Starting phenix.real_space_refine on Wed Sep 17 10:26:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn3_39413/09_2025/8yn3_39413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn3_39413/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yn3_39413/09_2025/8yn3_39413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn3_39413/09_2025/8yn3_39413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yn3_39413/09_2025/8yn3_39413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn3_39413/09_2025/8yn3_39413.map" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'GLN:plan1': 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: 1.97, per 1000 atoms: 0.24 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: 0.50 Conformation dependent library (CDL) restraints added in 405.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.27 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: 1.26 Time building geometry restraints manager: 0.74 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: 0.490 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- 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 8365 Z= 0.135 Angle : 0.465 7.096 11350 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 385 TYR 0.008 0.001 TYR A 339 PHE 0.013 0.001 PHE B 151 TRP 0.012 0.002 TRP A 234 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8362) covalent geometry : angle 0.46428 (11344) SS BOND : bond 0.00180 ( 3) SS BOND : angle 1.04897 ( 6) hydrogen bonds : bond 0.22556 ( 456) hydrogen bonds : angle 7.42316 ( 1284) *********************** 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 : 0.321 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: 0.6436 time to fit residues: 115.0785 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 : 0.224 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 155 ASN B 220 GLN B 259 GLN N 31 ASN N 123 GLN R 92 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.101825 restraints weight = 8803.405| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.83 r_work: 0.2925 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8365 Z= 0.242 Angle : 0.601 5.323 11350 Z= 0.333 Chirality : 0.046 0.180 1299 Planarity : 0.005 0.054 1440 Dihedral : 5.110 55.471 1216 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.82 % Allowed : 7.68 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.26), residues: 1028 helix: 2.27 (0.26), residues: 397 sheet: 0.46 (0.32), residues: 221 loop : 0.15 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 385 TYR 0.016 0.002 TYR A 339 PHE 0.021 0.002 PHE R 254 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 8362) covalent geometry : angle 0.60109 (11344) SS BOND : bond 0.00272 ( 3) SS BOND : angle 0.75148 ( 6) hydrogen bonds : bond 0.06368 ( 456) hydrogen bonds : angle 5.42453 ( 1284) *********************** 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 162 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.356 Fit side-chains REVERT: B 23 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8128 (tptm) REVERT: B 32 GLN cc_start: 0.8225 (mt0) cc_final: 0.8019 (mt0) REVERT: B 59 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: B 134 ARG cc_start: 0.7848 (ppt170) cc_final: 0.7197 (ptm-80) REVERT: B 137 ARG cc_start: 0.8005 (mmt-90) cc_final: 0.7650 (tpt90) REVERT: B 226 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8562 (mt-10) REVERT: N 19 ARG cc_start: 0.7953 (ttt180) cc_final: 0.7588 (ttt-90) REVERT: N 105 ARG cc_start: 0.7799 (mmm-85) cc_final: 0.7417 (mmm-85) REVERT: R 111 MET cc_start: 0.8978 (mmm) cc_final: 0.8718 (mmp) REVERT: R 121 MET cc_start: 0.9138 (mmm) cc_final: 0.8747 (mmm) REVERT: R 141 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7923 (mp) REVERT: R 198 MET cc_start: 0.8847 (mtp) cc_final: 0.8392 (mtm) outliers start: 25 outliers final: 11 residues processed: 148 average time/residue: 0.6028 time to fit residues: 94.2916 Evaluate side-chains 137 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR 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 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 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 74 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 91 HIS B 155 ASN B 268 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.104728 restraints weight = 8786.477| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.06 r_work: 0.3005 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8365 Z= 0.127 Angle : 0.485 5.064 11350 Z= 0.271 Chirality : 0.042 0.179 1299 Planarity : 0.004 0.051 1440 Dihedral : 4.703 54.003 1211 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.37 % Allowed : 9.49 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.26), residues: 1028 helix: 2.76 (0.26), residues: 385 sheet: 0.35 (0.32), residues: 221 loop : 0.07 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.012 0.001 TYR A 339 PHE 0.014 0.001 PHE A 376 TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8362) covalent geometry : angle 0.48508 (11344) SS BOND : bond 0.00156 ( 3) SS BOND : angle 0.47882 ( 6) hydrogen bonds : bond 0.04978 ( 456) hydrogen bonds : angle 4.97314 ( 1284) *********************** 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 156 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.265 Fit side-chains REVERT: A 24 LYS cc_start: 0.7732 (mptt) cc_final: 0.7291 (ttmt) REVERT: B 23 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7983 (tptm) REVERT: B 59 TYR cc_start: 0.9177 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: B 134 ARG cc_start: 0.7810 (ppt170) cc_final: 0.7161 (ptm-80) REVERT: B 137 ARG cc_start: 0.7933 (mmt-90) cc_final: 0.7687 (tpt90) REVERT: B 197 ARG cc_start: 0.8379 (mtp180) cc_final: 0.8146 (mtp180) REVERT: B 226 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8521 (mt-10) REVERT: N 19 ARG cc_start: 0.7810 (ttt180) cc_final: 0.7610 (ttt-90) REVERT: N 80 TYR cc_start: 0.8568 (m-80) cc_final: 0.8306 (m-80) REVERT: N 85 SER cc_start: 0.8750 (t) cc_final: 0.8277 (m) REVERT: N 105 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.7326 (mmm-85) REVERT: R 111 MET cc_start: 0.8838 (mmm) cc_final: 0.8608 (mmp) REVERT: R 121 MET cc_start: 0.9135 (mmm) cc_final: 0.8501 (mmm) REVERT: R 198 MET cc_start: 0.8837 (mtp) cc_final: 0.8364 (mtm) outliers start: 21 outliers final: 9 residues processed: 146 average time/residue: 0.6165 time to fit residues: 95.2478 Evaluate side-chains 140 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.140446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104267 restraints weight = 8893.860| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.03 r_work: 0.2994 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8365 Z= 0.140 Angle : 0.491 5.107 11350 Z= 0.272 Chirality : 0.042 0.180 1299 Planarity : 0.004 0.052 1440 Dihedral : 4.664 54.311 1211 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.71 % Allowed : 10.28 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.26), residues: 1028 helix: 2.85 (0.26), residues: 386 sheet: 0.28 (0.32), residues: 223 loop : 0.03 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.011 0.001 TYR R 250 PHE 0.015 0.002 PHE A 376 TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8362) covalent geometry : angle 0.49057 (11344) SS BOND : bond 0.00172 ( 3) SS BOND : angle 0.52551 ( 6) hydrogen bonds : bond 0.04937 ( 456) hydrogen bonds : angle 4.91531 ( 1284) *********************** 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 156 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.300 Fit side-chains REVERT: A 331 ASP cc_start: 0.8114 (t0) cc_final: 0.7877 (t70) REVERT: B 19 ARG cc_start: 0.8384 (ttp80) cc_final: 0.7441 (ttp-110) REVERT: B 23 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7934 (tptm) REVERT: B 59 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: B 134 ARG cc_start: 0.7829 (ppt170) cc_final: 0.7152 (ptm-80) REVERT: B 137 ARG cc_start: 0.7914 (mmt-90) cc_final: 0.7582 (tpt170) REVERT: B 197 ARG cc_start: 0.8379 (mtp180) cc_final: 0.8105 (mtp180) REVERT: B 226 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8586 (mt-10) REVERT: N 19 ARG cc_start: 0.7816 (ttt180) cc_final: 0.7559 (ttt-90) REVERT: N 85 SER cc_start: 0.8736 (t) cc_final: 0.8293 (m) REVERT: N 105 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.7360 (mmm-85) REVERT: R 121 MET cc_start: 0.9153 (mmm) cc_final: 0.8640 (mmm) REVERT: R 198 MET cc_start: 0.8832 (mtp) cc_final: 0.8376 (mtm) outliers start: 24 outliers final: 13 residues processed: 143 average time/residue: 0.6158 time to fit residues: 93.1295 Evaluate side-chains 141 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 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 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.139863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.103570 restraints weight = 8903.736| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.04 r_work: 0.2981 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8365 Z= 0.150 Angle : 0.497 5.096 11350 Z= 0.276 Chirality : 0.042 0.181 1299 Planarity : 0.004 0.050 1440 Dihedral : 4.689 54.872 1211 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.71 % Allowed : 11.19 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.26), residues: 1028 helix: 2.84 (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 ARG 0.007 0.000 ARG B 19 TYR 0.012 0.001 TYR A 339 PHE 0.018 0.002 PHE R 254 TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8362) covalent geometry : angle 0.49746 (11344) SS BOND : bond 0.00212 ( 3) SS BOND : angle 0.51665 ( 6) hydrogen bonds : bond 0.04968 ( 456) hydrogen bonds : angle 4.91908 ( 1284) *********************** 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 152 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.314 Fit side-chains REVERT: A 331 ASP cc_start: 0.8089 (t0) cc_final: 0.7850 (t70) REVERT: B 19 ARG cc_start: 0.8373 (ttp80) cc_final: 0.7446 (ttp-110) REVERT: B 23 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7943 (tptm) REVERT: B 59 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: B 134 ARG cc_start: 0.7825 (ppt170) cc_final: 0.7143 (ptm-80) REVERT: B 137 ARG cc_start: 0.7931 (mmt-90) cc_final: 0.7583 (tpt170) REVERT: B 226 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8607 (mt-10) REVERT: B 234 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: N 19 ARG cc_start: 0.7826 (ttt180) cc_final: 0.7536 (ttt-90) REVERT: N 85 SER cc_start: 0.8745 (t) cc_final: 0.8332 (m) REVERT: N 105 ARG cc_start: 0.7740 (mmm-85) cc_final: 0.7354 (mmm-85) REVERT: R 121 MET cc_start: 0.9154 (mmm) cc_final: 0.8616 (mmm) REVERT: R 198 MET cc_start: 0.8852 (mtp) cc_final: 0.8408 (mtm) outliers start: 24 outliers final: 14 residues processed: 142 average time/residue: 0.6027 time to fit residues: 90.4115 Evaluate side-chains 141 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 46 ARG 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 30 optimal weight: 0.0470 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 overall best weight: 2.7084 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.136960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.100436 restraints weight = 8910.832| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.99 r_work: 0.2944 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8365 Z= 0.251 Angle : 0.589 5.256 11350 Z= 0.323 Chirality : 0.046 0.189 1299 Planarity : 0.004 0.052 1440 Dihedral : 5.035 56.399 1211 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.94 % Allowed : 11.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.26), residues: 1028 helix: 2.59 (0.25), residues: 385 sheet: 0.23 (0.33), residues: 217 loop : -0.11 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 385 TYR 0.015 0.002 TYR R 250 PHE 0.019 0.002 PHE R 254 TRP 0.016 0.002 TRP A 234 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 8362) covalent geometry : angle 0.58880 (11344) SS BOND : bond 0.00395 ( 3) SS BOND : angle 0.78766 ( 6) hydrogen bonds : bond 0.05763 ( 456) hydrogen bonds : angle 5.19600 ( 1284) *********************** 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 155 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.331 Fit side-chains REVERT: A 331 ASP cc_start: 0.8182 (t70) cc_final: 0.7900 (t70) REVERT: B 19 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7498 (ttp-110) REVERT: B 23 LYS cc_start: 0.8332 (ttmm) cc_final: 0.7960 (tptm) REVERT: B 57 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8976 (pttp) REVERT: B 59 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: B 70 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8838 (pp) REVERT: B 134 ARG cc_start: 0.7884 (ppt170) cc_final: 0.7187 (ptm-80) REVERT: B 137 ARG cc_start: 0.8033 (mmt-90) cc_final: 0.7698 (tpt90) REVERT: B 226 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8599 (mt-10) REVERT: N 19 ARG cc_start: 0.7863 (ttt180) cc_final: 0.7630 (ttt-90) REVERT: N 85 SER cc_start: 0.8828 (t) cc_final: 0.8417 (m) REVERT: R 53 THR cc_start: 0.7602 (p) cc_final: 0.7181 (m) REVERT: R 121 MET cc_start: 0.9180 (mmm) cc_final: 0.8878 (mmm) REVERT: R 198 MET cc_start: 0.8848 (mtp) cc_final: 0.8409 (mtm) outliers start: 26 outliers final: 18 residues processed: 142 average time/residue: 0.6085 time to fit residues: 91.5480 Evaluate side-chains 144 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 357 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.105702 restraints weight = 8951.791| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.01 r_work: 0.3022 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8365 Z= 0.110 Angle : 0.460 6.971 11350 Z= 0.254 Chirality : 0.041 0.177 1299 Planarity : 0.003 0.051 1440 Dihedral : 4.523 54.404 1211 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.82 % Allowed : 11.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.26), residues: 1028 helix: 2.91 (0.26), residues: 386 sheet: 0.42 (0.33), residues: 212 loop : -0.13 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.012 0.001 TYR A 339 PHE 0.013 0.001 PHE R 254 TRP 0.018 0.002 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8362) covalent geometry : angle 0.46034 (11344) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.36955 ( 6) hydrogen bonds : bond 0.04345 ( 456) hydrogen bonds : angle 4.74945 ( 1284) *********************** 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 155 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.274 Fit side-chains REVERT: A 331 ASP cc_start: 0.7948 (t70) cc_final: 0.7727 (t70) REVERT: B 23 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8112 (tptm) REVERT: B 59 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8597 (m-80) REVERT: B 134 ARG cc_start: 0.7822 (ppt170) cc_final: 0.7135 (ptm-80) REVERT: B 137 ARG cc_start: 0.7945 (mmt-90) cc_final: 0.7607 (tpt170) REVERT: B 234 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: B 259 GLN cc_start: 0.9108 (pt0) cc_final: 0.8823 (pt0) REVERT: C 32 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7804 (ttpt) REVERT: N 19 ARG cc_start: 0.7785 (ttt180) cc_final: 0.7467 (ttt-90) REVERT: N 85 SER cc_start: 0.8743 (t) cc_final: 0.8350 (m) REVERT: R 121 MET cc_start: 0.9150 (mmm) cc_final: 0.8662 (mmm) REVERT: R 198 MET cc_start: 0.8830 (mtp) cc_final: 0.8393 (mtm) outliers start: 25 outliers final: 12 residues processed: 145 average time/residue: 0.5958 time to fit residues: 91.3751 Evaluate side-chains 139 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 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 79 LEU 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 327 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.139004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102614 restraints weight = 8841.787| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.03 r_work: 0.2968 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8365 Z= 0.182 Angle : 0.526 6.287 11350 Z= 0.289 Chirality : 0.044 0.184 1299 Planarity : 0.004 0.051 1440 Dihedral : 4.767 55.652 1211 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.60 % Allowed : 11.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.26), residues: 1028 helix: 2.79 (0.26), residues: 386 sheet: 0.29 (0.33), residues: 216 loop : -0.13 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.014 0.002 TYR B 124 PHE 0.016 0.002 PHE R 254 TRP 0.015 0.002 TRP A 234 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8362) covalent geometry : angle 0.52555 (11344) SS BOND : bond 0.00256 ( 3) SS BOND : angle 0.58934 ( 6) hydrogen bonds : bond 0.05120 ( 456) hydrogen bonds : angle 4.96251 ( 1284) *********************** 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 147 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.321 Fit side-chains REVERT: A 331 ASP cc_start: 0.8018 (t70) cc_final: 0.7761 (t70) REVERT: B 19 ARG cc_start: 0.8459 (ttp80) cc_final: 0.7654 (ttp-110) REVERT: B 23 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7946 (tptm) REVERT: B 59 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.8536 (m-80) REVERT: B 134 ARG cc_start: 0.7831 (ppt170) cc_final: 0.7150 (ptm-80) REVERT: B 137 ARG cc_start: 0.7987 (mmt-90) cc_final: 0.7579 (tpt170) REVERT: B 234 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8166 (m-80) REVERT: N 19 ARG cc_start: 0.7874 (ttt180) cc_final: 0.7646 (ttt-90) REVERT: N 85 SER cc_start: 0.8810 (t) cc_final: 0.8432 (m) REVERT: R 121 MET cc_start: 0.9156 (mmm) cc_final: 0.8599 (mmm) REVERT: R 198 MET cc_start: 0.8846 (mtp) cc_final: 0.8418 (mtm) outliers start: 23 outliers final: 14 residues processed: 136 average time/residue: 0.6123 time to fit residues: 88.1758 Evaluate side-chains 138 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.139668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.103828 restraints weight = 8849.178| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.91 r_work: 0.2987 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8365 Z= 0.150 Angle : 0.501 6.296 11350 Z= 0.277 Chirality : 0.042 0.183 1299 Planarity : 0.004 0.051 1440 Dihedral : 4.706 55.567 1211 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.03 % Allowed : 12.66 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.26), residues: 1028 helix: 2.82 (0.26), residues: 386 sheet: 0.23 (0.32), residues: 218 loop : -0.14 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.012 0.001 TYR R 250 PHE 0.015 0.002 PHE R 254 TRP 0.016 0.002 TRP A 234 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8362) covalent geometry : angle 0.50057 (11344) SS BOND : bond 0.00219 ( 3) SS BOND : angle 0.48569 ( 6) hydrogen bonds : bond 0.04843 ( 456) hydrogen bonds : angle 4.88544 ( 1284) *********************** 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 140 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.344 Fit side-chains REVERT: A 331 ASP cc_start: 0.8009 (t70) cc_final: 0.7748 (t70) REVERT: B 23 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8008 (tptm) REVERT: B 59 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.8565 (m-80) REVERT: B 134 ARG cc_start: 0.7820 (ppt170) cc_final: 0.7134 (ptm-80) REVERT: B 137 ARG cc_start: 0.7997 (mmt-90) cc_final: 0.7613 (tpt170) REVERT: B 234 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: N 19 ARG cc_start: 0.7872 (ttt180) cc_final: 0.7636 (ttt-90) REVERT: N 85 SER cc_start: 0.8818 (t) cc_final: 0.8457 (m) REVERT: R 121 MET cc_start: 0.9142 (mmm) cc_final: 0.8612 (mmm) REVERT: R 198 MET cc_start: 0.8840 (mtp) cc_final: 0.8412 (mtm) outliers start: 18 outliers final: 14 residues processed: 132 average time/residue: 0.6713 time to fit residues: 93.6243 Evaluate side-chains 134 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS 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 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 128 VAL Chi-restraints excluded: chain R residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.101634 restraints weight = 8820.099| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.04 r_work: 0.2960 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8365 Z= 0.195 Angle : 0.545 6.277 11350 Z= 0.300 Chirality : 0.044 0.184 1299 Planarity : 0.004 0.051 1440 Dihedral : 4.875 56.666 1211 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.37 % Allowed : 12.66 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.26), residues: 1028 helix: 2.70 (0.26), residues: 386 sheet: 0.25 (0.33), residues: 216 loop : -0.14 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.013 0.002 TYR R 250 PHE 0.017 0.002 PHE R 254 TRP 0.015 0.002 TRP A 234 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 8362) covalent geometry : angle 0.54523 (11344) SS BOND : bond 0.00272 ( 3) SS BOND : angle 0.64135 ( 6) hydrogen bonds : bond 0.05259 ( 456) hydrogen bonds : angle 5.02616 ( 1284) ********************** 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: 21 poor density : 123 time to evaluate : 0.384 Fit side-chains REVERT: A 331 ASP cc_start: 0.8019 (t70) cc_final: 0.7757 (t70) REVERT: B 23 LYS cc_start: 0.8333 (ttmm) cc_final: 0.7936 (tptm) REVERT: B 59 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8537 (m-80) REVERT: B 70 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8824 (pp) REVERT: B 134 ARG cc_start: 0.7869 (ppt170) cc_final: 0.7166 (ptm-80) REVERT: B 137 ARG cc_start: 0.7982 (mmt-90) cc_final: 0.7738 (tpt90) REVERT: B 234 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: N 19 ARG cc_start: 0.7886 (ttt180) cc_final: 0.7649 (ttt-90) REVERT: N 85 SER cc_start: 0.8830 (t) cc_final: 0.8459 (m) REVERT: R 53 THR cc_start: 0.7609 (p) cc_final: 0.7192 (m) REVERT: R 121 MET cc_start: 0.9137 (mmm) cc_final: 0.8553 (mmm) REVERT: R 198 MET cc_start: 0.8842 (mtp) cc_final: 0.8417 (mtm) outliers start: 21 outliers final: 13 residues processed: 133 average time/residue: 0.6581 time to fit residues: 92.4601 Evaluate side-chains 136 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR 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 70 LEU 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 R residue 30 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 87 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 0.1980 chunk 76 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3619 r_free = 0.3619 target = 0.141752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.105717 restraints weight = 8825.764| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.05 r_work: 0.3018 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8365 Z= 0.113 Angle : 0.471 6.306 11350 Z= 0.260 Chirality : 0.041 0.180 1299 Planarity : 0.003 0.052 1440 Dihedral : 4.562 55.464 1211 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.69 % Allowed : 13.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.26), residues: 1028 helix: 2.93 (0.26), residues: 386 sheet: 0.22 (0.33), residues: 218 loop : -0.11 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 19 TYR 0.011 0.001 TYR R 250 PHE 0.014 0.001 PHE A 376 TRP 0.017 0.002 TRP B 82 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8362) covalent geometry : angle 0.47077 (11344) SS BOND : bond 0.00123 ( 3) SS BOND : angle 0.39125 ( 6) hydrogen bonds : bond 0.04356 ( 456) hydrogen bonds : angle 4.73846 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3575.65 seconds wall clock time: 61 minutes 33.10 seconds (3693.10 seconds total)