Starting phenix.real_space_refine on Wed Mar 12 16:20:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn3_39413/03_2025/8yn3_39413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn3_39413/03_2025/8yn3_39413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yn3_39413/03_2025/8yn3_39413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn3_39413/03_2025/8yn3_39413.map" model { file = "/net/cci-nas-00/data/ceres_data/8yn3_39413/03_2025/8yn3_39413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn3_39413/03_2025/8yn3_39413.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 52 5.16 5 C 5195 2.51 5 N 1429 2.21 5 O 1525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8201 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1954 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2180 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'CLR': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.14, per 1000 atoms: 0.63 Number of scatterers: 8201 At special positions: 0 Unit cell: (101.65, 97.37, 119.84, 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 52 16.00 O 1525 8.00 N 1429 7.00 C 5195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 91 " - pdb=" SG CYS R 174 " 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: 2.24 Conformation dependent library (CDL) restraints added in 991.6 milliseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1962 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 43.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 9 through 40 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.586A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.907A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.054A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.957A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.528A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 15 through 46 removed outlier: 3.636A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' Processing helix chain 'R' and resid 54 through 71 Processing helix chain 'R' and resid 71 through 82 Processing helix chain 'R' and resid 87 through 122 removed outlier: 3.514A pdb=" N ILE R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 130 Processing helix chain 'R' and resid 131 through 156 removed outlier: 3.925A pdb=" N LEU R 152 " --> pdb=" O THR R 148 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 191 Processing helix chain 'R' and resid 191 through 218 Processing helix chain 'R' and resid 230 through 261 Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 266 through 288 removed outlier: 3.504A pdb=" N GLY R 277 " --> pdb=" O VAL R 273 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER R 281 " --> pdb=" O GLY R 277 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 292 through 302 removed outlier: 3.622A pdb=" N GLN R 300 " --> pdb=" O ARG R 296 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN R 301 " --> pdb=" O THR R 297 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.360A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.673A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.516A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.076A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.338A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.329A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.037A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.679A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 5.690A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1284 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: 2.47 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2697 1.34 - 1.46: 1913 1.46 - 1.58: 3681 1.58 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 8362 Sorted by residual: bond pdb=" C5 CLR R 702 " pdb=" C6 CLR R 702 " ideal model delta sigma weight residual 1.332 1.299 0.033 2.00e-02 2.50e+03 2.80e+00 bond pdb=" C10 CLR R 702 " pdb=" C9 CLR R 702 " ideal model delta sigma weight residual 1.551 1.521 0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" CA HSM R 701 " pdb=" CB HSM R 701 " ideal model delta sigma weight residual 1.533 1.506 0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C10 CLR R 702 " pdb=" C5 CLR R 702 " ideal model delta sigma weight residual 1.519 1.495 0.024 2.00e-02 2.50e+03 1.48e+00 bond pdb=" CE1 HSM R 701 " pdb=" NE2 HSM R 701 " ideal model delta sigma weight residual 1.354 1.330 0.024 2.00e-02 2.50e+03 1.43e+00 ... (remaining 8357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 11153 1.42 - 2.84: 156 2.84 - 4.26: 24 4.26 - 5.68: 10 5.68 - 7.10: 1 Bond angle restraints: 11344 Sorted by residual: angle pdb=" C13 CLR R 702 " pdb=" C17 CLR R 702 " pdb=" C20 CLR R 702 " ideal model delta sigma weight residual 119.60 112.50 7.10 3.00e+00 1.11e-01 5.60e+00 angle pdb=" N GLY A 225 " pdb=" CA GLY A 225 " pdb=" C GLY A 225 " ideal model delta sigma weight residual 113.18 117.91 -4.73 2.37e+00 1.78e-01 3.99e+00 angle pdb=" C23 CLR R 702 " pdb=" C24 CLR R 702 " pdb=" C25 CLR R 702 " ideal model delta sigma weight residual 115.14 109.82 5.32 3.00e+00 1.11e-01 3.14e+00 angle pdb=" CA TRP A 234 " pdb=" CB TRP A 234 " pdb=" CG TRP A 234 " ideal model delta sigma weight residual 113.60 116.94 -3.34 1.90e+00 2.77e-01 3.10e+00 angle pdb=" C13 CLR R 702 " pdb=" C14 CLR R 702 " pdb=" C8 CLR R 702 " ideal model delta sigma weight residual 115.50 110.41 5.09 3.00e+00 1.11e-01 2.88e+00 ... (remaining 11339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.98: 4702 13.98 - 27.96: 254 27.96 - 41.94: 59 41.94 - 55.92: 16 55.92 - 69.90: 4 Dihedral angle restraints: 5035 sinusoidal: 2000 harmonic: 3035 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -160.45 -19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1228 0.092 - 0.184: 68 0.184 - 0.276: 1 0.276 - 0.368: 1 0.368 - 0.460: 1 Chirality restraints: 1299 Sorted by residual: chirality pdb=" C14 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C15 CLR R 702 " pdb=" C8 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" C10 CLR R 702 " pdb=" C1 CLR R 702 " pdb=" C5 CLR R 702 " pdb=" C9 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.85 -2.49 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" C17 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C16 CLR R 702 " pdb=" C20 CLR R 702 " both_signs ideal model delta sigma weight residual False 2.55 2.82 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1296 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 236 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 193 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO R 194 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO R 194 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 194 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO B 194 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.016 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1710 2.78 - 3.31: 7787 3.31 - 3.84: 13978 3.84 - 4.37: 17402 4.37 - 4.90: 29257 Nonbonded interactions: 70134 Sorted by model distance: nonbonded pdb=" OG SER R 75 " pdb=" OH TYR R 94 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.254 3.040 nonbonded pdb=" O ASN A 50 " pdb=" NZ LYS A 293 " model vdw 2.262 3.120 nonbonded pdb=" O THR R 32 " pdb=" ND2 ASN R 36 " model vdw 2.269 3.120 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.297 3.120 ... (remaining 70129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.680 Find NCS groups from input model: 0.070 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:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 0.003 0.036 8362 Z= 0.203 Angle : 0.464 7.096 11344 Z= 0.239 Chirality : 0.046 0.460 1299 Planarity : 0.003 0.049 1440 Dihedral : 9.760 69.903 3064 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.79 % Allowed : 4.07 % Favored : 95.14 % 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: 1.26 (0.26), residues: 1028 helix: 1.74 (0.26), residues: 387 sheet: 0.62 (0.32), residues: 232 loop : 0.21 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.001 PHE B 151 TYR 0.008 0.001 TYR A 339 ARG 0.003 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 1.001 Fit side-chains REVERT: A 21 GLU cc_start: 0.7494 (tp30) cc_final: 0.7163 (tp30) REVERT: A 24 LYS cc_start: 0.7736 (mptt) cc_final: 0.7437 (ttmt) REVERT: A 390 GLN cc_start: 0.8791 (tt0) cc_final: 0.8493 (tt0) REVERT: B 19 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7665 (ttp-110) REVERT: B 32 GLN cc_start: 0.8249 (mt0) cc_final: 0.8043 (mt0) REVERT: B 59 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: B 137 ARG cc_start: 0.7891 (mmt-90) cc_final: 0.7567 (tpt170) REVERT: B 259 GLN cc_start: 0.9014 (pt0) cc_final: 0.8718 (pt0) REVERT: N 105 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7442 (mmm-85) REVERT: R 111 MET cc_start: 0.9095 (mmm) cc_final: 0.8841 (mmp) REVERT: R 121 MET cc_start: 0.9183 (mmm) cc_final: 0.8809 (mmm) REVERT: R 198 MET cc_start: 0.9050 (mtp) cc_final: 0.8576 (mtm) REVERT: R 260 ARG cc_start: 0.8026 (mmt90) cc_final: 0.7816 (mmt90) REVERT: R 267 GLU cc_start: 0.7792 (tt0) cc_final: 0.7564 (tt0) outliers start: 7 outliers final: 4 residues processed: 170 average time/residue: 1.5903 time to fit residues: 285.1483 Evaluate side-chains 136 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 264 ASN A 279 ASN B 17 GLN B 44 GLN B 91 HIS B 155 ASN B 220 GLN B 259 GLN N 31 ASN N 123 GLN R 92 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104742 restraints weight = 8791.462| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.86 r_work: 0.2982 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8362 Z= 0.243 Angle : 0.539 5.222 11344 Z= 0.300 Chirality : 0.044 0.160 1299 Planarity : 0.004 0.051 1440 Dihedral : 4.884 54.206 1216 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.37 % Allowed : 8.36 % Favored : 89.27 % 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: 1.65 (0.26), residues: 1028 helix: 2.43 (0.26), residues: 397 sheet: 0.61 (0.32), residues: 228 loop : 0.10 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.017 0.002 PHE R 254 TYR 0.015 0.001 TYR A 339 ARG 0.006 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.897 Fit side-chains REVERT: A 24 LYS cc_start: 0.7791 (mptt) cc_final: 0.7308 (ttpm) REVERT: B 23 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8109 (tptm) REVERT: B 32 GLN cc_start: 0.8203 (mt0) cc_final: 0.7992 (mt0) REVERT: B 59 TYR cc_start: 0.9176 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: B 134 ARG cc_start: 0.7846 (ppt170) cc_final: 0.7197 (ptm-80) REVERT: B 137 ARG cc_start: 0.7977 (mmt-90) cc_final: 0.7677 (tpt90) REVERT: B 226 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8451 (mt-10) REVERT: C 48 ASP cc_start: 0.8636 (t0) cc_final: 0.8342 (t0) REVERT: N 19 ARG cc_start: 0.7872 (ttt180) cc_final: 0.7563 (ttt-90) REVERT: N 105 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.7439 (mmm-85) REVERT: R 111 MET cc_start: 0.8939 (mmm) cc_final: 0.8690 (mmp) REVERT: R 121 MET cc_start: 0.9136 (mmm) cc_final: 0.8493 (mmm) REVERT: R 141 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7899 (mp) REVERT: R 198 MET cc_start: 0.8828 (mtp) cc_final: 0.8360 (mtm) REVERT: R 260 ARG cc_start: 0.8324 (mmt90) cc_final: 0.8054 (mmt90) outliers start: 21 outliers final: 8 residues processed: 145 average time/residue: 1.3472 time to fit residues: 206.6250 Evaluate side-chains 138 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 17 GLN B 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.137921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.101457 restraints weight = 8880.804| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.01 r_work: 0.2941 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8362 Z= 0.333 Angle : 0.572 5.240 11344 Z= 0.316 Chirality : 0.045 0.163 1299 Planarity : 0.004 0.053 1440 Dihedral : 4.999 55.622 1211 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.16 % Allowed : 8.25 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1028 helix: 2.47 (0.26), residues: 391 sheet: 0.37 (0.32), residues: 221 loop : 0.09 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.002 PHE R 254 TYR 0.014 0.002 TYR A 339 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.822 Fit side-chains REVERT: B 19 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7448 (ttp-110) REVERT: B 23 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8091 (tptm) REVERT: B 59 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.8529 (m-80) REVERT: B 134 ARG cc_start: 0.7899 (ppt170) cc_final: 0.7266 (ptm-80) REVERT: B 137 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.7675 (tpt90) REVERT: B 226 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8600 (mt-10) REVERT: N 19 ARG cc_start: 0.7877 (ttt180) cc_final: 0.7658 (ttt-90) REVERT: N 85 SER cc_start: 0.8792 (t) cc_final: 0.8350 (m) REVERT: N 105 ARG cc_start: 0.7719 (mmm-85) cc_final: 0.7330 (mmm-85) REVERT: R 53 THR cc_start: 0.7577 (p) cc_final: 0.7111 (m) REVERT: R 111 MET cc_start: 0.8905 (mmm) cc_final: 0.8656 (mmp) REVERT: R 121 MET cc_start: 0.9133 (mmm) cc_final: 0.8780 (mmm) REVERT: R 198 MET cc_start: 0.8850 (mtp) cc_final: 0.8342 (mtp) outliers start: 28 outliers final: 17 residues processed: 141 average time/residue: 1.3061 time to fit residues: 194.8897 Evaluate side-chains 144 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 0.0170 chunk 55 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 17 GLN B 44 GLN B 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.105536 restraints weight = 8803.323| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.06 r_work: 0.3010 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8362 Z= 0.159 Angle : 0.473 6.962 11344 Z= 0.261 Chirality : 0.041 0.143 1299 Planarity : 0.003 0.050 1440 Dihedral : 4.621 54.373 1211 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.71 % Allowed : 9.94 % Favored : 87.34 % 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: 1.73 (0.26), residues: 1028 helix: 2.84 (0.26), residues: 382 sheet: 0.30 (0.32), residues: 223 loop : 0.09 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.002 0.001 HIS B 62 PHE 0.014 0.001 PHE A 376 TYR 0.011 0.001 TYR A 339 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.928 Fit side-chains REVERT: B 19 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7442 (ttp-110) REVERT: B 23 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7909 (tptm) REVERT: B 59 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: B 134 ARG cc_start: 0.7806 (ppt170) cc_final: 0.7115 (ptm-80) REVERT: B 137 ARG cc_start: 0.7896 (mmt-90) cc_final: 0.7557 (tpt170) REVERT: B 197 ARG cc_start: 0.8310 (mtp180) cc_final: 0.8092 (mtp180) REVERT: B 226 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8555 (mt-10) REVERT: N 19 ARG cc_start: 0.7798 (ttt180) cc_final: 0.7569 (ttt-90) REVERT: N 85 SER cc_start: 0.8739 (t) cc_final: 0.8324 (m) REVERT: N 105 ARG cc_start: 0.7667 (mmm-85) cc_final: 0.7305 (mmm-85) REVERT: R 111 MET cc_start: 0.8840 (mmm) cc_final: 0.8628 (mmp) REVERT: R 121 MET cc_start: 0.9146 (mmm) cc_final: 0.8564 (mmm) REVERT: R 198 MET cc_start: 0.8825 (mtp) cc_final: 0.8364 (mtm) outliers start: 24 outliers final: 10 residues processed: 145 average time/residue: 1.2197 time to fit residues: 187.8088 Evaluate side-chains 133 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 17 GLN B 44 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.142676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.106777 restraints weight = 8711.961| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.07 r_work: 0.3028 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8362 Z= 0.144 Angle : 0.455 5.547 11344 Z= 0.251 Chirality : 0.041 0.138 1299 Planarity : 0.003 0.050 1440 Dihedral : 4.500 54.003 1211 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.49 % Allowed : 10.85 % Favored : 86.67 % 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: 1.83 (0.26), residues: 1028 helix: 3.02 (0.26), residues: 386 sheet: 0.32 (0.32), residues: 220 loop : 0.03 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.002 0.001 HIS R 218 PHE 0.014 0.001 PHE A 376 TYR 0.010 0.001 TYR R 250 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.868 Fit side-chains REVERT: B 19 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7416 (ttp-110) REVERT: B 23 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8098 (tptm) REVERT: B 59 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.8533 (m-80) REVERT: B 134 ARG cc_start: 0.7795 (ppt170) cc_final: 0.7091 (ptm-80) REVERT: B 137 ARG cc_start: 0.7929 (mmt-90) cc_final: 0.7612 (tpt170) REVERT: B 186 ASP cc_start: 0.8417 (m-30) cc_final: 0.8174 (m-30) REVERT: B 197 ARG cc_start: 0.8307 (mtp180) cc_final: 0.8074 (mtp180) REVERT: B 226 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8547 (mt-10) REVERT: B 234 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: C 32 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7686 (ttpt) REVERT: N 3 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: N 85 SER cc_start: 0.8730 (t) cc_final: 0.8342 (m) REVERT: R 121 MET cc_start: 0.9148 (mmm) cc_final: 0.8617 (mmm) REVERT: R 198 MET cc_start: 0.8825 (mtp) cc_final: 0.8379 (mtm) outliers start: 22 outliers final: 10 residues processed: 142 average time/residue: 1.2313 time to fit residues: 185.5914 Evaluate side-chains 136 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 17 GLN B 44 GLN N 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.140199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103635 restraints weight = 8830.817| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.03 r_work: 0.2992 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8362 Z= 0.221 Angle : 0.501 5.132 11344 Z= 0.277 Chirality : 0.042 0.146 1299 Planarity : 0.003 0.050 1440 Dihedral : 4.662 54.298 1211 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.71 % Allowed : 11.53 % Favored : 85.76 % 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: 1.75 (0.26), residues: 1028 helix: 2.93 (0.26), residues: 386 sheet: 0.41 (0.32), residues: 216 loop : -0.06 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.003 0.001 HIS B 62 PHE 0.017 0.002 PHE R 254 TYR 0.013 0.002 TYR A 311 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7784 (mptt) cc_final: 0.7492 (mmtm) REVERT: B 19 ARG cc_start: 0.8315 (ttp80) cc_final: 0.7455 (ttp-110) REVERT: B 23 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8003 (tptm) REVERT: B 59 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: B 134 ARG cc_start: 0.7800 (ppt170) cc_final: 0.7104 (ptm-80) REVERT: B 137 ARG cc_start: 0.7967 (mmt-90) cc_final: 0.7602 (tpt170) REVERT: B 197 ARG cc_start: 0.8366 (mtp180) cc_final: 0.8102 (mtp180) REVERT: B 226 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8604 (mt-10) REVERT: B 234 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: C 32 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7478 (ttmm) REVERT: N 3 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: N 85 SER cc_start: 0.8778 (t) cc_final: 0.8411 (m) REVERT: R 121 MET cc_start: 0.9141 (mmm) cc_final: 0.8642 (mmm) REVERT: R 198 MET cc_start: 0.8840 (mtp) cc_final: 0.8406 (mtm) outliers start: 24 outliers final: 12 residues processed: 136 average time/residue: 1.2531 time to fit residues: 180.7002 Evaluate side-chains 137 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.0000 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 17 GLN B 44 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.105498 restraints weight = 8788.723| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.05 r_work: 0.3009 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8362 Z= 0.169 Angle : 0.468 5.190 11344 Z= 0.259 Chirality : 0.041 0.140 1299 Planarity : 0.003 0.049 1440 Dihedral : 4.552 54.460 1211 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.60 % Allowed : 11.53 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.26), residues: 1028 helix: 3.01 (0.26), residues: 386 sheet: 0.39 (0.32), residues: 216 loop : -0.08 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.002 0.001 HIS B 62 PHE 0.016 0.001 PHE R 254 TYR 0.015 0.001 TYR A 311 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.842 Fit side-chains REVERT: A 24 LYS cc_start: 0.7770 (mptt) cc_final: 0.7458 (mmtm) REVERT: B 23 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7980 (tptm) REVERT: B 59 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8558 (m-80) REVERT: B 134 ARG cc_start: 0.7807 (ppt170) cc_final: 0.7105 (ptm-80) REVERT: B 137 ARG cc_start: 0.7954 (mmt-90) cc_final: 0.7594 (tpt170) REVERT: B 186 ASP cc_start: 0.8466 (m-30) cc_final: 0.8261 (m-30) REVERT: B 226 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8617 (mt-10) REVERT: B 234 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: N 85 SER cc_start: 0.8760 (t) cc_final: 0.8393 (m) REVERT: R 121 MET cc_start: 0.9140 (mmm) cc_final: 0.8666 (mmm) REVERT: R 198 MET cc_start: 0.8834 (mtp) cc_final: 0.8388 (mtm) outliers start: 23 outliers final: 14 residues processed: 138 average time/residue: 1.2653 time to fit residues: 185.5060 Evaluate side-chains 140 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.4980 chunk 49 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 17 GLN B 32 GLN B 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.105683 restraints weight = 8870.317| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.00 r_work: 0.3016 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8362 Z= 0.160 Angle : 0.463 5.065 11344 Z= 0.256 Chirality : 0.041 0.139 1299 Planarity : 0.003 0.049 1440 Dihedral : 4.510 54.914 1211 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.82 % Allowed : 11.64 % Favored : 85.54 % 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: 1.81 (0.26), residues: 1028 helix: 3.05 (0.26), residues: 386 sheet: 0.38 (0.32), residues: 216 loop : -0.07 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.015 0.001 PHE R 254 TYR 0.016 0.001 TYR A 311 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.868 Fit side-chains REVERT: A 24 LYS cc_start: 0.7777 (mptt) cc_final: 0.7457 (mmtm) REVERT: B 23 LYS cc_start: 0.8349 (ttmm) cc_final: 0.7979 (tptm) REVERT: B 59 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: B 134 ARG cc_start: 0.7838 (ppt170) cc_final: 0.7133 (ptm-80) REVERT: B 137 ARG cc_start: 0.7943 (mmt-90) cc_final: 0.7595 (tpt170) REVERT: B 186 ASP cc_start: 0.8435 (m-30) cc_final: 0.8218 (m-30) REVERT: B 226 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8652 (mt-10) REVERT: B 234 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: B 303 ASP cc_start: 0.7769 (m-30) cc_final: 0.7523 (m-30) REVERT: C 32 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7439 (ttmm) REVERT: N 85 SER cc_start: 0.8756 (t) cc_final: 0.8408 (m) REVERT: R 121 MET cc_start: 0.9146 (mmm) cc_final: 0.8782 (mmm) REVERT: R 198 MET cc_start: 0.8819 (mtp) cc_final: 0.8377 (mtm) outliers start: 25 outliers final: 16 residues processed: 137 average time/residue: 1.2469 time to fit residues: 181.2497 Evaluate side-chains 142 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 85 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 44 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.104648 restraints weight = 8937.964| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.04 r_work: 0.2998 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8362 Z= 0.184 Angle : 0.477 5.092 11344 Z= 0.264 Chirality : 0.041 0.141 1299 Planarity : 0.003 0.050 1440 Dihedral : 4.568 55.204 1211 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.49 % Allowed : 12.09 % Favored : 85.42 % 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: 1.78 (0.26), residues: 1028 helix: 3.01 (0.26), residues: 386 sheet: 0.38 (0.32), residues: 216 loop : -0.09 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.002 0.001 HIS B 62 PHE 0.015 0.002 PHE R 254 TYR 0.016 0.001 TYR A 311 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.933 Fit side-chains REVERT: A 24 LYS cc_start: 0.7786 (mptt) cc_final: 0.7495 (mmtm) REVERT: A 331 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: B 23 LYS cc_start: 0.8359 (ttmm) cc_final: 0.7983 (tptm) REVERT: B 59 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: B 137 ARG cc_start: 0.7937 (mmt-90) cc_final: 0.7622 (tpt170) REVERT: B 226 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8624 (mt-10) REVERT: B 234 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: B 259 GLN cc_start: 0.8971 (pt0) cc_final: 0.8616 (pt0) REVERT: B 303 ASP cc_start: 0.7773 (m-30) cc_final: 0.7537 (m-30) REVERT: C 32 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7462 (ttmm) REVERT: N 85 SER cc_start: 0.8768 (t) cc_final: 0.8430 (m) REVERT: R 121 MET cc_start: 0.9143 (mmm) cc_final: 0.8760 (mmm) REVERT: R 198 MET cc_start: 0.8828 (mtp) cc_final: 0.8394 (mtm) outliers start: 22 outliers final: 14 residues processed: 140 average time/residue: 1.2875 time to fit residues: 192.1268 Evaluate side-chains 142 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 17 GLN B 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.105909 restraints weight = 8748.458| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.02 r_work: 0.3011 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8362 Z= 0.167 Angle : 0.469 5.107 11344 Z= 0.259 Chirality : 0.041 0.139 1299 Planarity : 0.003 0.050 1440 Dihedral : 4.525 55.494 1211 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.15 % Allowed : 12.66 % Favored : 85.20 % 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: 1.80 (0.26), residues: 1028 helix: 3.04 (0.26), residues: 386 sheet: 0.39 (0.33), residues: 216 loop : -0.09 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS R 218 PHE 0.015 0.001 PHE R 254 TYR 0.016 0.001 TYR A 311 ARG 0.010 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.216 Fit side-chains REVERT: A 24 LYS cc_start: 0.7738 (mptt) cc_final: 0.7441 (mmtm) REVERT: A 331 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: B 23 LYS cc_start: 0.8375 (ttmm) cc_final: 0.7989 (tptm) REVERT: B 59 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: B 137 ARG cc_start: 0.7985 (mmt-90) cc_final: 0.7620 (tpt170) REVERT: B 186 ASP cc_start: 0.8386 (m-30) cc_final: 0.8165 (m-30) REVERT: B 226 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8623 (mt-10) REVERT: B 234 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: B 259 GLN cc_start: 0.8980 (pt0) cc_final: 0.8687 (pt0) REVERT: B 303 ASP cc_start: 0.7792 (m-30) cc_final: 0.7556 (m-30) REVERT: C 32 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7475 (ttmm) REVERT: N 85 SER cc_start: 0.8766 (t) cc_final: 0.8435 (m) REVERT: R 121 MET cc_start: 0.9149 (mmm) cc_final: 0.8784 (mmm) REVERT: R 198 MET cc_start: 0.8824 (mtp) cc_final: 0.8378 (mtm) outliers start: 19 outliers final: 14 residues processed: 135 average time/residue: 1.4391 time to fit residues: 206.5143 Evaluate side-chains 142 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 0.0470 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105578 restraints weight = 8920.718| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.05 r_work: 0.3020 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8362 Z= 0.158 Angle : 0.462 5.099 11344 Z= 0.256 Chirality : 0.041 0.138 1299 Planarity : 0.003 0.050 1440 Dihedral : 4.505 55.651 1211 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.26 % Allowed : 12.54 % Favored : 85.20 % 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: 1.83 (0.26), residues: 1028 helix: 3.07 (0.26), residues: 386 sheet: 0.41 (0.33), residues: 216 loop : -0.08 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.014 0.001 PHE R 254 TYR 0.016 0.001 TYR A 311 ARG 0.010 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7518.48 seconds wall clock time: 131 minutes 10.51 seconds (7870.51 seconds total)