Starting phenix.real_space_refine on Sun Dec 29 06:27:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btx_30190/12_2024/7btx_30190.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btx_30190/12_2024/7btx_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_30190/12_2024/7btx_30190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btx_30190/12_2024/7btx_30190.map" model { file = "/net/cci-nas-00/data/ceres_data/7btx_30190/12_2024/7btx_30190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btx_30190/12_2024/7btx_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-5532/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: 5.70, per 1000 atoms: 0.56 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 1.1 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: 1.16 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: 3.57 Time building geometry restraints manager: 2.87 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.080 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- 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= 0.493 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 *********************** 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 : 1.166 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: 1.0976 time to fit residues: 209.5221 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 : 1.150 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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= 0.378 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 *********************** 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 : 1.205 Fit side-chains REVERT: A 138 GLU cc_start: 0.7575 (tp30) cc_final: 0.7167 (mm-30) REVERT: A 314 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: B 196 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7414 (mtmt) REVERT: B 255 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7266 (tt0) REVERT: C 97 GLU cc_start: 0.5537 (OUTLIER) cc_final: 0.5269 (mt-10) REVERT: C 267 ASP cc_start: 0.7896 (t70) cc_final: 0.7086 (t0) REVERT: L 169 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8496 (tt) REVERT: L 239 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8350 (tt) REVERT: L 315 GLN cc_start: 0.6680 (tp-100) cc_final: 0.6320 (tt0) REVERT: L 434 LYS cc_start: 0.7939 (ttpt) cc_final: 0.6964 (mptt) outliers start: 30 outliers final: 11 residues processed: 139 average time/residue: 0.9298 time to fit residues: 142.7323 Evaluate side-chains 118 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 239 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** B 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10386 Z= 0.345 Angle : 0.721 8.224 14034 Z= 0.385 Chirality : 0.045 0.159 1573 Planarity : 0.006 0.095 1764 Dihedral : 7.024 47.773 1360 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.45 % Favored : 91.22 % Rotamer: Outliers : 3.52 % Allowed : 14.54 % Favored : 81.94 % 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: -2.33 (0.22), residues: 1242 helix: -0.08 (0.25), residues: 396 sheet: -1.21 (0.26), residues: 387 loop : -3.12 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 323 HIS 0.005 0.001 HIS A 169 PHE 0.025 0.002 PHE L 313 TYR 0.014 0.002 TYR B 164 ARG 0.007 0.000 ARG L 66 *********************** 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 152 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 1.219 Fit side-chains REVERT: A 138 GLU cc_start: 0.7541 (tp30) cc_final: 0.7132 (mm-30) REVERT: A 169 HIS cc_start: 0.7098 (OUTLIER) cc_final: 0.6274 (m-70) REVERT: A 314 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: B 196 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7386 (mtmt) REVERT: B 255 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7269 (tt0) REVERT: C 267 ASP cc_start: 0.7898 (t70) cc_final: 0.7041 (t0) REVERT: C 302 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7960 (mp) REVERT: L 169 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8505 (tt) REVERT: L 298 PHE cc_start: 0.7208 (t80) cc_final: 0.6872 (t80) REVERT: L 315 GLN cc_start: 0.6744 (tp-100) cc_final: 0.6364 (tt0) REVERT: L 434 LYS cc_start: 0.7929 (ttpt) cc_final: 0.6953 (mptt) outliers start: 40 outliers final: 17 residues processed: 134 average time/residue: 1.0785 time to fit residues: 157.9975 Evaluate side-chains 123 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 314 GLN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 471 ILE 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 196 LYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 66 ASP 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 169 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 111 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10386 Z= 0.347 Angle : 0.709 7.957 14034 Z= 0.377 Chirality : 0.045 0.154 1573 Planarity : 0.006 0.093 1764 Dihedral : 6.882 47.967 1360 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.70 % Favored : 90.98 % Rotamer: Outliers : 4.41 % Allowed : 15.24 % 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 (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: -1.93 (0.23), residues: 1242 helix: 0.52 (0.26), residues: 397 sheet: -1.07 (0.26), residues: 391 loop : -3.10 (0.24), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 323 HIS 0.005 0.001 HIS A 169 PHE 0.019 0.002 PHE B 68 TYR 0.017 0.002 TYR L 296 ARG 0.007 0.000 ARG L 66 *********************** 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 165 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 115 time to evaluate : 1.188 Fit side-chains REVERT: A 138 GLU cc_start: 0.7568 (tp30) cc_final: 0.7172 (mm-30) REVERT: A 203 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8885 (mp) REVERT: A 314 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: B 255 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7250 (tt0) REVERT: C 267 ASP cc_start: 0.7857 (t70) cc_final: 0.6983 (t0) REVERT: L 7 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6916 (pt0) REVERT: L 169 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8510 (tt) REVERT: L 239 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8440 (tt) REVERT: L 298 PHE cc_start: 0.7229 (t80) cc_final: 0.6911 (t80) REVERT: L 315 GLN cc_start: 0.6711 (tp-100) cc_final: 0.6346 (tt0) REVERT: L 434 LYS cc_start: 0.7897 (ttpt) cc_final: 0.6958 (mttt) outliers start: 50 outliers final: 23 residues processed: 144 average time/residue: 0.9326 time to fit residues: 147.8487 Evaluate side-chains 137 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 197 TRP Chi-restraints excluded: chain A residue 203 LEU 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 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 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 134 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10386 Z= 0.244 Angle : 0.657 7.740 14034 Z= 0.350 Chirality : 0.042 0.136 1573 Planarity : 0.006 0.089 1764 Dihedral : 6.601 45.930 1360 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.29 % Favored : 91.47 % Rotamer: Outliers : 3.70 % Allowed : 16.48 % Favored : 79.82 % 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: -1.56 (0.24), residues: 1242 helix: 0.94 (0.27), residues: 401 sheet: -0.93 (0.26), residues: 396 loop : -3.00 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.007 0.001 HIS A 169 PHE 0.027 0.001 PHE L 313 TYR 0.014 0.001 TYR L 185 ARG 0.002 0.000 ARG L 66 *********************** 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 162 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 1.275 Fit side-chains REVERT: A 138 GLU cc_start: 0.7574 (tp30) cc_final: 0.7196 (mm-30) REVERT: A 213 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8556 (m) REVERT: B 255 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7240 (tt0) REVERT: C 267 ASP cc_start: 0.7843 (t70) cc_final: 0.7014 (t0) REVERT: C 302 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7868 (mp) REVERT: L 7 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6852 (pt0) REVERT: L 66 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7278 (ptp-110) REVERT: L 169 LEU cc_start: 0.8732 (mt) cc_final: 0.8518 (tt) REVERT: L 239 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8422 (tt) REVERT: L 298 PHE cc_start: 0.7093 (t80) cc_final: 0.6799 (t80) REVERT: L 315 GLN cc_start: 0.6666 (tp-100) cc_final: 0.6311 (tt0) REVERT: L 434 LYS cc_start: 0.7887 (ttpt) cc_final: 0.6977 (mttp) outliers start: 42 outliers final: 17 residues processed: 145 average time/residue: 1.0830 time to fit residues: 172.1579 Evaluate side-chains 130 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 181 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 292 CYS 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 C residue 20 VAL Chi-restraints excluded: chain C residue 62 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 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 40 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 0.0670 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2391 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= 0.298 Angle : 0.688 8.959 14034 Z= 0.363 Chirality : 0.044 0.145 1573 Planarity : 0.006 0.089 1764 Dihedral : 6.481 47.233 1358 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.94 % Favored : 90.82 % Rotamer: Outliers : 4.41 % Allowed : 15.95 % Favored : 79.65 % 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: -1.42 (0.24), residues: 1242 helix: 1.07 (0.26), residues: 403 sheet: -0.87 (0.26), residues: 396 loop : -2.92 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 236 HIS 0.004 0.001 HIS A 310 PHE 0.018 0.002 PHE B 68 TYR 0.013 0.002 TYR B 164 ARG 0.005 0.000 ARG A 397 *********************** 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 163 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 113 time to evaluate : 1.141 Fit side-chains REVERT: A 138 GLU cc_start: 0.7548 (tp30) cc_final: 0.7176 (mm-30) REVERT: A 213 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8561 (m) REVERT: A 314 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: B 255 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7239 (tt0) REVERT: C 302 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7904 (mp) REVERT: L 7 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6877 (pt0) REVERT: L 66 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7313 (ptp-110) REVERT: L 148 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7344 (p90) REVERT: L 169 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8521 (tt) REVERT: L 239 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8451 (tt) REVERT: L 298 PHE cc_start: 0.7127 (t80) cc_final: 0.6839 (t80) REVERT: L 315 GLN cc_start: 0.6687 (tp-100) cc_final: 0.6483 (mt0) REVERT: L 434 LYS cc_start: 0.7890 (ttpt) cc_final: 0.6974 (mttt) outliers start: 50 outliers final: 23 residues processed: 144 average time/residue: 0.9808 time to fit residues: 155.0402 Evaluate side-chains 140 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 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 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 132 LEU 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 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 242 VAL 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 115 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 0.0010 chunk 119 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 0.0270 chunk 55 optimal weight: 0.0030 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 421 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN C 300 ASN L 49 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10386 Z= 0.138 Angle : 0.594 7.643 14034 Z= 0.315 Chirality : 0.040 0.141 1573 Planarity : 0.005 0.080 1764 Dihedral : 5.934 42.803 1358 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.57 % Favored : 92.19 % Rotamer: Outliers : 2.47 % Allowed : 18.15 % Favored : 79.38 % 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: -0.97 (0.24), residues: 1242 helix: 1.56 (0.27), residues: 406 sheet: -0.65 (0.26), residues: 398 loop : -2.82 (0.27), residues: 438 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 0.023 0.001 PHE L 313 TYR 0.010 0.001 TYR B 164 ARG 0.004 0.000 ARG A 397 *********************** 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 160 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7536 (tp30) cc_final: 0.7213 (pt0) REVERT: B 139 ILE cc_start: 0.8663 (mp) cc_final: 0.8285 (mm) REVERT: B 255 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7268 (tt0) REVERT: L 434 LYS cc_start: 0.7869 (ttpt) cc_final: 0.6961 (mttp) outliers start: 28 outliers final: 10 residues processed: 148 average time/residue: 1.0594 time to fit residues: 171.5964 Evaluate side-chains 129 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 181 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 123 ASN 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 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 0.0020 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10386 Z= 0.243 Angle : 0.651 7.654 14034 Z= 0.342 Chirality : 0.042 0.143 1573 Planarity : 0.005 0.089 1764 Dihedral : 6.091 46.179 1358 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.37 % Favored : 91.38 % Rotamer: Outliers : 2.29 % Allowed : 19.12 % Favored : 78.59 % 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: -0.92 (0.24), residues: 1242 helix: 1.64 (0.27), residues: 405 sheet: -0.65 (0.26), residues: 401 loop : -2.78 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 236 HIS 0.004 0.001 HIS L 44 PHE 0.016 0.001 PHE A 237 TYR 0.014 0.002 TYR L 254 ARG 0.008 0.000 ARG C 272 *********************** 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 142 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.199 Fit side-chains REVERT: A 138 GLU cc_start: 0.7576 (tp30) cc_final: 0.7180 (mm-30) REVERT: A 304 GLU cc_start: 0.7547 (tt0) cc_final: 0.7138 (tt0) REVERT: A 314 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: B 255 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7276 (tt0) REVERT: C 111 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: L 85 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6303 (mmp) REVERT: L 239 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8372 (tt) REVERT: L 434 LYS cc_start: 0.7886 (ttpt) cc_final: 0.6973 (mttp) outliers start: 26 outliers final: 14 residues processed: 131 average time/residue: 1.0290 time to fit residues: 148.4793 Evaluate side-chains 123 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 181 SER Chi-restraints excluded: chain A residue 197 TRP 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 123 ASN 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 111 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 105 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10386 Z= 0.241 Angle : 0.650 7.690 14034 Z= 0.341 Chirality : 0.042 0.143 1573 Planarity : 0.005 0.087 1764 Dihedral : 6.107 45.218 1358 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.29 % Favored : 91.47 % Rotamer: Outliers : 2.29 % Allowed : 19.03 % 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: -0.92 (0.24), residues: 1242 helix: 1.66 (0.26), residues: 405 sheet: -0.69 (0.26), residues: 403 loop : -2.77 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 236 HIS 0.004 0.001 HIS A 310 PHE 0.024 0.001 PHE L 313 TYR 0.014 0.001 TYR L 254 ARG 0.007 0.000 ARG C 272 *********************** 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 134 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.510 Fit side-chains REVERT: A 138 GLU cc_start: 0.7587 (tp30) cc_final: 0.7169 (mm-30) REVERT: A 314 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: B 255 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7260 (tt0) REVERT: L 85 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6257 (mmp) REVERT: L 239 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (tt) REVERT: L 298 PHE cc_start: 0.7155 (t80) cc_final: 0.6843 (t80) REVERT: L 434 LYS cc_start: 0.7890 (ttpt) cc_final: 0.6979 (mttp) outliers start: 26 outliers final: 17 residues processed: 127 average time/residue: 0.9308 time to fit residues: 130.9125 Evaluate side-chains 124 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 181 SER Chi-restraints excluded: chain A residue 197 TRP 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 123 ASN 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 173 ILE Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 85 MET 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 117 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10386 Z= 0.259 Angle : 0.663 8.077 14034 Z= 0.347 Chirality : 0.043 0.149 1573 Planarity : 0.005 0.088 1764 Dihedral : 6.154 46.398 1358 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.37 % Favored : 91.38 % Rotamer: Outliers : 2.03 % Allowed : 19.56 % Favored : 78.41 % 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: -0.94 (0.24), residues: 1242 helix: 1.65 (0.26), residues: 404 sheet: -0.71 (0.26), residues: 403 loop : -2.79 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 236 HIS 0.004 0.001 HIS L 44 PHE 0.023 0.001 PHE L 313 TYR 0.014 0.002 TYR L 296 ARG 0.006 0.000 ARG C 272 ********************** 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 131 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.988 Fit side-chains REVERT: A 138 GLU cc_start: 0.7576 (tp30) cc_final: 0.7186 (mm-30) REVERT: A 304 GLU cc_start: 0.7610 (tt0) cc_final: 0.7218 (tt0) REVERT: A 314 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: B 255 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7248 (tt0) REVERT: L 85 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6214 (mmp) REVERT: L 239 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8427 (tt) REVERT: L 298 PHE cc_start: 0.7179 (t80) cc_final: 0.6867 (t80) REVERT: L 313 PHE cc_start: 0.7498 (t80) cc_final: 0.7202 (t80) REVERT: L 434 LYS cc_start: 0.7871 (ttpt) cc_final: 0.6974 (mttp) outliers start: 23 outliers final: 15 residues processed: 124 average time/residue: 0.9261 time to fit residues: 126.9674 Evaluate side-chains 123 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 181 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 123 ASN 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 173 ILE Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 85 MET 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 104 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** 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 = 0.3661 r_free = 0.3661 target = 0.143984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110089 restraints weight = 11833.704| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.05 r_work: 0.3067 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2982 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= 0.171 Angle : 0.619 8.596 14034 Z= 0.325 Chirality : 0.041 0.235 1573 Planarity : 0.005 0.085 1764 Dihedral : 5.893 43.475 1358 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.73 % Favored : 92.03 % Rotamer: Outliers : 1.50 % Allowed : 20.26 % Favored : 78.24 % 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: -0.77 (0.25), residues: 1242 helix: 1.83 (0.27), residues: 405 sheet: -0.55 (0.26), residues: 399 loop : -2.80 (0.27), residues: 438 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 0.021 0.001 PHE L 313 TYR 0.013 0.001 TYR L 254 ARG 0.007 0.000 ARG C 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.36 seconds wall clock time: 61 minutes 22.93 seconds (3682.93 seconds total)