Starting phenix.real_space_refine on Wed Mar 4 01:54:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btx_30190/03_2026/7btx_30190.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btx_30190/03_2026/7btx_30190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7btx_30190/03_2026/7btx_30190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btx_30190/03_2026/7btx_30190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7btx_30190/03_2026/7btx_30190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btx_30190/03_2026/7btx_30190.map" } resolution = 2.8 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6512 2.51 5 N 1724 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10168 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2775 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2399 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain breaks: 2 Chain: "C" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2439 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2555 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.54, per 1000 atoms: 0.25 Number of scatterers: 10168 At special positions: 0 Unit cell: (106.24, 101.26, 101.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1888 8.00 N 1724 7.00 C 6512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.87 Conformation dependent library (CDL) restraints added in 633.0 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 33.8% alpha, 39.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.601A pdb=" N LYS A 201 " --> pdb=" O TRP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.503A pdb=" N LYS A 356 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.872A pdb=" N ILE A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 119 through 123 removed outlier: 3.546A pdb=" N ASN B 123 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 153 removed outlier: 3.677A pdb=" N ARG B 153 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 181 removed outlier: 3.539A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.571A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.637A pdb=" N GLU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 225 Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 242 Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.658A pdb=" N GLN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 283 through 297 removed outlier: 3.581A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 removed outlier: 3.543A pdb=" N PHE B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.770A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.813A pdb=" N LEU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 187 through 194 Processing helix chain 'C' and resid 204 through 241 removed outlier: 3.754A pdb=" N ASN C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 210 " --> pdb=" O HIS C 206 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 263 removed outlier: 3.572A pdb=" N LEU C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 279 removed outlier: 4.244A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.708A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 318 removed outlier: 3.853A pdb=" N SER C 318 " --> pdb=" O VAL C 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 315 through 318' Processing helix chain 'C' and resid 319 through 326 removed outlier: 3.865A pdb=" N TYR C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 16 Processing helix chain 'L' and resid 19 through 23 removed outlier: 3.609A pdb=" N ASN L 22 " --> pdb=" O SER L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.829A pdb=" N LYS L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129 removed outlier: 7.544A pdb=" N ALA A 139 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG A 164 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N SER A 170 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 194 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 296 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A 440 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 129 removed outlier: 7.544A pdb=" N ALA A 139 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG A 164 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N SER A 170 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 194 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 296 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A 440 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 21 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 7 removed outlier: 4.196A pdb=" N THR C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 194 through 199 removed outlier: 3.538A pdb=" N LEU L 179 " --> pdb=" O SER L 174 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR L 165 " --> pdb=" O LEU L 161 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N TYR L 491 " --> pdb=" O HIS L 44 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN L 46 " --> pdb=" O TYR L 491 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 209 through 211 removed outlier: 3.540A pdb=" N GLU L 236 " --> pdb=" O SER L 249 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 209 through 211 removed outlier: 3.540A pdb=" N GLU L 236 " --> pdb=" O SER L 249 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU L 269 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG L 263 " --> pdb=" O SER L 258 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN L 306 " --> pdb=" O ASP L 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 313 through 316 649 hydrogen bonds defined for protein. 1848 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: 1.57 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1632 1.28 - 1.41: 2707 1.41 - 1.55: 5952 1.55 - 1.68: 30 1.68 - 1.82: 65 Bond restraints: 10386 Sorted by residual: bond pdb=" CA ASN A 135 " pdb=" C ASN A 135 " ideal model delta sigma weight residual 1.523 1.423 0.100 1.34e-02 5.57e+03 5.57e+01 bond pdb=" C ASP A 134 " pdb=" O ASP A 134 " ideal model delta sigma weight residual 1.235 1.154 0.081 1.14e-02 7.69e+03 5.07e+01 bond pdb=" C ASN A 135 " pdb=" O ASN A 135 " ideal model delta sigma weight residual 1.235 1.168 0.068 1.26e-02 6.30e+03 2.88e+01 bond pdb=" CG ASN A 135 " pdb=" ND2 ASN A 135 " ideal model delta sigma weight residual 1.328 1.218 0.110 2.10e-02 2.27e+03 2.72e+01 bond pdb=" N ASN A 135 " pdb=" CA ASN A 135 " ideal model delta sigma weight residual 1.457 1.395 0.063 1.29e-02 6.01e+03 2.37e+01 ... (remaining 10381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 13886 4.13 - 8.26: 136 8.26 - 12.39: 9 12.39 - 16.52: 2 16.52 - 20.65: 1 Bond angle restraints: 14034 Sorted by residual: angle pdb=" N GLU C 98 " pdb=" CA GLU C 98 " pdb=" C GLU C 98 " ideal model delta sigma weight residual 109.06 129.71 -20.65 1.70e+00 3.46e-01 1.48e+02 angle pdb=" C LEU A 152 " pdb=" N LYS A 153 " pdb=" CA LYS A 153 " ideal model delta sigma weight residual 121.54 135.70 -14.16 1.91e+00 2.74e-01 5.49e+01 angle pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta sigma weight residual 122.95 132.10 -9.15 1.44e+00 4.82e-01 4.04e+01 angle pdb=" N THR C 87 " pdb=" CA THR C 87 " pdb=" C THR C 87 " ideal model delta sigma weight residual 110.80 123.76 -12.96 2.13e+00 2.20e-01 3.70e+01 angle pdb=" C TYR C 150 " pdb=" N PHE C 151 " pdb=" CA PHE C 151 " ideal model delta sigma weight residual 120.58 128.56 -7.98 1.32e+00 5.74e-01 3.65e+01 ... (remaining 14029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5514 17.47 - 34.95: 534 34.95 - 52.42: 106 52.42 - 69.89: 19 69.89 - 87.37: 13 Dihedral angle restraints: 6186 sinusoidal: 2480 harmonic: 3706 Sorted by residual: dihedral pdb=" CA LEU B 128 " pdb=" C LEU B 128 " pdb=" N PRO B 129 " pdb=" CA PRO B 129 " ideal model delta harmonic sigma weight residual 180.00 123.89 56.11 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA LEU C 60 " pdb=" C LEU C 60 " pdb=" N PRO C 61 " pdb=" CA PRO C 61 " ideal model delta harmonic sigma weight residual 180.00 129.92 50.08 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA TYR L 148 " pdb=" C TYR L 148 " pdb=" N PRO L 149 " pdb=" CA PRO L 149 " ideal model delta harmonic sigma weight residual 180.00 133.14 46.86 0 5.00e+00 4.00e-02 8.79e+01 ... (remaining 6183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 1555 0.166 - 0.331: 15 0.331 - 0.497: 0 0.497 - 0.663: 2 0.663 - 0.828: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" CA THR C 87 " pdb=" N THR C 87 " pdb=" C THR C 87 " pdb=" CB THR C 87 " both_signs ideal model delta sigma weight residual False 2.53 1.70 0.83 2.00e-01 2.50e+01 1.72e+01 chirality pdb=" CA GLU C 98 " pdb=" N GLU C 98 " pdb=" C GLU C 98 " pdb=" CB GLU C 98 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CA PHE B 18 " pdb=" N PHE B 18 " pdb=" C PHE B 18 " pdb=" CB PHE B 18 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 ... (remaining 1570 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " -0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO C 61 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 86 " -0.023 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C CYS C 86 " 0.077 2.00e-02 2.50e+03 pdb=" O CYS C 86 " -0.028 2.00e-02 2.50e+03 pdb=" N THR C 87 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 128 " -0.071 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO B 129 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.061 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2791 2.80 - 3.33: 8218 3.33 - 3.85: 16487 3.85 - 4.38: 20074 4.38 - 4.90: 35542 Nonbonded interactions: 83112 Sorted by model distance: nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASP B 80 " pdb=" OH TYR B 192 " model vdw 2.297 3.040 nonbonded pdb=" O SER L 230 " pdb=" OG SER L 230 " model vdw 2.306 3.040 nonbonded pdb=" O SER L 302 " pdb=" OG SER L 302 " model vdw 2.315 3.040 nonbonded pdb=" O LEU C 109 " pdb=" OG SER C 113 " model vdw 2.317 3.040 ... (remaining 83107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.750 Find NCS groups from input model: 0.100 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:8.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 10386 Z= 0.375 Angle : 1.094 20.654 14034 Z= 0.629 Chirality : 0.063 0.828 1573 Planarity : 0.008 0.114 1764 Dihedral : 14.926 87.369 3786 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.13 % Favored : 91.14 % Rotamer: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.66 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.57 % 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: -4.94 (0.18), residues: 1242 helix: -4.14 (0.12), residues: 389 sheet: -1.85 (0.24), residues: 397 loop : -3.55 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 409 TYR 0.018 0.002 TYR B 245 PHE 0.026 0.003 PHE B 68 TRP 0.023 0.002 TRP A 323 HIS 0.014 0.002 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00764 (10386) covalent geometry : angle 1.09413 (14034) hydrogen bonds : bond 0.24697 ( 505) hydrogen bonds : angle 9.51081 ( 1848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 0.420 Fit side-chains REVERT: A 138 GLU cc_start: 0.7629 (tp30) cc_final: 0.7241 (mm-30) REVERT: A 169 HIS cc_start: 0.6932 (m90) cc_final: 0.6711 (m90) REVERT: B 248 HIS cc_start: 0.8311 (t70) cc_final: 0.8058 (t70) REVERT: B 255 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7454 (tt0) REVERT: C 267 ASP cc_start: 0.7849 (t70) cc_final: 0.7382 (t0) REVERT: L 434 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7936 (tttm) outliers start: 3 outliers final: 1 residues processed: 176 average time/residue: 0.5036 time to fit residues: 95.7988 Evaluate side-chains 121 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 159 ASN A 175 ASN A 187 ASN A 200 ASN A 207 GLN A 280 HIS A 318 ASN A 369 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN A 466 HIS B 87 GLN B 94 ASN B 256 GLN C 7 HIS C 50 ASN C 84 ASN C 136 ASN C 160 GLN C 208 ASN C 218 GLN C 222 ASN C 224 GLN C 277 GLN C 300 ASN C 301 ASN C 314 ASN L 22 ASN L 57 ASN L 180 ASN L 490 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109355 restraints weight = 11842.014| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.02 r_work: 0.3139 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10386 Z= 0.140 Angle : 0.674 9.311 14034 Z= 0.366 Chirality : 0.042 0.144 1573 Planarity : 0.006 0.089 1764 Dihedral : 7.041 46.526 1360 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.73 % Favored : 91.95 % Rotamer: Outliers : 1.76 % Allowed : 12.69 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % 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: -3.09 (0.21), residues: 1242 helix: -1.37 (0.22), residues: 404 sheet: -1.25 (0.25), residues: 383 loop : -3.30 (0.23), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 120 TYR 0.013 0.001 TYR L 296 PHE 0.021 0.001 PHE A 237 TRP 0.016 0.001 TRP A 323 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00287 (10386) covalent geometry : angle 0.67353 (14034) hydrogen bonds : bond 0.04112 ( 505) hydrogen bonds : angle 4.97529 ( 1848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.295 Fit side-chains REVERT: A 138 GLU cc_start: 0.7716 (tp30) cc_final: 0.7367 (mm-30) REVERT: B 211 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 255 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7513 (tt0) REVERT: C 97 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6195 (mt-10) REVERT: C 267 ASP cc_start: 0.8195 (t70) cc_final: 0.7354 (t0) REVERT: L 169 LEU cc_start: 0.8990 (mt) cc_final: 0.8690 (tt) REVERT: L 434 LYS cc_start: 0.8167 (ttpt) cc_final: 0.6837 (mptt) outliers start: 20 outliers final: 5 residues processed: 146 average time/residue: 0.4555 time to fit residues: 72.7574 Evaluate side-chains 119 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 81 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 342 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111463 restraints weight = 11901.264| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.03 r_work: 0.3173 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10386 Z= 0.114 Angle : 0.607 8.031 14034 Z= 0.326 Chirality : 0.040 0.141 1573 Planarity : 0.005 0.087 1764 Dihedral : 6.398 46.682 1360 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.81 % Favored : 91.87 % Rotamer: Outliers : 2.91 % Allowed : 14.27 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % 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: -2.01 (0.23), residues: 1242 helix: 0.15 (0.26), residues: 400 sheet: -0.85 (0.26), residues: 387 loop : -3.12 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 376 TYR 0.019 0.001 TYR C 140 PHE 0.019 0.001 PHE L 313 TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00242 (10386) covalent geometry : angle 0.60715 (14034) hydrogen bonds : bond 0.03329 ( 505) hydrogen bonds : angle 4.30641 ( 1848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.394 Fit side-chains REVERT: A 136 ASP cc_start: 0.7585 (t0) cc_final: 0.7175 (m-30) REVERT: A 138 GLU cc_start: 0.7631 (tp30) cc_final: 0.7261 (mm-30) REVERT: A 169 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.5935 (m-70) REVERT: B 196 LYS cc_start: 0.7666 (mtmt) cc_final: 0.7281 (mttt) REVERT: B 211 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8089 (mp) REVERT: B 255 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7512 (tt0) REVERT: C 267 ASP cc_start: 0.8134 (t70) cc_final: 0.7342 (t0) REVERT: C 276 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8319 (mt-10) REVERT: L 169 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8709 (tt) REVERT: L 231 LEU cc_start: 0.8445 (tp) cc_final: 0.8239 (tm) REVERT: L 434 LYS cc_start: 0.8132 (ttpt) cc_final: 0.6887 (mttp) outliers start: 33 outliers final: 10 residues processed: 148 average time/residue: 0.4084 time to fit residues: 66.4861 Evaluate side-chains 126 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain L residue 169 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 207 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN L 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.105438 restraints weight = 12037.321| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.03 r_work: 0.3082 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10386 Z= 0.223 Angle : 0.693 7.849 14034 Z= 0.369 Chirality : 0.044 0.146 1573 Planarity : 0.006 0.093 1764 Dihedral : 6.662 47.898 1360 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.62 % Favored : 91.14 % Rotamer: Outliers : 3.96 % Allowed : 14.89 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % 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: -1.73 (0.23), residues: 1242 helix: 0.61 (0.27), residues: 398 sheet: -0.95 (0.25), residues: 403 loop : -2.97 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 66 TYR 0.012 0.002 TYR A 262 PHE 0.022 0.002 PHE L 313 TRP 0.014 0.001 TRP A 197 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00512 (10386) covalent geometry : angle 0.69348 (14034) hydrogen bonds : bond 0.03857 ( 505) hydrogen bonds : angle 4.47050 ( 1848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.421 Fit side-chains REVERT: A 138 GLU cc_start: 0.7699 (tp30) cc_final: 0.7272 (mm-30) REVERT: A 169 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.6023 (m-70) REVERT: B 150 MET cc_start: 0.9309 (mmp) cc_final: 0.9068 (mmt) REVERT: B 255 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7526 (tt0) REVERT: C 267 ASP cc_start: 0.8234 (t70) cc_final: 0.7337 (t0) REVERT: C 302 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7565 (mp) REVERT: L 169 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8725 (tt) REVERT: L 239 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8417 (tt) REVERT: L 434 LYS cc_start: 0.8170 (ttpt) cc_final: 0.6883 (mttt) outliers start: 45 outliers final: 21 residues processed: 142 average time/residue: 0.4372 time to fit residues: 68.1090 Evaluate side-chains 132 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 90 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.112559 restraints weight = 11844.264| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.05 r_work: 0.3132 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10386 Z= 0.146 Angle : 0.621 7.621 14034 Z= 0.331 Chirality : 0.041 0.137 1573 Planarity : 0.005 0.088 1764 Dihedral : 6.352 44.874 1360 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.81 % Favored : 91.95 % Rotamer: Outliers : 3.61 % Allowed : 16.21 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % 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: -1.40 (0.24), residues: 1242 helix: 1.05 (0.27), residues: 398 sheet: -0.75 (0.26), residues: 399 loop : -2.96 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 66 TYR 0.012 0.001 TYR L 254 PHE 0.023 0.001 PHE L 313 TRP 0.012 0.001 TRP A 197 HIS 0.005 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00327 (10386) covalent geometry : angle 0.62064 (14034) hydrogen bonds : bond 0.03312 ( 505) hydrogen bonds : angle 4.19948 ( 1848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 136 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7394 (m-30) REVERT: A 138 GLU cc_start: 0.7701 (tp30) cc_final: 0.7303 (mm-30) REVERT: A 169 HIS cc_start: 0.6776 (OUTLIER) cc_final: 0.5896 (m-70) REVERT: A 213 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8775 (m) REVERT: B 150 MET cc_start: 0.9282 (mmp) cc_final: 0.9029 (mmp) REVERT: B 255 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7509 (tt0) REVERT: C 218 GLN cc_start: 0.6144 (OUTLIER) cc_final: 0.5938 (tm-30) REVERT: C 267 ASP cc_start: 0.8225 (t70) cc_final: 0.7339 (t0) REVERT: L 169 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8726 (tt) REVERT: L 239 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8388 (tp) REVERT: L 434 LYS cc_start: 0.8151 (ttpt) cc_final: 0.6855 (mttp) outliers start: 41 outliers final: 20 residues processed: 144 average time/residue: 0.4371 time to fit residues: 68.9458 Evaluate side-chains 140 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 342 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.144427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110788 restraints weight = 11963.013| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.04 r_work: 0.3112 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10386 Z= 0.116 Angle : 0.596 7.712 14034 Z= 0.317 Chirality : 0.040 0.138 1573 Planarity : 0.005 0.085 1764 Dihedral : 5.959 44.410 1358 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.13 % Favored : 91.63 % Rotamer: Outliers : 3.44 % Allowed : 16.21 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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: -1.07 (0.24), residues: 1242 helix: 1.41 (0.27), residues: 401 sheet: -0.62 (0.26), residues: 401 loop : -2.86 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 66 TYR 0.011 0.001 TYR L 254 PHE 0.020 0.001 PHE L 313 TRP 0.012 0.001 TRP A 197 HIS 0.005 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00253 (10386) covalent geometry : angle 0.59610 (14034) hydrogen bonds : bond 0.03009 ( 505) hydrogen bonds : angle 4.02267 ( 1848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 136 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: A 138 GLU cc_start: 0.7712 (tp30) cc_final: 0.7358 (mm-30) REVERT: A 169 HIS cc_start: 0.6709 (OUTLIER) cc_final: 0.5893 (m-70) REVERT: A 213 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8756 (m) REVERT: B 255 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7495 (tt0) REVERT: C 132 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8715 (mt) REVERT: C 218 GLN cc_start: 0.6102 (OUTLIER) cc_final: 0.5888 (tm-30) REVERT: C 267 ASP cc_start: 0.8153 (t70) cc_final: 0.7308 (t0) REVERT: L 7 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6655 (pt0) REVERT: L 169 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8733 (tt) REVERT: L 239 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8366 (tp) REVERT: L 434 LYS cc_start: 0.8109 (ttpt) cc_final: 0.6815 (mttp) outliers start: 39 outliers final: 14 residues processed: 146 average time/residue: 0.4602 time to fit residues: 73.3874 Evaluate side-chains 133 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 118 optimal weight: 0.1980 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 0.0060 chunk 112 optimal weight: 5.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 301 ASN L 257 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108414 restraints weight = 11851.697| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.02 r_work: 0.3099 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10386 Z= 0.166 Angle : 0.640 7.748 14034 Z= 0.340 Chirality : 0.042 0.142 1573 Planarity : 0.005 0.087 1764 Dihedral : 6.092 46.174 1358 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.21 % Favored : 91.55 % Rotamer: Outliers : 3.26 % Allowed : 16.83 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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: -0.99 (0.24), residues: 1242 helix: 1.40 (0.27), residues: 406 sheet: -0.58 (0.26), residues: 403 loop : -2.78 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 66 TYR 0.013 0.001 TYR B 164 PHE 0.020 0.001 PHE L 313 TRP 0.013 0.001 TRP A 197 HIS 0.005 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00378 (10386) covalent geometry : angle 0.64006 (14034) hydrogen bonds : bond 0.03323 ( 505) hydrogen bonds : angle 4.13759 ( 1848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 136 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: A 138 GLU cc_start: 0.7663 (tp30) cc_final: 0.7294 (mm-30) REVERT: A 169 HIS cc_start: 0.6780 (OUTLIER) cc_final: 0.5978 (m-70) REVERT: A 213 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8792 (m) REVERT: A 277 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8702 (tt) REVERT: A 304 GLU cc_start: 0.8219 (tt0) cc_final: 0.7769 (tt0) REVERT: B 255 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7529 (tt0) REVERT: C 218 GLN cc_start: 0.6149 (OUTLIER) cc_final: 0.5947 (tm-30) REVERT: C 267 ASP cc_start: 0.8162 (t70) cc_final: 0.7263 (t0) REVERT: L 7 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6761 (pt0) REVERT: L 169 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8732 (tt) REVERT: L 239 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8382 (tp) REVERT: L 298 PHE cc_start: 0.7464 (t80) cc_final: 0.7103 (t80) REVERT: L 434 LYS cc_start: 0.8134 (ttpt) cc_final: 0.6836 (mttp) outliers start: 37 outliers final: 19 residues processed: 139 average time/residue: 0.4711 time to fit residues: 71.4207 Evaluate side-chains 137 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 66 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 80 optimal weight: 30.0000 chunk 90 optimal weight: 0.2980 chunk 71 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 301 ASN L 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107236 restraints weight = 11891.879| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.03 r_work: 0.3103 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10386 Z= 0.180 Angle : 0.655 7.796 14034 Z= 0.346 Chirality : 0.043 0.141 1573 Planarity : 0.005 0.087 1764 Dihedral : 6.154 46.315 1358 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.62 % Favored : 91.14 % Rotamer: Outliers : 3.52 % Allowed : 16.48 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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: -0.97 (0.24), residues: 1242 helix: 1.49 (0.27), residues: 401 sheet: -0.58 (0.26), residues: 403 loop : -2.77 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 66 TYR 0.013 0.001 TYR B 164 PHE 0.019 0.001 PHE L 313 TRP 0.013 0.001 TRP A 197 HIS 0.005 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00411 (10386) covalent geometry : angle 0.65479 (14034) hydrogen bonds : bond 0.03388 ( 505) hydrogen bonds : angle 4.16853 ( 1848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.398 Fit side-chains REVERT: A 136 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: A 138 GLU cc_start: 0.7687 (tp30) cc_final: 0.7273 (mm-30) REVERT: A 169 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.5942 (m-70) REVERT: A 213 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8800 (m) REVERT: A 277 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8690 (tt) REVERT: A 472 ARG cc_start: 0.7926 (tpp80) cc_final: 0.7711 (tpp-160) REVERT: B 255 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7506 (tt0) REVERT: C 267 ASP cc_start: 0.8172 (t70) cc_final: 0.7224 (t0) REVERT: L 7 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6734 (pt0) REVERT: L 169 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8727 (tt) REVERT: L 239 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8409 (tt) REVERT: L 298 PHE cc_start: 0.7505 (t80) cc_final: 0.7121 (t80) REVERT: L 434 LYS cc_start: 0.8148 (ttpt) cc_final: 0.6841 (mttp) outliers start: 40 outliers final: 25 residues processed: 137 average time/residue: 0.4580 time to fit residues: 68.6625 Evaluate side-chains 140 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 411 ILE Chi-restraints excluded: chain L residue 425 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 0.0970 chunk 101 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 overall best weight: 2.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 342 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.138986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104812 restraints weight = 11914.050| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.03 r_work: 0.3081 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10386 Z= 0.246 Angle : 0.712 8.249 14034 Z= 0.377 Chirality : 0.045 0.154 1573 Planarity : 0.006 0.089 1764 Dihedral : 6.384 47.804 1358 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.50 % Rotamer: Outliers : 3.26 % Allowed : 17.00 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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: -1.08 (0.24), residues: 1242 helix: 1.36 (0.27), residues: 399 sheet: -0.68 (0.26), residues: 406 loop : -2.75 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 472 TYR 0.014 0.002 TYR B 164 PHE 0.021 0.002 PHE L 313 TRP 0.014 0.001 TRP A 197 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00571 (10386) covalent geometry : angle 0.71198 (14034) hydrogen bonds : bond 0.03737 ( 505) hydrogen bonds : angle 4.32656 ( 1848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.336 Fit side-chains REVERT: A 138 GLU cc_start: 0.7698 (tp30) cc_final: 0.7250 (mm-30) REVERT: A 213 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8813 (m) REVERT: A 472 ARG cc_start: 0.8080 (tpp80) cc_final: 0.7856 (tpp-160) REVERT: B 255 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7497 (tt0) REVERT: C 111 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: C 267 ASP cc_start: 0.8202 (t70) cc_final: 0.7982 (m-30) REVERT: L 7 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6753 (pt0) REVERT: L 169 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8690 (tt) REVERT: L 239 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8441 (tt) REVERT: L 298 PHE cc_start: 0.7534 (t80) cc_final: 0.7148 (t80) REVERT: L 434 LYS cc_start: 0.8138 (ttpt) cc_final: 0.6857 (mttt) outliers start: 37 outliers final: 23 residues processed: 129 average time/residue: 0.4598 time to fit residues: 64.7767 Evaluate side-chains 135 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 58 optimal weight: 0.0270 chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.143522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.109150 restraints weight = 11786.946| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.08 r_work: 0.3115 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10386 Z= 0.120 Angle : 0.616 8.008 14034 Z= 0.326 Chirality : 0.041 0.137 1573 Planarity : 0.005 0.084 1764 Dihedral : 5.950 44.227 1358 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.65 % Favored : 92.11 % Rotamer: Outliers : 2.20 % Allowed : 18.06 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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 (0.24), residues: 1242 helix: 1.70 (0.27), residues: 399 sheet: -0.50 (0.26), residues: 401 loop : -2.71 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 472 TYR 0.012 0.001 TYR L 254 PHE 0.017 0.001 PHE L 313 TRP 0.011 0.001 TRP A 197 HIS 0.006 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00264 (10386) covalent geometry : angle 0.61564 (14034) hydrogen bonds : bond 0.03019 ( 505) hydrogen bonds : angle 4.03130 ( 1848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.395 Fit side-chains REVERT: A 136 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: A 138 GLU cc_start: 0.7661 (tp30) cc_final: 0.7283 (mm-30) REVERT: A 277 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 304 GLU cc_start: 0.8184 (tt0) cc_final: 0.7714 (tt0) REVERT: B 255 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7506 (tt0) REVERT: C 104 ARG cc_start: 0.6633 (mmm160) cc_final: 0.6357 (mmm160) REVERT: C 267 ASP cc_start: 0.8148 (t70) cc_final: 0.7216 (t0) REVERT: L 169 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8703 (tt) REVERT: L 434 LYS cc_start: 0.8098 (ttpt) cc_final: 0.6764 (mttp) outliers start: 25 outliers final: 13 residues processed: 126 average time/residue: 0.4603 time to fit residues: 63.4996 Evaluate side-chains 127 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 207 GLN A 411 HIS ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103161 restraints weight = 12038.201| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.06 r_work: 0.3033 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 10386 Z= 0.306 Angle : 0.757 8.114 14034 Z= 0.397 Chirality : 0.047 0.162 1573 Planarity : 0.006 0.091 1764 Dihedral : 6.473 48.860 1358 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.74 % Rotamer: Outliers : 1.67 % Allowed : 18.24 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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: -1.16 (0.24), residues: 1242 helix: 1.27 (0.26), residues: 401 sheet: -0.77 (0.26), residues: 392 loop : -2.68 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 120 TYR 0.017 0.002 TYR L 148 PHE 0.021 0.002 PHE L 313 TRP 0.015 0.002 TRP A 197 HIS 0.005 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00715 (10386) covalent geometry : angle 0.75745 (14034) hydrogen bonds : bond 0.03971 ( 505) hydrogen bonds : angle 4.40496 ( 1848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.68 seconds wall clock time: 57 minutes 32.19 seconds (3452.19 seconds total)