Starting phenix.real_space_refine on Thu Feb 13 12:36:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kfz_37209/02_2025/8kfz_37209.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kfz_37209/02_2025/8kfz_37209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kfz_37209/02_2025/8kfz_37209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kfz_37209/02_2025/8kfz_37209.map" model { file = "/net/cci-nas-00/data/ceres_data/8kfz_37209/02_2025/8kfz_37209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kfz_37209/02_2025/8kfz_37209.cif" } resolution = 3.3 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= 0.001 sd= 0.023 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 66 5.16 5 C 5733 2.51 5 N 1503 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8966 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2342 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 5, 'TRANS': 282} Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 5.58, per 1000 atoms: 0.62 Number of scatterers: 8966 At special positions: 0 Unit cell: (87.36, 122.72, 125.84, 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 66 16.00 O 1664 8.00 N 1503 7.00 C 5733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 39.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'R' and resid 30 through 62 Processing helix chain 'R' and resid 68 through 86 Processing helix chain 'R' and resid 86 through 97 removed outlier: 4.228A pdb=" N PHE R 90 " --> pdb=" O PHE R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 5.113A pdb=" N LYS R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 170 Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 188 through 205 removed outlier: 4.142A pdb=" N LYS R 193 " --> pdb=" O GLN R 189 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TRP R 194 " --> pdb=" O GLN R 190 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN R 203 " --> pdb=" O ASN R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 removed outlier: 3.704A pdb=" N ILE R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 250 removed outlier: 3.550A pdb=" N LEU R 248 " --> pdb=" O VAL R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 266 removed outlier: 3.914A pdb=" N ASN R 255 " --> pdb=" O TRP R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 290 Processing helix chain 'R' and resid 291 through 301 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.017A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.944A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.566A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.596A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.819A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.542A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.855A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.566A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 172 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.523A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.882A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.590A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.277A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.984A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.086A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.702A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 5.704A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.258A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.258A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.465A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 135 through 136 removed outlier: 3.591A pdb=" N GLN S 219 " --> pdb=" O THR S 226 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 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: 1.22 - 1.34: 2859 1.34 - 1.46: 2059 1.46 - 1.58: 4140 1.58 - 1.70: 1 1.70 - 1.81: 95 Bond restraints: 9154 Sorted by residual: bond pdb=" N PRO S 169 " pdb=" CD PRO S 169 " ideal model delta sigma weight residual 1.473 1.418 0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" CB PRO S 169 " pdb=" CG PRO S 169 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.11e+00 bond pdb=" CG PRO S 169 " pdb=" CD PRO S 169 " ideal model delta sigma weight residual 1.503 1.552 -0.049 3.40e-02 8.65e+02 2.12e+00 bond pdb=" CB MET S 218 " pdb=" CG MET S 218 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" C VAL A 201 " pdb=" O VAL A 201 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.19e+00 ... (remaining 9149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 12233 2.46 - 4.92: 135 4.92 - 7.38: 16 7.38 - 9.85: 4 9.85 - 12.31: 2 Bond angle restraints: 12390 Sorted by residual: angle pdb=" CA PRO S 169 " pdb=" N PRO S 169 " pdb=" CD PRO S 169 " ideal model delta sigma weight residual 112.00 118.38 -6.38 1.40e+00 5.10e-01 2.08e+01 angle pdb=" C VAL R 85 " pdb=" N PHE R 86 " pdb=" CA PHE R 86 " ideal model delta sigma weight residual 120.28 114.93 5.35 1.44e+00 4.82e-01 1.38e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.37e+01 angle pdb=" CA LEU R 159 " pdb=" CB LEU R 159 " pdb=" CG LEU R 159 " ideal model delta sigma weight residual 116.30 128.61 -12.31 3.50e+00 8.16e-02 1.24e+01 angle pdb=" N PHE R 86 " pdb=" CA PHE R 86 " pdb=" CB PHE R 86 " ideal model delta sigma weight residual 110.22 115.51 -5.29 1.54e+00 4.22e-01 1.18e+01 ... (remaining 12385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4739 17.90 - 35.81: 526 35.81 - 53.71: 140 53.71 - 71.61: 16 71.61 - 89.52: 2 Dihedral angle restraints: 5423 sinusoidal: 2109 harmonic: 3314 Sorted by residual: dihedral pdb=" CA PHE R 290 " pdb=" C PHE R 290 " pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA MET R 266 " pdb=" C MET R 266 " pdb=" N HIS R 267 " pdb=" CA HIS R 267 " ideal model delta harmonic sigma weight residual 180.00 155.48 24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN S 159 " pdb=" C ASN S 159 " pdb=" N THR S 160 " pdb=" CA THR S 160 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1270 0.072 - 0.145: 135 0.145 - 0.217: 8 0.217 - 0.290: 0 0.290 - 0.362: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB ILE R 115 " pdb=" CA ILE R 115 " pdb=" CG1 ILE R 115 " pdb=" CG2 ILE R 115 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CG LEU A 268 " pdb=" CB LEU A 268 " pdb=" CD1 LEU A 268 " pdb=" CD2 LEU A 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL A 339 " pdb=" CA VAL A 339 " pdb=" CG1 VAL A 339 " pdb=" CG2 VAL A 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 1411 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 251 " -0.026 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP R 251 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP R 251 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP R 251 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 251 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 251 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 251 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 251 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 251 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP R 251 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 86 " 0.029 2.00e-02 2.50e+03 2.46e-02 1.05e+01 pdb=" CG PHE R 86 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE R 86 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 86 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE R 86 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE R 86 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.57e+00 pdb=" N PRO C 49 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.029 5.00e-02 4.00e+02 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1029 2.75 - 3.28: 9143 3.28 - 3.82: 15574 3.82 - 4.36: 18629 4.36 - 4.90: 31446 Nonbonded interactions: 75821 Sorted by model distance: nonbonded pdb=" O SER S 85 " pdb=" NH1 ARG S 87 " model vdw 2.206 3.120 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.233 3.120 nonbonded pdb=" O LYS R 306 " pdb=" ND1 HIS R 310 " model vdw 2.257 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.258 3.040 nonbonded pdb=" O PHE R 88 " pdb=" OG1 THR R 92 " model vdw 2.259 3.040 ... (remaining 75816 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: 3.080 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 24.200 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 0.004 0.101 9154 Z= 0.228 Angle : 0.667 12.307 12390 Z= 0.356 Chirality : 0.045 0.362 1414 Planarity : 0.004 0.053 1554 Dihedral : 15.611 89.516 3276 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.10 % Allowed : 28.85 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1125 helix: 1.73 (0.26), residues: 399 sheet: 0.05 (0.29), residues: 284 loop : -0.16 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP R 251 HIS 0.004 0.001 HIS S 155 PHE 0.056 0.002 PHE R 86 TYR 0.022 0.002 TYR S 178 ARG 0.008 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 121 MET cc_start: 0.7320 (mmt) cc_final: 0.7027 (mmt) REVERT: R 131 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7923 (mtt180) REVERT: R 132 TYR cc_start: 0.8680 (t80) cc_final: 0.8449 (t80) REVERT: B 57 LYS cc_start: 0.7624 (mtmt) cc_final: 0.7149 (mtmt) REVERT: B 130 GLU cc_start: 0.7745 (mp0) cc_final: 0.7297 (mp0) REVERT: B 169 TRP cc_start: 0.7798 (m100) cc_final: 0.7593 (m100) REVERT: S 38 ARG cc_start: 0.7426 (ptt180) cc_final: 0.7031 (ptt180) REVERT: S 90 ASP cc_start: 0.7234 (m-30) cc_final: 0.6980 (m-30) REVERT: S 167 GLN cc_start: 0.8221 (tt0) cc_final: 0.7951 (tp40) outliers start: 1 outliers final: 1 residues processed: 304 average time/residue: 0.2706 time to fit residues: 106.9634 Evaluate side-chains 292 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 183 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 GLN R 76 ASN R 230 ASN A 347 ASN B 132 ASN B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.155225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126702 restraints weight = 15164.027| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.67 r_work: 0.3492 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9154 Z= 0.279 Angle : 0.633 8.271 12390 Z= 0.339 Chirality : 0.044 0.236 1414 Planarity : 0.004 0.055 1554 Dihedral : 4.872 28.358 1227 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.85 % Allowed : 24.49 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1125 helix: 1.69 (0.26), residues: 407 sheet: 0.10 (0.29), residues: 285 loop : -0.31 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 251 HIS 0.005 0.001 HIS A 244 PHE 0.043 0.002 PHE R 86 TYR 0.018 0.002 TYR R 118 ARG 0.006 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 73 TYR cc_start: 0.7338 (m-10) cc_final: 0.7096 (m-10) REVERT: R 86 PHE cc_start: 0.7285 (m-80) cc_final: 0.6810 (m-80) REVERT: R 121 MET cc_start: 0.7408 (mmt) cc_final: 0.6642 (mmt) REVERT: R 127 MET cc_start: 0.6754 (mtp) cc_final: 0.6541 (mtm) REVERT: R 132 TYR cc_start: 0.8264 (t80) cc_final: 0.8056 (t80) REVERT: A 197 LYS cc_start: 0.7399 (mtmt) cc_final: 0.7025 (mtmt) REVERT: A 243 MET cc_start: 0.8410 (mmm) cc_final: 0.7770 (tpp) REVERT: A 336 PHE cc_start: 0.7955 (t80) cc_final: 0.7641 (t80) REVERT: A 349 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7629 (ttmt) REVERT: B 130 GLU cc_start: 0.7916 (mp0) cc_final: 0.7399 (mp0) REVERT: B 183 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7120 (t-170) REVERT: B 283 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7755 (mmm-85) REVERT: S 34 MET cc_start: 0.7695 (mmm) cc_final: 0.7032 (mmm) REVERT: S 38 ARG cc_start: 0.7547 (ptt180) cc_final: 0.7134 (ptt180) REVERT: S 46 GLU cc_start: 0.7575 (tt0) cc_final: 0.7322 (tt0) REVERT: S 90 ASP cc_start: 0.7296 (m-30) cc_final: 0.6994 (m-30) REVERT: S 171 GLN cc_start: 0.6507 (mm-40) cc_final: 0.6219 (tm-30) outliers start: 38 outliers final: 27 residues processed: 316 average time/residue: 0.2617 time to fit residues: 109.8075 Evaluate side-chains 325 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 220 GLN B 239 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127118 restraints weight = 15303.632| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.71 r_work: 0.3516 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9154 Z= 0.226 Angle : 0.599 10.932 12390 Z= 0.317 Chirality : 0.043 0.247 1414 Planarity : 0.004 0.049 1554 Dihedral : 4.788 28.057 1227 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.54 % Allowed : 25.81 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1125 helix: 1.80 (0.26), residues: 407 sheet: 0.04 (0.29), residues: 286 loop : -0.31 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 251 HIS 0.004 0.001 HIS R 310 PHE 0.028 0.002 PHE R 86 TYR 0.016 0.002 TYR S 178 ARG 0.005 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 293 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 73 TYR cc_start: 0.7352 (m-10) cc_final: 0.7053 (m-10) REVERT: R 86 PHE cc_start: 0.7323 (m-80) cc_final: 0.6738 (m-80) REVERT: R 121 MET cc_start: 0.7429 (mmt) cc_final: 0.6703 (mmt) REVERT: R 127 MET cc_start: 0.6891 (mtp) cc_final: 0.6666 (mtm) REVERT: R 220 LYS cc_start: 0.8260 (mmmm) cc_final: 0.7861 (mmmm) REVERT: R 237 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7648 (tt) REVERT: A 197 LYS cc_start: 0.7381 (mtmt) cc_final: 0.7042 (mtmt) REVERT: A 349 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7573 (ttmt) REVERT: B 130 GLU cc_start: 0.7976 (mp0) cc_final: 0.7626 (mp0) REVERT: B 183 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7107 (t-170) REVERT: S 18 ARG cc_start: 0.7235 (tmm-80) cc_final: 0.6851 (ttp80) REVERT: S 38 ARG cc_start: 0.7479 (ptt180) cc_final: 0.7107 (ptt180) REVERT: S 90 ASP cc_start: 0.7312 (m-30) cc_final: 0.7003 (m-30) outliers start: 35 outliers final: 26 residues processed: 307 average time/residue: 0.2278 time to fit residues: 93.2367 Evaluate side-chains 318 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 290 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 204 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 HIS ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 155 ASN B 220 GLN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.155722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.127008 restraints weight = 15190.595| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.70 r_work: 0.3508 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9154 Z= 0.251 Angle : 0.603 11.777 12390 Z= 0.320 Chirality : 0.043 0.264 1414 Planarity : 0.004 0.051 1554 Dihedral : 4.765 28.474 1227 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.45 % Allowed : 24.90 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1125 helix: 1.79 (0.26), residues: 407 sheet: -0.03 (0.29), residues: 288 loop : -0.32 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 251 HIS 0.004 0.001 HIS R 231 PHE 0.023 0.002 PHE B 253 TYR 0.016 0.002 TYR S 178 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 73 TYR cc_start: 0.7346 (m-10) cc_final: 0.7041 (m-10) REVERT: R 86 PHE cc_start: 0.7480 (m-80) cc_final: 0.6839 (m-80) REVERT: R 121 MET cc_start: 0.7406 (mmt) cc_final: 0.6747 (mmt) REVERT: R 127 MET cc_start: 0.6808 (mtp) cc_final: 0.6544 (mtm) REVERT: R 149 MET cc_start: 0.7367 (tpt) cc_final: 0.6823 (tpt) REVERT: R 159 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6862 (mp) REVERT: R 220 LYS cc_start: 0.8234 (mmmm) cc_final: 0.7824 (mmmm) REVERT: R 249 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6549 (mm) REVERT: A 197 LYS cc_start: 0.7332 (mtmt) cc_final: 0.6993 (mtmt) REVERT: A 321 THR cc_start: 0.8343 (m) cc_final: 0.7984 (t) REVERT: A 349 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7613 (ttmt) REVERT: B 130 GLU cc_start: 0.7964 (mp0) cc_final: 0.7559 (mp0) REVERT: B 183 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7193 (t-170) REVERT: S 18 ARG cc_start: 0.7286 (tmm-80) cc_final: 0.7045 (tmm-80) REVERT: S 38 ARG cc_start: 0.7535 (ptt180) cc_final: 0.7177 (ptt180) REVERT: S 90 ASP cc_start: 0.7323 (m-30) cc_final: 0.7022 (m-30) REVERT: S 168 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7866 (ttm-80) outliers start: 44 outliers final: 31 residues processed: 315 average time/residue: 0.2438 time to fit residues: 102.1362 Evaluate side-chains 326 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 292 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 204 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 0.0170 chunk 68 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 155 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.155489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126417 restraints weight = 15116.140| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.68 r_work: 0.3504 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9154 Z= 0.255 Angle : 0.612 12.594 12390 Z= 0.322 Chirality : 0.043 0.281 1414 Planarity : 0.004 0.053 1554 Dihedral : 4.786 28.718 1227 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.96 % Allowed : 25.61 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1125 helix: 1.77 (0.26), residues: 407 sheet: -0.08 (0.29), residues: 288 loop : -0.35 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 251 HIS 0.004 0.001 HIS R 310 PHE 0.018 0.002 PHE B 253 TYR 0.015 0.002 TYR S 178 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 297 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 73 TYR cc_start: 0.7388 (m-10) cc_final: 0.7119 (m-10) REVERT: R 86 PHE cc_start: 0.7520 (m-80) cc_final: 0.6963 (m-80) REVERT: R 121 MET cc_start: 0.7455 (mmt) cc_final: 0.6716 (mmt) REVERT: R 127 MET cc_start: 0.6793 (mtp) cc_final: 0.6538 (mtp) REVERT: R 149 MET cc_start: 0.7361 (tpt) cc_final: 0.7110 (tpt) REVERT: R 159 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6857 (mp) REVERT: R 207 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.4935 (tt) REVERT: R 211 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6519 (m-80) REVERT: R 249 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6544 (mm) REVERT: R 306 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7032 (pttm) REVERT: A 197 LYS cc_start: 0.7376 (mtmt) cc_final: 0.6987 (mtmt) REVERT: A 277 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7086 (tttt) REVERT: A 321 THR cc_start: 0.8344 (m) cc_final: 0.8003 (t) REVERT: A 349 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7620 (ttmt) REVERT: B 52 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7288 (mmm-85) REVERT: B 175 GLN cc_start: 0.7161 (mm-40) cc_final: 0.6954 (mm-40) REVERT: B 183 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7270 (t-170) REVERT: B 296 VAL cc_start: 0.8102 (t) cc_final: 0.7858 (m) REVERT: S 18 ARG cc_start: 0.7274 (tmm-80) cc_final: 0.7018 (tmm-80) REVERT: S 38 ARG cc_start: 0.7552 (ptt180) cc_final: 0.7197 (ptt180) REVERT: S 90 ASP cc_start: 0.7322 (m-30) cc_final: 0.7021 (m-30) outliers start: 49 outliers final: 35 residues processed: 321 average time/residue: 0.2284 time to fit residues: 98.6297 Evaluate side-chains 335 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 141 GLU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 204 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.0070 chunk 102 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** S 155 HIS ** 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 = 0.4058 r_free = 0.4058 target = 0.156067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127421 restraints weight = 15058.202| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.67 r_work: 0.3494 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9154 Z= 0.216 Angle : 0.613 12.871 12390 Z= 0.321 Chirality : 0.043 0.300 1414 Planarity : 0.004 0.053 1554 Dihedral : 4.743 29.047 1227 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.06 % Allowed : 25.81 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1125 helix: 1.82 (0.26), residues: 401 sheet: -0.06 (0.29), residues: 284 loop : -0.38 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 251 HIS 0.004 0.001 HIS R 310 PHE 0.033 0.002 PHE R 88 TYR 0.012 0.001 TYR S 103 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 73 TYR cc_start: 0.7358 (m-10) cc_final: 0.7060 (m-10) REVERT: R 86 PHE cc_start: 0.7429 (m-80) cc_final: 0.6849 (m-80) REVERT: R 118 TYR cc_start: 0.6922 (m-80) cc_final: 0.6326 (m-80) REVERT: R 121 MET cc_start: 0.7448 (mmt) cc_final: 0.6786 (mmt) REVERT: R 149 MET cc_start: 0.7340 (tpt) cc_final: 0.7078 (tpt) REVERT: R 159 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6886 (mp) REVERT: R 207 LEU cc_start: 0.5305 (OUTLIER) cc_final: 0.4892 (tt) REVERT: R 211 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6496 (m-80) REVERT: R 220 LYS cc_start: 0.8198 (mmmm) cc_final: 0.7759 (mmmm) REVERT: R 249 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6501 (mm) REVERT: R 306 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7034 (pttm) REVERT: A 197 LYS cc_start: 0.7397 (mtmt) cc_final: 0.6973 (mtmt) REVERT: A 270 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7943 (mmtm) REVERT: A 277 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7001 (tttt) REVERT: A 321 THR cc_start: 0.8315 (m) cc_final: 0.7990 (t) REVERT: A 349 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7510 (ttmt) REVERT: B 52 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7244 (mmm-85) REVERT: B 175 GLN cc_start: 0.7158 (mm-40) cc_final: 0.6913 (mm-40) REVERT: B 183 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7290 (t-170) REVERT: B 296 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7840 (m) REVERT: S 18 ARG cc_start: 0.7257 (tmm-80) cc_final: 0.7030 (tmm-80) REVERT: S 38 ARG cc_start: 0.7485 (ptt180) cc_final: 0.7175 (ptt180) REVERT: S 90 ASP cc_start: 0.7328 (m-30) cc_final: 0.7075 (m-30) REVERT: S 215 TYR cc_start: 0.7956 (m-10) cc_final: 0.7697 (m-10) outliers start: 50 outliers final: 33 residues processed: 307 average time/residue: 0.2268 time to fit residues: 93.0628 Evaluate side-chains 330 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain R residue 300 TYR Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 141 GLU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 0.0370 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 chunk 108 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 239 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.156664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.127706 restraints weight = 15272.130| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.72 r_work: 0.3497 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9154 Z= 0.199 Angle : 0.612 13.708 12390 Z= 0.317 Chirality : 0.043 0.267 1414 Planarity : 0.004 0.053 1554 Dihedral : 4.655 29.290 1227 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.96 % Allowed : 26.11 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1125 helix: 1.89 (0.26), residues: 401 sheet: 0.00 (0.30), residues: 282 loop : -0.34 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 251 HIS 0.004 0.001 HIS R 310 PHE 0.028 0.002 PHE R 88 TYR 0.012 0.001 TYR A 302 ARG 0.006 0.000 ARG S 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 288 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 73 TYR cc_start: 0.7346 (m-10) cc_final: 0.7029 (m-10) REVERT: R 86 PHE cc_start: 0.7441 (m-80) cc_final: 0.6862 (m-80) REVERT: R 118 TYR cc_start: 0.7013 (m-80) cc_final: 0.6466 (m-80) REVERT: R 121 MET cc_start: 0.7449 (mmt) cc_final: 0.6784 (mmt) REVERT: R 127 MET cc_start: 0.6769 (mtp) cc_final: 0.6561 (mtp) REVERT: R 149 MET cc_start: 0.7328 (tpt) cc_final: 0.7060 (tpt) REVERT: R 159 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6893 (mp) REVERT: R 207 LEU cc_start: 0.5271 (OUTLIER) cc_final: 0.4876 (tt) REVERT: R 211 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: R 220 LYS cc_start: 0.8181 (mmmm) cc_final: 0.7820 (mmmm) REVERT: R 249 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6427 (mm) REVERT: R 306 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7016 (pttm) REVERT: A 197 LYS cc_start: 0.7453 (mtmt) cc_final: 0.7031 (mtmt) REVERT: A 270 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7838 (mmtm) REVERT: A 277 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6991 (tttt) REVERT: A 321 THR cc_start: 0.8322 (m) cc_final: 0.8004 (t) REVERT: A 332 VAL cc_start: 0.8057 (m) cc_final: 0.7781 (p) REVERT: A 349 LYS cc_start: 0.7864 (mtmt) cc_final: 0.7553 (ttmt) REVERT: B 29 THR cc_start: 0.7934 (t) cc_final: 0.7510 (p) REVERT: B 52 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7225 (mmm-85) REVERT: B 175 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6848 (mm-40) REVERT: B 183 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7298 (t-170) REVERT: S 38 ARG cc_start: 0.7480 (ptt180) cc_final: 0.7160 (ptt180) REVERT: S 90 ASP cc_start: 0.7307 (m-30) cc_final: 0.7051 (m-30) REVERT: S 215 TYR cc_start: 0.7955 (m-10) cc_final: 0.7705 (m-10) outliers start: 49 outliers final: 32 residues processed: 310 average time/residue: 0.2412 time to fit residues: 99.2635 Evaluate side-chains 324 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 284 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain R residue 300 TYR Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 141 GLU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 0.0870 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 220 GLN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.156128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127342 restraints weight = 15408.961| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.72 r_work: 0.3508 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9154 Z= 0.231 Angle : 0.626 13.375 12390 Z= 0.326 Chirality : 0.043 0.246 1414 Planarity : 0.004 0.058 1554 Dihedral : 4.692 28.847 1227 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.96 % Allowed : 26.11 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1125 helix: 1.87 (0.26), residues: 401 sheet: -0.05 (0.30), residues: 284 loop : -0.38 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 251 HIS 0.004 0.001 HIS R 310 PHE 0.025 0.002 PHE A 336 TYR 0.011 0.001 TYR R 300 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7469 (m-10) REVERT: R 73 TYR cc_start: 0.7383 (m-10) cc_final: 0.7049 (m-10) REVERT: R 86 PHE cc_start: 0.7536 (m-80) cc_final: 0.6897 (m-80) REVERT: R 118 TYR cc_start: 0.7045 (m-80) cc_final: 0.6543 (m-80) REVERT: R 121 MET cc_start: 0.7480 (mmt) cc_final: 0.6734 (mmt) REVERT: R 149 MET cc_start: 0.7358 (tpt) cc_final: 0.6920 (tpt) REVERT: R 152 THR cc_start: 0.6825 (m) cc_final: 0.6624 (t) REVERT: R 159 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6909 (mp) REVERT: R 207 LEU cc_start: 0.5460 (OUTLIER) cc_final: 0.5037 (tt) REVERT: R 211 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: R 220 LYS cc_start: 0.8215 (mmmm) cc_final: 0.7870 (mmmm) REVERT: R 249 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6469 (mm) REVERT: R 306 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7031 (pttm) REVERT: A 197 LYS cc_start: 0.7472 (mtmt) cc_final: 0.7064 (mtmt) REVERT: A 270 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7796 (mmtm) REVERT: A 277 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7045 (tttt) REVERT: A 321 THR cc_start: 0.8338 (m) cc_final: 0.8025 (t) REVERT: A 332 VAL cc_start: 0.8047 (m) cc_final: 0.7787 (p) REVERT: A 349 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7627 (ttmt) REVERT: B 29 THR cc_start: 0.7957 (t) cc_final: 0.7532 (p) REVERT: B 52 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7245 (mmm-85) REVERT: B 175 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6936 (mm-40) REVERT: B 183 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7362 (t-170) REVERT: S 38 ARG cc_start: 0.7587 (ptt180) cc_final: 0.7301 (ptt180) REVERT: S 90 ASP cc_start: 0.7251 (m-30) cc_final: 0.6993 (m-30) REVERT: S 167 GLN cc_start: 0.7907 (tp40) cc_final: 0.7558 (tp-100) REVERT: S 215 TYR cc_start: 0.7960 (m-10) cc_final: 0.7668 (m-10) outliers start: 49 outliers final: 34 residues processed: 315 average time/residue: 0.2353 time to fit residues: 99.8265 Evaluate side-chains 338 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 295 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain R residue 300 TYR Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 141 GLU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** 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 = 0.4056 r_free = 0.4056 target = 0.156133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127656 restraints weight = 15218.878| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.70 r_work: 0.3509 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9154 Z= 0.229 Angle : 0.641 14.554 12390 Z= 0.332 Chirality : 0.044 0.233 1414 Planarity : 0.004 0.057 1554 Dihedral : 4.717 28.899 1227 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.76 % Allowed : 26.72 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1125 helix: 1.81 (0.26), residues: 401 sheet: -0.02 (0.30), residues: 284 loop : -0.40 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 251 HIS 0.003 0.001 HIS R 310 PHE 0.027 0.002 PHE A 336 TYR 0.018 0.001 TYR R 300 ARG 0.008 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7465 (m-10) REVERT: R 73 TYR cc_start: 0.7377 (m-10) cc_final: 0.7023 (m-80) REVERT: R 86 PHE cc_start: 0.7554 (m-80) cc_final: 0.6918 (m-80) REVERT: R 118 TYR cc_start: 0.7077 (m-80) cc_final: 0.6557 (m-80) REVERT: R 121 MET cc_start: 0.7482 (mmt) cc_final: 0.6736 (mmt) REVERT: R 149 MET cc_start: 0.7366 (tpt) cc_final: 0.6915 (tpt) REVERT: R 152 THR cc_start: 0.6824 (m) cc_final: 0.6620 (t) REVERT: R 159 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6937 (mp) REVERT: R 207 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.5069 (tt) REVERT: R 211 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6457 (m-80) REVERT: R 220 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7909 (mmmm) REVERT: R 249 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6459 (mm) REVERT: R 306 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7032 (pttm) REVERT: A 197 LYS cc_start: 0.7483 (mtmt) cc_final: 0.7081 (mtmt) REVERT: A 270 LYS cc_start: 0.8188 (mmtm) cc_final: 0.7832 (mmtm) REVERT: A 277 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7049 (tttt) REVERT: A 321 THR cc_start: 0.8365 (m) cc_final: 0.8057 (t) REVERT: A 332 VAL cc_start: 0.8053 (m) cc_final: 0.7756 (p) REVERT: A 349 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7580 (ttmt) REVERT: B 29 THR cc_start: 0.7971 (t) cc_final: 0.7554 (p) REVERT: B 49 ARG cc_start: 0.8239 (mmt-90) cc_final: 0.7975 (mpt180) REVERT: B 52 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7254 (mmm-85) REVERT: B 130 GLU cc_start: 0.7946 (mp0) cc_final: 0.7475 (mp0) REVERT: B 175 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6918 (mm-40) REVERT: B 183 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7371 (t-170) REVERT: S 38 ARG cc_start: 0.7576 (ptt180) cc_final: 0.7306 (ptt180) REVERT: S 90 ASP cc_start: 0.7243 (m-30) cc_final: 0.6989 (m-30) REVERT: S 215 TYR cc_start: 0.7956 (m-10) cc_final: 0.7666 (m-10) REVERT: S 227 PHE cc_start: 0.7216 (m-80) cc_final: 0.6856 (m-80) outliers start: 47 outliers final: 34 residues processed: 309 average time/residue: 0.2463 time to fit residues: 101.1282 Evaluate side-chains 325 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 282 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 141 GLU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.155949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127256 restraints weight = 15296.585| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.70 r_work: 0.3507 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9154 Z= 0.244 Angle : 0.653 14.834 12390 Z= 0.338 Chirality : 0.044 0.230 1414 Planarity : 0.004 0.056 1554 Dihedral : 4.745 28.810 1227 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.55 % Allowed : 26.42 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1125 helix: 1.65 (0.26), residues: 407 sheet: -0.05 (0.30), residues: 284 loop : -0.39 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP R 251 HIS 0.004 0.001 HIS R 310 PHE 0.029 0.002 PHE A 336 TYR 0.023 0.002 TYR R 300 ARG 0.007 0.001 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 296 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7469 (m-10) REVERT: R 86 PHE cc_start: 0.7555 (m-80) cc_final: 0.6948 (m-80) REVERT: R 118 TYR cc_start: 0.7104 (m-80) cc_final: 0.6570 (m-80) REVERT: R 121 MET cc_start: 0.7461 (mmt) cc_final: 0.6728 (mmt) REVERT: R 149 MET cc_start: 0.7357 (tpt) cc_final: 0.6868 (tpt) REVERT: R 152 THR cc_start: 0.6824 (m) cc_final: 0.6611 (t) REVERT: R 159 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6927 (mp) REVERT: R 207 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5123 (tt) REVERT: R 211 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: R 249 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6461 (mm) REVERT: R 254 PHE cc_start: 0.7667 (t80) cc_final: 0.7447 (t80) REVERT: R 295 VAL cc_start: 0.7964 (t) cc_final: 0.7657 (p) REVERT: R 306 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7042 (pttm) REVERT: A 197 LYS cc_start: 0.7487 (mtmt) cc_final: 0.7094 (mtmt) REVERT: A 270 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7878 (mmtm) REVERT: A 277 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7119 (tttt) REVERT: A 321 THR cc_start: 0.8369 (m) cc_final: 0.8069 (t) REVERT: A 332 VAL cc_start: 0.8060 (m) cc_final: 0.7760 (p) REVERT: A 349 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7589 (ttmt) REVERT: B 29 THR cc_start: 0.7972 (t) cc_final: 0.7539 (p) REVERT: B 52 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7284 (mmm-85) REVERT: B 75 GLN cc_start: 0.8203 (mm110) cc_final: 0.7879 (mm110) REVERT: B 129 ARG cc_start: 0.7761 (mmm160) cc_final: 0.7509 (mtp85) REVERT: B 130 GLU cc_start: 0.7991 (mp0) cc_final: 0.7480 (mp0) REVERT: B 175 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6928 (mm-40) REVERT: B 183 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7445 (t-170) REVERT: S 38 ARG cc_start: 0.7621 (ptt180) cc_final: 0.7369 (ptt180) REVERT: S 90 ASP cc_start: 0.7233 (m-30) cc_final: 0.6996 (m-30) REVERT: S 215 TYR cc_start: 0.7955 (m-10) cc_final: 0.7621 (m-10) REVERT: S 227 PHE cc_start: 0.7245 (m-80) cc_final: 0.6899 (m-80) outliers start: 45 outliers final: 35 residues processed: 316 average time/residue: 0.2300 time to fit residues: 97.7879 Evaluate side-chains 337 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 293 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 141 GLU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** 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 = 0.4052 r_free = 0.4052 target = 0.155504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126706 restraints weight = 15286.329| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.71 r_work: 0.3510 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9154 Z= 0.230 Angle : 0.646 15.037 12390 Z= 0.336 Chirality : 0.044 0.226 1414 Planarity : 0.004 0.055 1554 Dihedral : 4.716 28.884 1227 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.76 % Allowed : 26.62 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1125 helix: 1.67 (0.26), residues: 407 sheet: -0.03 (0.30), residues: 284 loop : -0.40 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP R 251 HIS 0.003 0.001 HIS R 310 PHE 0.028 0.002 PHE A 336 TYR 0.021 0.002 TYR R 300 ARG 0.004 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4560.74 seconds wall clock time: 82 minutes 5.31 seconds (4925.31 seconds total)