Starting phenix.real_space_refine on Mon Jul 28 04:19:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btx_30190/07_2025/7btx_30190.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btx_30190/07_2025/7btx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7btx_30190/07_2025/7btx_30190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btx_30190/07_2025/7btx_30190.map" model { file = "/net/cci-nas-00/data/ceres_data/7btx_30190/07_2025/7btx_30190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btx_30190/07_2025/7btx_30190.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'GLU:plan': 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: 6.34, per 1000 atoms: 0.62 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: 2.56 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.34 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: 3.30 Time building geometry restraints manager: 3.03 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: 0.960 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.640 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.370 ------------------------------------------------------------------------------- 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 : 4.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.002 TRP A 323 HIS 0.014 0.002 HIS A 422 PHE 0.026 0.003 PHE B 68 TYR 0.018 0.002 TYR B 245 ARG 0.016 0.001 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.24697 ( 505) hydrogen bonds : angle 9.51081 ( 1848) covalent geometry : bond 0.00764 (10386) covalent geometry : angle 1.09413 (14034) *********************** 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 : 1.191 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: 0.6710 (m90) REVERT: B 248 HIS cc_start: 0.8311 (t70) cc_final: 0.8057 (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 315 GLN cc_start: 0.7116 (tp-100) cc_final: 0.6796 (tt0) REVERT: L 434 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7938 (tttm) outliers start: 3 outliers final: 1 residues processed: 176 average time/residue: 1.0730 time to fit residues: 205.0197 Evaluate side-chains 124 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 104 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 A 424 ASN A 466 HIS B 87 GLN B 94 ASN 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 164 GLN L 180 ASN L 490 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.137729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103923 restraints weight = 11939.325| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.01 r_work: 0.3070 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1706 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= 0.257 Angle : 0.767 8.581 14034 Z= 0.413 Chirality : 0.046 0.170 1573 Planarity : 0.007 0.097 1764 Dihedral : 7.356 50.180 1360 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.78 % Favored : 90.90 % Rotamer: Outliers : 2.64 % Allowed : 12.78 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.21), residues: 1242 helix: -1.49 (0.22), residues: 403 sheet: -1.33 (0.25), residues: 387 loop : -3.32 (0.23), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 323 HIS 0.005 0.001 HIS A 422 PHE 0.022 0.002 PHE C 225 TYR 0.016 0.002 TYR L 148 ARG 0.006 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 505) hydrogen bonds : angle 5.14326 ( 1848) covalent geometry : bond 0.00588 (10386) covalent geometry : angle 0.76671 (14034) *********************** 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 148 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.134 Fit side-chains REVERT: A 138 GLU cc_start: 0.7712 (tp30) cc_final: 0.7249 (mm-30) REVERT: A 314 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: B 196 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7469 (mtmt) REVERT: B 255 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7541 (tt0) REVERT: C 97 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6285 (mt-10) REVERT: C 267 ASP cc_start: 0.8297 (t70) cc_final: 0.7346 (t0) REVERT: L 169 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8739 (tt) REVERT: L 298 PHE cc_start: 0.7452 (t80) cc_final: 0.7194 (t80) REVERT: L 315 GLN cc_start: 0.7059 (tp-100) cc_final: 0.6519 (tt0) REVERT: L 434 LYS cc_start: 0.8228 (ttpt) cc_final: 0.6913 (mptt) outliers start: 30 outliers final: 11 residues processed: 139 average time/residue: 0.9174 time to fit residues: 140.5884 Evaluate side-chains 118 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 197 TRP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 457 LEU 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 B residue 196 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain L residue 169 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 0.1980 chunk 89 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.107618 restraints weight = 11969.911| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.03 r_work: 0.3111 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2116 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= 0.151 Angle : 0.648 8.104 14034 Z= 0.347 Chirality : 0.042 0.138 1573 Planarity : 0.006 0.090 1764 Dihedral : 6.728 46.278 1360 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.73 % Favored : 92.03 % Rotamer: Outliers : 2.73 % Allowed : 14.54 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.23), residues: 1242 helix: -0.01 (0.26), residues: 404 sheet: -1.09 (0.26), residues: 382 loop : -3.13 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.005 0.001 HIS A 169 PHE 0.023 0.001 PHE L 313 TYR 0.016 0.001 TYR L 185 ARG 0.004 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 505) hydrogen bonds : angle 4.49139 ( 1848) covalent geometry : bond 0.00336 (10386) covalent geometry : angle 0.64752 (14034) *********************** 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 153 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.093 Fit side-chains REVERT: A 138 GLU cc_start: 0.7687 (tp30) cc_final: 0.7216 (mm-30) REVERT: A 169 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.5962 (m-70) REVERT: B 255 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7526 (tt0) REVERT: C 267 ASP cc_start: 0.8201 (t70) cc_final: 0.7293 (t0) REVERT: C 302 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7671 (mp) REVERT: L 169 LEU cc_start: 0.8987 (mt) cc_final: 0.8740 (tt) REVERT: L 296 TYR cc_start: 0.8179 (t80) cc_final: 0.7960 (t80) REVERT: L 315 GLN cc_start: 0.7051 (tp-100) cc_final: 0.6515 (tt0) REVERT: L 434 LYS cc_start: 0.8166 (ttpt) cc_final: 0.6902 (mttt) outliers start: 31 outliers final: 10 residues processed: 139 average time/residue: 0.9883 time to fit residues: 150.2744 Evaluate side-chains 121 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 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 C residue 134 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 46 optimal weight: 0.0010 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 207 GLN A 342 ASN ** 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 67 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 = 0.3578 r_free = 0.3578 target = 0.137015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.102656 restraints weight = 12023.181| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.03 r_work: 0.3050 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 10386 Z= 0.303 Angle : 0.761 7.944 14034 Z= 0.402 Chirality : 0.047 0.162 1573 Planarity : 0.006 0.097 1764 Dihedral : 6.983 48.641 1360 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.62 % Favored : 91.06 % Rotamer: Outliers : 4.14 % Allowed : 15.24 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.23), residues: 1242 helix: 0.39 (0.26), residues: 397 sheet: -1.18 (0.26), residues: 386 loop : -3.05 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 197 HIS 0.005 0.001 HIS L 191 PHE 0.023 0.002 PHE B 68 TYR 0.015 0.002 TYR C 140 ARG 0.008 0.001 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 505) hydrogen bonds : angle 4.63655 ( 1848) covalent geometry : bond 0.00702 (10386) covalent geometry : angle 0.76125 (14034) *********************** 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 154 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 1.432 Fit side-chains REVERT: A 138 GLU cc_start: 0.7672 (tp30) cc_final: 0.7220 (mm-30) REVERT: A 203 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8889 (mp) REVERT: A 314 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: B 255 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7524 (tt0) REVERT: C 267 ASP cc_start: 0.8271 (t70) cc_final: 0.7228 (t0) REVERT: L 169 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8727 (tt) REVERT: L 239 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8441 (tt) REVERT: L 298 PHE cc_start: 0.7590 (t80) cc_final: 0.7231 (t80) REVERT: L 315 GLN cc_start: 0.7063 (tp-100) cc_final: 0.6534 (tt0) REVERT: L 434 LYS cc_start: 0.8182 (ttpt) cc_final: 0.6856 (mptt) outliers start: 47 outliers final: 28 residues processed: 137 average time/residue: 1.0168 time to fit residues: 153.4945 Evaluate side-chains 136 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 203 LEU 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 292 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 471 ILE 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 B residue 212 LEU 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 66 ASP Chi-restraints excluded: chain C residue 132 LEU 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 C residue 251 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104056 restraints weight = 11909.073| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.04 r_work: 0.3076 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10386 Z= 0.216 Angle : 0.690 7.860 14034 Z= 0.366 Chirality : 0.044 0.151 1573 Planarity : 0.006 0.092 1764 Dihedral : 6.738 46.715 1360 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.45 % Favored : 91.30 % Rotamer: Outliers : 4.67 % Allowed : 15.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.23), residues: 1242 helix: 0.82 (0.26), residues: 396 sheet: -1.01 (0.26), residues: 399 loop : -2.99 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.004 0.001 HIS A 310 PHE 0.027 0.002 PHE L 313 TYR 0.015 0.002 TYR L 296 ARG 0.002 0.000 ARG A 376 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 505) hydrogen bonds : angle 4.41631 ( 1848) covalent geometry : bond 0.00498 (10386) covalent geometry : angle 0.68958 (14034) *********************** 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 164 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 111 time to evaluate : 1.249 Fit side-chains REVERT: A 138 GLU cc_start: 0.7710 (tp30) cc_final: 0.7257 (mm-30) REVERT: A 169 HIS cc_start: 0.6754 (OUTLIER) cc_final: 0.6256 (m90) REVERT: A 203 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8913 (mp) REVERT: A 314 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: B 255 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7521 (tt0) REVERT: C 267 ASP cc_start: 0.8256 (t70) cc_final: 0.7985 (m-30) REVERT: C 302 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7795 (mp) REVERT: L 7 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6694 (pt0) REVERT: L 66 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7395 (ptp-110) REVERT: L 169 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8741 (tt) REVERT: L 239 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8458 (tt) REVERT: L 298 PHE cc_start: 0.7525 (t80) cc_final: 0.7192 (t80) REVERT: L 315 GLN cc_start: 0.7076 (tp-100) cc_final: 0.6563 (tt0) REVERT: L 434 LYS cc_start: 0.8178 (ttpt) cc_final: 0.6925 (mttt) outliers start: 53 outliers final: 28 residues processed: 143 average time/residue: 0.9528 time to fit residues: 149.5626 Evaluate side-chains 143 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 144 GLU 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 203 LEU 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 292 CYS Chi-restraints excluded: chain A residue 314 GLN 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 20 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 132 LEU 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 C residue 302 LEU Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 66 ARG Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU 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 88 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 80 optimal weight: 30.0000 chunk 101 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 342 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.105958 restraints weight = 11907.270| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.03 r_work: 0.3105 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2398 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 : 0.668 8.201 14034 Z= 0.353 Chirality : 0.043 0.138 1573 Planarity : 0.006 0.090 1764 Dihedral : 6.560 46.429 1360 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.53 % Favored : 91.22 % Rotamer: Outliers : 3.96 % Allowed : 16.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.24), residues: 1242 helix: 1.04 (0.26), residues: 402 sheet: -0.89 (0.26), residues: 398 loop : -2.93 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 197 HIS 0.004 0.001 HIS A 310 PHE 0.017 0.001 PHE B 68 TYR 0.013 0.001 TYR B 164 ARG 0.005 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 505) hydrogen bonds : angle 4.30290 ( 1848) covalent geometry : bond 0.00412 (10386) covalent geometry : angle 0.66794 (14034) *********************** 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 162 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 117 time to evaluate : 2.376 Fit side-chains REVERT: A 138 GLU cc_start: 0.7691 (tp30) cc_final: 0.7237 (mm-30) REVERT: A 169 HIS cc_start: 0.6683 (OUTLIER) cc_final: 0.6193 (m90) REVERT: A 213 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8801 (m) REVERT: A 314 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: B 255 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7494 (tt0) REVERT: C 267 ASP cc_start: 0.8228 (t70) cc_final: 0.7224 (t0) REVERT: C 302 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7779 (mp) REVERT: L 7 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6667 (pt0) REVERT: L 66 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7587 (ptp-110) REVERT: L 148 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7639 (p90) REVERT: L 169 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8752 (tt) REVERT: L 298 PHE cc_start: 0.7479 (t80) cc_final: 0.7128 (t80) REVERT: L 315 GLN cc_start: 0.7034 (tp-100) cc_final: 0.6320 (mt0) REVERT: L 434 LYS cc_start: 0.8169 (ttpt) cc_final: 0.6898 (mttt) outliers start: 45 outliers final: 24 residues processed: 145 average time/residue: 1.3893 time to fit residues: 221.5429 Evaluate side-chains 143 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 144 GLU 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 314 GLN 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 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 134 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 66 ARG Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN L 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.106218 restraints weight = 11982.072| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.05 r_work: 0.3122 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2542 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= 0.153 Angle : 0.643 9.153 14034 Z= 0.339 Chirality : 0.042 0.138 1573 Planarity : 0.005 0.088 1764 Dihedral : 6.246 45.427 1358 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.37 % Favored : 91.38 % Rotamer: Outliers : 3.26 % Allowed : 17.27 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.24), residues: 1242 helix: 1.20 (0.27), residues: 406 sheet: -0.78 (0.26), residues: 399 loop : -2.86 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 197 HIS 0.004 0.001 HIS A 310 PHE 0.023 0.001 PHE L 313 TYR 0.013 0.001 TYR B 164 ARG 0.003 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 505) hydrogen bonds : angle 4.19216 ( 1848) covalent geometry : bond 0.00345 (10386) covalent geometry : angle 0.64325 (14034) *********************** 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 155 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 1.270 Fit side-chains REVERT: A 136 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: A 138 GLU cc_start: 0.7695 (tp30) cc_final: 0.7311 (mm-30) REVERT: A 169 HIS cc_start: 0.6689 (OUTLIER) cc_final: 0.6185 (m90) REVERT: A 213 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8803 (m) REVERT: A 314 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: B 255 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7539 (tt0) REVERT: C 267 ASP cc_start: 0.8218 (t70) cc_final: 0.7232 (t0) REVERT: C 302 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7785 (mp) REVERT: L 7 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: L 66 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7726 (ptp-110) REVERT: L 169 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8761 (tt) REVERT: L 298 PHE cc_start: 0.7479 (t80) cc_final: 0.7137 (t80) REVERT: L 315 GLN cc_start: 0.7028 (tp-100) cc_final: 0.6334 (mt0) REVERT: L 434 LYS cc_start: 0.8188 (ttpt) cc_final: 0.6924 (mttp) outliers start: 37 outliers final: 15 residues processed: 139 average time/residue: 1.0414 time to fit residues: 159.0940 Evaluate side-chains 131 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 213 SER Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 314 GLN 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 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 134 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 66 ARG Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 29 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** 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 = 0.3616 r_free = 0.3616 target = 0.140131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.106080 restraints weight = 11950.358| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.04 r_work: 0.3076 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2592 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= 0.168 Angle : 0.651 7.612 14034 Z= 0.344 Chirality : 0.042 0.137 1573 Planarity : 0.005 0.089 1764 Dihedral : 6.217 46.092 1358 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.62 % Favored : 91.14 % Rotamer: Outliers : 3.44 % Allowed : 17.53 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.24), residues: 1242 helix: 1.38 (0.27), residues: 400 sheet: -0.78 (0.26), residues: 401 loop : -2.81 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 197 HIS 0.004 0.001 HIS A 310 PHE 0.016 0.001 PHE B 68 TYR 0.013 0.001 TYR L 254 ARG 0.003 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 505) hydrogen bonds : angle 4.19478 ( 1848) covalent geometry : bond 0.00384 (10386) covalent geometry : angle 0.65086 (14034) *********************** 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 147 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 1.115 Fit side-chains REVERT: A 138 GLU cc_start: 0.7691 (tp30) cc_final: 0.7319 (mm-30) REVERT: A 169 HIS cc_start: 0.6656 (OUTLIER) cc_final: 0.6162 (m90) REVERT: A 213 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8796 (m) REVERT: A 314 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: B 255 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7516 (tt0) REVERT: C 111 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: C 267 ASP cc_start: 0.8195 (t70) cc_final: 0.7891 (m-30) REVERT: C 302 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7837 (mp) REVERT: L 7 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6662 (pt0) REVERT: L 66 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7717 (ptp-110) REVERT: L 169 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8751 (tt) REVERT: L 239 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8381 (tp) REVERT: L 298 PHE cc_start: 0.7482 (t80) cc_final: 0.7100 (t80) REVERT: L 315 GLN cc_start: 0.6970 (tp-100) cc_final: 0.6300 (mt0) REVERT: L 434 LYS cc_start: 0.8159 (ttpt) cc_final: 0.6875 (mttp) outliers start: 39 outliers final: 18 residues processed: 133 average time/residue: 0.9527 time to fit residues: 139.2347 Evaluate side-chains 133 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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 213 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 314 GLN 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 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 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 302 LEU 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 66 ARG Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 61 optimal weight: 0.0040 chunk 89 optimal weight: 0.1980 overall best weight: 1.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** 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 = 0.3601 r_free = 0.3601 target = 0.138969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.104502 restraints weight = 11943.381| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.06 r_work: 0.3075 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10386 Z= 0.202 Angle : 0.681 8.185 14034 Z= 0.357 Chirality : 0.044 0.139 1573 Planarity : 0.005 0.089 1764 Dihedral : 6.337 46.903 1358 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.62 % Favored : 91.14 % Rotamer: Outliers : 3.26 % Allowed : 17.62 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.24), residues: 1242 helix: 1.34 (0.26), residues: 401 sheet: -0.76 (0.26), residues: 399 loop : -2.81 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 197 HIS 0.004 0.001 HIS A 310 PHE 0.025 0.002 PHE L 313 TYR 0.017 0.002 TYR L 185 ARG 0.004 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 505) hydrogen bonds : angle 4.26499 ( 1848) covalent geometry : bond 0.00466 (10386) covalent geometry : angle 0.68078 (14034) *********************** 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 142 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.113 Fit side-chains REVERT: A 138 GLU cc_start: 0.7725 (tp30) cc_final: 0.7274 (mm-30) REVERT: A 169 HIS cc_start: 0.6627 (OUTLIER) cc_final: 0.6166 (m90) REVERT: A 213 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8818 (m) REVERT: A 314 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: B 255 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7532 (tt0) REVERT: C 111 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: C 267 ASP cc_start: 0.8244 (t70) cc_final: 0.7880 (m-30) REVERT: C 302 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7889 (mp) REVERT: L 7 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6705 (pt0) REVERT: L 66 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7749 (ptp-110) REVERT: L 169 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8726 (tt) REVERT: L 239 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8435 (tp) REVERT: L 298 PHE cc_start: 0.7505 (t80) cc_final: 0.7129 (t80) REVERT: L 315 GLN cc_start: 0.7014 (tp-100) cc_final: 0.6369 (mt0) REVERT: L 434 LYS cc_start: 0.8165 (ttpt) cc_final: 0.6912 (mttt) outliers start: 37 outliers final: 22 residues processed: 128 average time/residue: 0.9910 time to fit residues: 139.1905 Evaluate side-chains 135 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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 213 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 314 GLN 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 20 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 302 LEU 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 66 ARG Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU 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 13 optimal weight: 0.3980 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 50 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108552 restraints weight = 11848.199| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.04 r_work: 0.3090 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2788 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= 0.128 Angle : 0.609 7.493 14034 Z= 0.323 Chirality : 0.041 0.139 1573 Planarity : 0.005 0.086 1764 Dihedral : 6.002 44.205 1358 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.89 % Favored : 91.87 % Rotamer: Outliers : 2.64 % Allowed : 18.68 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1242 helix: 1.62 (0.27), residues: 400 sheet: -0.69 (0.26), residues: 401 loop : -2.80 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 236 HIS 0.004 0.001 HIS A 310 PHE 0.022 0.001 PHE L 313 TYR 0.012 0.001 TYR B 164 ARG 0.003 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 505) hydrogen bonds : angle 4.03873 ( 1848) covalent geometry : bond 0.00286 (10386) covalent geometry : angle 0.60940 (14034) ********************** 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 148 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.305 Fit side-chains REVERT: A 138 GLU cc_start: 0.7691 (tp30) cc_final: 0.7158 (mm-30) REVERT: A 169 HIS cc_start: 0.6604 (OUTLIER) cc_final: 0.6081 (m90) REVERT: A 314 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: A 472 ARG cc_start: 0.7895 (tpp-160) cc_final: 0.7612 (tpp80) REVERT: B 255 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7506 (tt0) REVERT: C 302 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7714 (mp) REVERT: L 169 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8744 (tt) REVERT: L 239 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8344 (tp) REVERT: L 313 PHE cc_start: 0.8068 (t80) cc_final: 0.7620 (t80) REVERT: L 315 GLN cc_start: 0.6935 (tp-100) cc_final: 0.6327 (mt0) REVERT: L 434 LYS cc_start: 0.8136 (ttpt) cc_final: 0.6833 (mttp) outliers start: 30 outliers final: 14 residues processed: 135 average time/residue: 0.9903 time to fit residues: 146.5686 Evaluate side-chains 128 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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 235 THR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 314 GLN 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 C residue 20 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 226 ASP 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 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.141004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.106974 restraints weight = 11821.151| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.03 r_work: 0.3106 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10386 Z= 0.164 Angle : 0.649 8.082 14034 Z= 0.341 Chirality : 0.042 0.137 1573 Planarity : 0.005 0.089 1764 Dihedral : 6.085 46.272 1358 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.05 % Favored : 91.71 % Rotamer: Outliers : 2.20 % Allowed : 18.94 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1242 helix: 1.65 (0.27), residues: 399 sheet: -0.69 (0.26), residues: 401 loop : -2.76 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 236 HIS 0.004 0.001 HIS A 310 PHE 0.023 0.001 PHE L 313 TYR 0.017 0.001 TYR L 185 ARG 0.003 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 505) hydrogen bonds : angle 4.10856 ( 1848) covalent geometry : bond 0.00375 (10386) covalent geometry : angle 0.64898 (14034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7461.34 seconds wall clock time: 130 minutes 20.86 seconds (7820.86 seconds total)