc_final: 0.7892 (t0) REVERT: B 201 SER cc_start: 0.9189 (m) cc_final: 0.8935 (p) REVERT: B 259 GLN cc_start: 0.8011 (pt0) cc_final: 0.7035 (pt0) REVERT: A 252 SER cc_start: 0.8702 (m) cc_final: 0.8432 (m) REVERT: A 306 GLN cc_start: 0.8041 (mm110) cc_final: 0.7702 (mt0) outliers start: 11 outliers final: 11 residues processed: 172 average time/residue: 0.1730 time to fit residues: 38.7008 Evaluate side-chains 177 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 2 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.149355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118632 restraints weight = 24149.045| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.33 r_work: 0.3136 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7039 Z= 0.120 Angle : 0.446 4.621 9568 Z= 0.243 Chirality : 0.038 0.135 1122 Planarity : 0.004 0.057 1204 Dihedral : 5.149 44.932 995 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.41 % Allowed : 14.99 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.29), residues: 892 helix: 2.78 (0.26), residues: 393 sheet: -0.55 (0.38), residues: 184 loop : -0.96 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 32 TYR 0.023 0.001 TYR A 302 PHE 0.008 0.001 PHE A 354 TRP 0.006 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 7036) covalent geometry : angle 0.44490 / 0.24 ( 9562) SS BOND : bond 0.00177 / 0.09 ( 3) SS BOND : angle 1.48003 / 0.87 ( 6) hydrogen bonds : bond 0.03676 / 2.47 ( 371) hydrogen bonds : angle 3.94502 / 2.79 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 152 ARG cc_start: 0.7414 (ptp90) cc_final: 0.6845 (ptt180) REVERT: B 83 ASP cc_start: 0.8371 (t0) cc_final: 0.7918 (t0) REVERT: B 201 SER cc_start: 0.9201 (m) cc_final: 0.8958 (p) REVERT: B 259 GLN cc_start: 0.8017 (pt0) cc_final: 0.7094 (pt0) REVERT: A 242 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7841 (mtp-110) REVERT: A 252 SER cc_start: 0.8756 (m) cc_final: 0.8485 (m) REVERT: A 306 GLN cc_start: 0.8092 (mm110) cc_final: 0.7785 (mt0) outliers start: 10 outliers final: 9 residues processed: 176 average time/residue: 0.1818 time to fit residues: 41.8572 Evaluate side-chains 178 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 2 optimal weight: 0.1980 chunk 17 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117209 restraints weight = 24372.280| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.32 r_work: 0.3135 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7039 Z= 0.118 Angle : 0.452 5.674 9568 Z= 0.245 Chirality : 0.038 0.168 1122 Planarity : 0.004 0.054 1204 Dihedral : 5.143 48.110 995 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.27 % Allowed : 15.84 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.29), residues: 892 helix: 2.86 (0.26), residues: 393 sheet: -0.52 (0.38), residues: 184 loop : -0.91 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG R 115 TYR 0.023 0.001 TYR A 302 PHE 0.008 0.001 PHE A 354 TRP 0.006 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7036) covalent geometry : angle 0.44994 / 0.24 ( 9562) SS BOND : bond 0.00064 / 0.03 ( 3) SS BOND : angle 1.87491 / 1.09 ( 6) hydrogen bonds : bond 0.03571 / 2.40 ( 371) hydrogen bonds : angle 3.91046 / 2.77 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3365.48 seconds wall clock time: 57 minutes 37.80 seconds (3457.80 seconds total)