Starting phenix.real_space_refine on Fri Jul 3 08:23:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7td2_25821/07_2026/7td2_25821_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7td2_25821/07_2026/7td2_25821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7td2_25821/07_2026/7td2_25821_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7td2_25821/07_2026/7td2_25821_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7td2_25821/07_2026/7td2_25821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7td2_25821/07_2026/7td2_25821.map" } resolution = 3.11 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= 0.001 sd= 1.055 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 60 5.16 5 C 4416 2.51 5 N 1156 2.21 5 O 1263 1.98 5 H 6632 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13528 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 4482 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 7, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 4863 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 4, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3394 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 760 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'NKP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.96, per 1000 atoms: 0.14 Number of scatterers: 13528 At special positions: 0 Unit cell: (94.696, 95.76, 128.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 1 15.00 O 1263 8.00 N 1156 7.00 C 4416 6.00 H 6632 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 190 " distance=2.03 Simple disulfide: pdb=" SG CYS R 188 " - pdb=" SG CYS R 195 " distance=1.95 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 287 " 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: 0.83 Conformation dependent library (CDL) restraints added in 365.9 milliseconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1714 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 45.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 29 through 37 removed outlier: 3.935A pdb=" N PHE R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER R 37 " --> pdb=" O PHE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 77 Processing helix chain 'R' and resid 82 through 106 Processing helix chain 'R' and resid 109 through 115 Processing helix chain 'R' and resid 117 through 151 removed outlier: 3.652A pdb=" N ILE R 128 " --> pdb=" O ARG R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 181 removed outlier: 4.349A pdb=" N VAL R 164 " --> pdb=" O SER R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 238 removed outlier: 3.932A pdb=" N LEU R 207 " --> pdb=" O SER R 203 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 284 removed outlier: 3.648A pdb=" N SER R 255 " --> pdb=" O ASP R 251 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 292 through 312 removed outlier: 3.983A pdb=" N SER R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA R 305 " --> pdb=" O GLU R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 322 removed outlier: 3.548A pdb=" N PHE R 322 " --> pdb=" O MET R 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 10 through 32 removed outlier: 3.825A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.120A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.670A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.225A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.623A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.764A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.871A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'G' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.652A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.775A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.530A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 150 removed outlier: 4.322A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.657A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.540A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.886A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.641A pdb=" N LEU A 268 " --> pdb=" O HIS A 322 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6607 1.03 - 1.23: 30 1.23 - 1.42: 2949 1.42 - 1.62: 3989 1.62 - 1.82: 90 Bond restraints: 13665 Sorted by residual: bond pdb=" OAD NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.696 1.509 0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.683 1.509 0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" CAH NKP R 401 " pdb=" OBC NKP R 401 " ideal model delta sigma weight residual 1.468 1.399 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C LYS A 349 " pdb=" O LYS A 349 " ideal model delta sigma weight residual 1.236 1.196 0.041 1.26e-02 6.30e+03 1.04e+01 bond pdb=" C LEU A 348 " pdb=" N LYS A 349 " ideal model delta sigma weight residual 1.335 1.293 0.042 1.38e-02 5.25e+03 9.26e+00 ... (remaining 13660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.28: 24557 11.28 - 22.57: 2 22.57 - 33.85: 0 33.85 - 45.14: 0 45.14 - 56.42: 1 Bond angle restraints: 24560 Sorted by residual: angle pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAD NKP R 401 " ideal model delta sigma weight residual 53.21 109.63 -56.42 3.00e+00 1.11e-01 3.54e+02 angle pdb=" OAA NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAB NKP R 401 " ideal model delta sigma weight residual 128.27 109.52 18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" OAA NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAD NKP R 401 " ideal model delta sigma weight residual 121.86 109.50 12.36 3.00e+00 1.11e-01 1.70e+01 angle pdb=" C LEU A 353 " pdb=" N PHE A 354 " pdb=" CA PHE A 354 " ideal model delta sigma weight residual 121.70 128.74 -7.04 1.80e+00 3.09e-01 1.53e+01 angle pdb=" CAL NKP R 401 " pdb=" CAK NKP R 401 " pdb=" OAE NKP R 401 " ideal model delta sigma weight residual 130.47 119.56 10.91 3.00e+00 1.11e-01 1.32e+01 ... (remaining 24555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 6059 17.77 - 35.53: 337 35.53 - 53.30: 79 53.30 - 71.07: 17 71.07 - 88.84: 5 Dihedral angle restraints: 6497 sinusoidal: 3353 harmonic: 3144 Sorted by residual: dihedral pdb=" CA CYS R 284 " pdb=" C CYS R 284 " pdb=" N PRO R 285 " pdb=" CA PRO R 285 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CB GLU B 226 " pdb=" CG GLU B 226 " pdb=" CD GLU B 226 " pdb=" OE1 GLU B 226 " ideal model delta sinusoidal sigma weight residual 0.00 -85.84 85.84 1 3.00e+01 1.11e-03 9.89e+00 dihedral pdb=" CA ASP R 204 " pdb=" CB ASP R 204 " pdb=" CG ASP R 204 " pdb=" OD1 ASP R 204 " ideal model delta sinusoidal sigma weight residual -30.00 -83.23 53.23 1 2.00e+01 2.50e-03 9.63e+00 ... (remaining 6494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1040 0.072 - 0.143: 80 0.143 - 0.215: 0 0.215 - 0.287: 0 0.287 - 0.358: 1 Chirality restraints: 1121 Sorted by residual: chirality pdb=" CAH NKP R 401 " pdb=" CAG NKP R 401 " pdb=" CAI NKP R 401 " pdb=" OBC NKP R 401 " both_signs ideal model delta sigma weight residual False -2.84 -2.49 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA LYS A 349 " pdb=" N LYS A 349 " pdb=" C LYS A 349 " pdb=" CB LYS A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1118 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 348 " -0.012 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" N LYS A 349 " 0.037 2.00e-02 2.50e+03 pdb=" CA LYS A 349 " -0.010 2.00e-02 2.50e+03 pdb=" H LYS A 349 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 353 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C LEU A 353 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A 353 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 354 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 348 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C LEU A 348 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 348 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 349 " -0.009 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 728 2.22 - 2.81: 28388 2.81 - 3.41: 34897 3.41 - 4.00: 46667 4.00 - 4.60: 72911 Nonbonded interactions: 183591 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" HG SER B 316 " model vdw 1.619 2.450 nonbonded pdb=" O ASP B 298 " pdb=" H ALA B 302 " model vdw 1.631 2.450 nonbonded pdb=" O ILE R 63 " pdb="HD22 ASN R 67 " model vdw 1.635 2.450 nonbonded pdb=" HA ASP R 315 " pdb=" HE2 PHE A 354 " model vdw 1.638 2.270 nonbonded pdb=" OG SER B 201 " pdb=" HE1 TRP B 211 " model vdw 1.642 2.450 ... (remaining 183586 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=0.00 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: 0.170 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: 0.050 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.280 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 7036 Z= 0.213 Angle : 0.781 56.419 9557 Z= 0.331 Chirality : 0.038 0.358 1121 Planarity : 0.002 0.020 1197 Dihedral : 12.099 88.835 2433 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.42 % Allowed : 5.64 % Favored : 93.94 % 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 are not related in a simple way. whole: -0.58 (0.27), residues: 890 helix: 0.95 (0.25), residues: 382 sheet: -1.03 (0.36), residues: 177 loop : -1.54 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 134 TYR 0.011 0.001 TYR R 231 PHE 0.005 0.001 PHE A 189 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.21 ( 7033) covalent geometry : angle 0.77975 / 0.33 ( 9551) SS BOND : bond 0.04629 / 2.20 ( 3) SS BOND : angle 2.14583 / 1.17 ( 6) hydrogen bonds : bond 0.12276 / 7.75 ( 385) hydrogen bonds : angle 4.46059 / 3.19 ( 1116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 ILE cc_start: 0.9097 (mm) cc_final: 0.8840 (mt) REVERT: B 186 ASP cc_start: 0.8580 (m-30) cc_final: 0.8022 (m-30) REVERT: B 220 GLN cc_start: 0.8020 (mt0) cc_final: 0.7799 (mt0) REVERT: A 207 GLU cc_start: 0.7001 (tp30) cc_final: 0.6737 (tp30) REVERT: G 21 MET cc_start: 0.3344 (mmm) cc_final: 0.3061 (mmt) outliers start: 3 outliers final: 1 residues processed: 192 average time/residue: 0.1441 time to fit residues: 37.1925 Evaluate side-chains 158 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.112006 restraints weight = 24255.569| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.41 r_work: 0.3053 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7036 Z= 0.229 Angle : 0.529 5.025 9557 Z= 0.295 Chirality : 0.041 0.150 1121 Planarity : 0.004 0.045 1197 Dihedral : 6.398 77.971 991 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.55 % Allowed : 11.71 % Favored : 86.74 % 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 are not related in a simple way. whole: 0.46 (0.29), residues: 890 helix: 1.89 (0.26), residues: 390 sheet: -0.67 (0.36), residues: 182 loop : -1.07 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.016 0.002 TYR R 231 PHE 0.013 0.001 PHE A 196 TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 ( 7033) covalent geometry : angle 0.52880 / 0.29 ( 9551) SS BOND : bond 0.00316 / 0.15 ( 3) SS BOND : angle 0.64321 / 0.38 ( 6) hydrogen bonds : bond 0.04598 / 3.00 ( 385) hydrogen bonds : angle 4.22530 / 3.07 ( 1116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 MET cc_start: 0.7245 (mmp) cc_final: 0.6977 (mmt) REVERT: B 186 ASP cc_start: 0.9038 (m-30) cc_final: 0.8480 (m-30) REVERT: B 220 GLN cc_start: 0.8460 (mt0) cc_final: 0.8075 (mt0) REVERT: B 268 ASN cc_start: 0.8532 (t0) cc_final: 0.8215 (m-40) REVERT: A 308 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8322 (mt-10) REVERT: A 309 ASP cc_start: 0.7980 (m-30) cc_final: 0.7760 (m-30) REVERT: G 61 PHE cc_start: 0.7035 (m-80) cc_final: 0.6766 (m-80) outliers start: 11 outliers final: 8 residues processed: 174 average time/residue: 0.1385 time to fit residues: 33.2765 Evaluate side-chains 164 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.138931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.109913 restraints weight = 24560.942| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.37 r_work: 0.3075 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7036 Z= 0.165 Angle : 0.459 4.488 9557 Z= 0.254 Chirality : 0.039 0.136 1121 Planarity : 0.003 0.031 1197 Dihedral : 6.128 72.841 991 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.97 % Allowed : 13.54 % Favored : 84.49 % 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 are not related in a simple way. whole: 0.82 (0.29), residues: 890 helix: 2.34 (0.27), residues: 381 sheet: -0.42 (0.37), residues: 182 loop : -1.05 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.011 0.001 TYR R 231 PHE 0.011 0.001 PHE A 196 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 7033) covalent geometry : angle 0.45912 / 0.25 ( 9551) SS BOND : bond 0.00248 / 0.12 ( 3) SS BOND : angle 0.51992 / 0.29 ( 6) hydrogen bonds : bond 0.04421 / 2.90 ( 385) hydrogen bonds : angle 4.05344 / 2.94 ( 1116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.8990 (m-30) cc_final: 0.8385 (m-30) REVERT: B 220 GLN cc_start: 0.8496 (mt0) cc_final: 0.8151 (mt0) REVERT: B 268 ASN cc_start: 0.8585 (t0) cc_final: 0.8283 (m-40) REVERT: A 229 ASP cc_start: 0.8558 (p0) cc_final: 0.8336 (p0) REVERT: A 308 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8274 (mt-10) REVERT: G 61 PHE cc_start: 0.7152 (m-80) cc_final: 0.6897 (m-80) outliers start: 14 outliers final: 10 residues processed: 170 average time/residue: 0.1574 time to fit residues: 35.9945 Evaluate side-chains 164 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 40.0000 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.136400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108156 restraints weight = 24648.745| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.35 r_work: 0.3040 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7036 Z= 0.199 Angle : 0.491 4.840 9557 Z= 0.273 Chirality : 0.040 0.138 1121 Planarity : 0.003 0.032 1197 Dihedral : 5.601 72.388 991 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.68 % Allowed : 14.67 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.29), residues: 890 helix: 2.33 (0.26), residues: 380 sheet: -0.32 (0.37), residues: 182 loop : -0.93 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.013 0.001 TYR R 231 PHE 0.012 0.001 PHE A 196 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 ( 7033) covalent geometry : angle 0.49131 / 0.27 ( 9551) SS BOND : bond 0.00260 / 0.13 ( 3) SS BOND : angle 0.41711 / 0.22 ( 6) hydrogen bonds : bond 0.04604 / 3.02 ( 385) hydrogen bonds : angle 4.10972 / 3.00 ( 1116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 MET cc_start: 0.7373 (mmp) cc_final: 0.6993 (mmt) REVERT: R 234 GLN cc_start: 0.8469 (tt0) cc_final: 0.8245 (tm-30) REVERT: B 44 GLN cc_start: 0.8565 (mp10) cc_final: 0.8334 (mp10) REVERT: B 268 ASN cc_start: 0.8693 (t0) cc_final: 0.8325 (m-40) REVERT: A 32 ARG cc_start: 0.8291 (ptm160) cc_final: 0.7891 (ptp90) REVERT: A 229 ASP cc_start: 0.8710 (p0) cc_final: 0.8469 (p0) REVERT: A 308 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8299 (mt-10) REVERT: G 61 PHE cc_start: 0.7223 (m-80) cc_final: 0.6996 (m-80) outliers start: 19 outliers final: 16 residues processed: 180 average time/residue: 0.1428 time to fit residues: 35.5706 Evaluate side-chains 177 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 67 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.138968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.110021 restraints weight = 24607.803| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.37 r_work: 0.3073 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7036 Z= 0.135 Angle : 0.447 4.455 9557 Z= 0.247 Chirality : 0.038 0.135 1121 Planarity : 0.003 0.031 1197 Dihedral : 5.468 71.831 991 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.12 % Allowed : 15.94 % Favored : 81.95 % 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 are not related in a simple way. whole: 1.18 (0.29), residues: 890 helix: 2.64 (0.26), residues: 380 sheet: -0.26 (0.38), residues: 177 loop : -0.84 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 283 TYR 0.010 0.001 TYR R 231 PHE 0.009 0.001 PHE A 196 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7033) covalent geometry : angle 0.44704 / 0.25 ( 9551) SS BOND : bond 0.00228 / 0.11 ( 3) SS BOND : angle 0.45589 / 0.29 ( 6) hydrogen bonds : bond 0.04173 / 2.74 ( 385) hydrogen bonds : angle 3.94056 / 2.88 ( 1116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 MET cc_start: 0.7470 (mmp) cc_final: 0.7269 (mmp) REVERT: R 234 GLN cc_start: 0.8492 (tt0) cc_final: 0.8278 (tm-30) REVERT: B 44 GLN cc_start: 0.8538 (mp10) cc_final: 0.8318 (mp10) REVERT: B 48 ARG cc_start: 0.8230 (mmt-90) cc_final: 0.7737 (mmt90) REVERT: B 268 ASN cc_start: 0.8677 (t0) cc_final: 0.8325 (m-40) REVERT: A 32 ARG cc_start: 0.8313 (ptm160) cc_final: 0.7925 (ptp90) REVERT: A 229 ASP cc_start: 0.8654 (p0) cc_final: 0.8410 (p0) REVERT: A 308 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8278 (mt-10) REVERT: G 61 PHE cc_start: 0.7209 (m-80) cc_final: 0.6996 (m-80) outliers start: 15 outliers final: 13 residues processed: 174 average time/residue: 0.1452 time to fit residues: 34.6860 Evaluate side-chains 176 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 2 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 0.0040 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 overall best weight: 1.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.138825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.109833 restraints weight = 24577.925| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.37 r_work: 0.3079 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7036 Z= 0.134 Angle : 0.441 4.542 9557 Z= 0.244 Chirality : 0.038 0.138 1121 Planarity : 0.003 0.031 1197 Dihedral : 5.320 70.219 991 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.54 % Allowed : 16.08 % Favored : 81.38 % 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 are not related in a simple way. whole: 1.33 (0.29), residues: 890 helix: 2.75 (0.26), residues: 384 sheet: -0.23 (0.37), residues: 182 loop : -0.77 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 283 TYR 0.010 0.001 TYR R 231 PHE 0.009 0.001 PHE A 196 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7033) covalent geometry : angle 0.44117 / 0.24 ( 9551) SS BOND : bond 0.00217 / 0.10 ( 3) SS BOND : angle 0.44592 / 0.26 ( 6) hydrogen bonds : bond 0.04063 / 2.67 ( 385) hydrogen bonds : angle 3.88715 / 2.84 ( 1116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 MET cc_start: 0.7570 (mmp) cc_final: 0.7224 (mmp) REVERT: R 234 GLN cc_start: 0.8497 (tt0) cc_final: 0.8291 (tm-30) REVERT: B 44 GLN cc_start: 0.8532 (mp10) cc_final: 0.8318 (mp10) REVERT: B 48 ARG cc_start: 0.8227 (mmt-90) cc_final: 0.7734 (mmt90) REVERT: B 220 GLN cc_start: 0.8539 (mt0) cc_final: 0.8321 (mt0) REVERT: B 268 ASN cc_start: 0.8669 (t0) cc_final: 0.8298 (m-40) REVERT: B 325 MET cc_start: 0.8117 (mmm) cc_final: 0.7904 (mmt) REVERT: A 32 ARG cc_start: 0.8279 (ptm160) cc_final: 0.7867 (ptp90) REVERT: A 229 ASP cc_start: 0.8787 (p0) cc_final: 0.8553 (p0) REVERT: A 308 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8255 (mt-10) REVERT: G 61 PHE cc_start: 0.7231 (m-80) cc_final: 0.7020 (m-80) outliers start: 18 outliers final: 15 residues processed: 181 average time/residue: 0.1516 time to fit residues: 37.5419 Evaluate side-chains 182 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.139612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.110520 restraints weight = 24379.462| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.38 r_work: 0.3040 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7036 Z= 0.117 Angle : 0.435 4.486 9557 Z= 0.240 Chirality : 0.038 0.137 1121 Planarity : 0.003 0.031 1197 Dihedral : 5.227 69.484 991 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.97 % Allowed : 17.35 % Favored : 80.68 % 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 are not related in a simple way. whole: 1.53 (0.30), residues: 890 helix: 2.94 (0.26), residues: 385 sheet: -0.19 (0.37), residues: 186 loop : -0.67 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 36 TYR 0.009 0.001 TYR B 59 PHE 0.008 0.001 PHE A 196 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7033) covalent geometry : angle 0.43475 / 0.24 ( 9551) SS BOND : bond 0.00209 / 0.10 ( 3) SS BOND : angle 0.44515 / 0.29 ( 6) hydrogen bonds : bond 0.03909 / 2.57 ( 385) hydrogen bonds : angle 3.84316 / 2.81 ( 1116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 MET cc_start: 0.7566 (mmp) cc_final: 0.7245 (mmp) REVERT: R 234 GLN cc_start: 0.8460 (tt0) cc_final: 0.8246 (tm-30) REVERT: B 48 ARG cc_start: 0.8198 (mmt-90) cc_final: 0.7725 (mmt90) REVERT: B 220 GLN cc_start: 0.8451 (mt0) cc_final: 0.8229 (mt0) REVERT: B 268 ASN cc_start: 0.8656 (t0) cc_final: 0.8258 (m-40) REVERT: A 32 ARG cc_start: 0.8227 (ptm160) cc_final: 0.7743 (ptp90) REVERT: A 229 ASP cc_start: 0.8667 (p0) cc_final: 0.8439 (p0) REVERT: A 308 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8172 (mt-10) outliers start: 14 outliers final: 14 residues processed: 182 average time/residue: 0.1492 time to fit residues: 37.4916 Evaluate side-chains 180 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.106215 restraints weight = 24666.745| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.38 r_work: 0.2987 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7036 Z= 0.239 Angle : 0.513 4.868 9557 Z= 0.286 Chirality : 0.040 0.148 1121 Planarity : 0.003 0.032 1197 Dihedral : 5.755 70.616 991 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.40 % Allowed : 17.35 % Favored : 80.25 % 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 are not related in a simple way. whole: 1.14 (0.29), residues: 890 helix: 2.56 (0.26), residues: 378 sheet: -0.26 (0.38), residues: 174 loop : -0.79 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 24 TYR 0.017 0.002 TYR R 231 PHE 0.016 0.002 PHE G 61 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.24 ( 7033) covalent geometry : angle 0.51309 / 0.29 ( 9551) SS BOND : bond 0.00321 / 0.15 ( 3) SS BOND : angle 0.36563 / 0.22 ( 6) hydrogen bonds : bond 0.04899 / 3.23 ( 385) hydrogen bonds : angle 4.11417 / 3.01 ( 1116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 MET cc_start: 0.7629 (mmp) cc_final: 0.7338 (mmp) REVERT: R 234 GLN cc_start: 0.8499 (tt0) cc_final: 0.8272 (tm-30) REVERT: B 44 GLN cc_start: 0.8542 (mp10) cc_final: 0.8319 (mp10) REVERT: B 127 LYS cc_start: 0.8239 (mmtp) cc_final: 0.7964 (mmtm) REVERT: B 220 GLN cc_start: 0.8526 (mt0) cc_final: 0.8299 (mt0) REVERT: B 268 ASN cc_start: 0.8699 (t0) cc_final: 0.8409 (m-40) REVERT: A 32 ARG cc_start: 0.8328 (ptm160) cc_final: 0.7890 (ptp90) REVERT: A 229 ASP cc_start: 0.8827 (p0) cc_final: 0.8592 (p0) REVERT: A 308 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8283 (mt-10) outliers start: 17 outliers final: 14 residues processed: 181 average time/residue: 0.1383 time to fit residues: 33.7786 Evaluate side-chains 177 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114411 restraints weight = 24563.182| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.35 r_work: 0.3028 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7036 Z= 0.097 Angle : 0.436 4.410 9557 Z= 0.240 Chirality : 0.038 0.139 1121 Planarity : 0.003 0.031 1197 Dihedral : 5.208 68.701 991 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.69 % Allowed : 18.48 % Favored : 79.83 % 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 are not related in a simple way. whole: 1.55 (0.30), residues: 890 helix: 3.00 (0.26), residues: 385 sheet: -0.26 (0.38), residues: 180 loop : -0.65 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.007 0.001 TYR B 59 PHE 0.009 0.001 PHE G 61 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 ( 7033) covalent geometry : angle 0.43623 / 0.24 ( 9551) SS BOND : bond 0.00219 / 0.11 ( 3) SS BOND : angle 0.57814 / 0.42 ( 6) hydrogen bonds : bond 0.03833 / 2.54 ( 385) hydrogen bonds : angle 3.84019 / 2.81 ( 1116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 MET cc_start: 0.7648 (mmp) cc_final: 0.7308 (mmp) REVERT: R 234 GLN cc_start: 0.8433 (tt0) cc_final: 0.8217 (tm-30) REVERT: B 197 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7698 (mmm160) REVERT: B 220 GLN cc_start: 0.8456 (mt0) cc_final: 0.8200 (mt0) REVERT: B 268 ASN cc_start: 0.8665 (t0) cc_final: 0.8287 (m-40) REVERT: B 325 MET cc_start: 0.8172 (tpp) cc_final: 0.7837 (tpp) REVERT: A 32 ARG cc_start: 0.8211 (ptm160) cc_final: 0.7753 (ptp90) REVERT: A 229 ASP cc_start: 0.8691 (p0) cc_final: 0.8475 (p0) REVERT: A 308 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8190 (mt-10) REVERT: G 38 MET cc_start: 0.7273 (mtp) cc_final: 0.7066 (mtm) outliers start: 12 outliers final: 11 residues processed: 179 average time/residue: 0.1434 time to fit residues: 34.6945 Evaluate side-chains 177 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 40.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.106429 restraints weight = 24791.451| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.39 r_work: 0.2970 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7036 Z= 0.214 Angle : 0.495 4.765 9557 Z= 0.276 Chirality : 0.040 0.143 1121 Planarity : 0.004 0.045 1197 Dihedral : 5.530 70.017 991 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.83 % Allowed : 18.19 % Favored : 79.97 % 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 are not related in a simple way. whole: 1.33 (0.29), residues: 890 helix: 2.73 (0.26), residues: 385 sheet: -0.21 (0.38), residues: 179 loop : -0.77 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 36 TYR 0.015 0.001 TYR R 231 PHE 0.013 0.001 PHE G 61 TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 ( 7033) covalent geometry : angle 0.49483 / 0.28 ( 9551) SS BOND : bond 0.00292 / 0.14 ( 3) SS BOND : angle 0.33882 / 0.18 ( 6) hydrogen bonds : bond 0.04645 / 3.06 ( 385) hydrogen bonds : angle 4.03823 / 2.95 ( 1116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 MET cc_start: 0.7611 (mmp) cc_final: 0.7286 (mmp) REVERT: R 234 GLN cc_start: 0.8469 (tt0) cc_final: 0.8242 (tm-30) REVERT: B 44 GLN cc_start: 0.8575 (mp10) cc_final: 0.8332 (mp10) REVERT: B 220 GLN cc_start: 0.8516 (mt0) cc_final: 0.8301 (mt0) REVERT: B 262 MET cc_start: 0.8558 (tpp) cc_final: 0.8268 (mtt) REVERT: B 268 ASN cc_start: 0.8719 (t0) cc_final: 0.8400 (m-40) REVERT: A 20 ASP cc_start: 0.8029 (m-30) cc_final: 0.7816 (m-30) REVERT: A 32 ARG cc_start: 0.8279 (ptm160) cc_final: 0.7816 (ptp90) REVERT: A 229 ASP cc_start: 0.8807 (p0) cc_final: 0.8605 (p0) REVERT: A 308 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8249 (mt-10) REVERT: G 29 LYS cc_start: 0.7308 (mmtt) cc_final: 0.6998 (mmmm) REVERT: G 38 MET cc_start: 0.7223 (mtp) cc_final: 0.7011 (mtm) outliers start: 13 outliers final: 13 residues processed: 178 average time/residue: 0.1549 time to fit residues: 37.9535 Evaluate side-chains 182 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.140510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111860 restraints weight = 24701.942| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.36 r_work: 0.3013 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7036 Z= 0.119 Angle : 0.445 4.417 9557 Z= 0.245 Chirality : 0.038 0.137 1121 Planarity : 0.003 0.040 1197 Dihedral : 5.259 68.197 991 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.55 % Allowed : 18.48 % Favored : 79.97 % 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 are not related in a simple way. whole: 1.55 (0.29), residues: 890 helix: 3.04 (0.26), residues: 380 sheet: -0.16 (0.38), residues: 179 loop : -0.72 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 36 TYR 0.008 0.001 TYR B 59 PHE 0.010 0.001 PHE G 61 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7033) covalent geometry : angle 0.44463 / 0.25 ( 9551) SS BOND : bond 0.00243 / 0.12 ( 3) SS BOND : angle 0.42369 / 0.30 ( 6) hydrogen bonds : bond 0.04019 / 2.65 ( 385) hydrogen bonds : angle 3.88356 / 2.84 ( 1116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3335.61 seconds wall clock time: 57 minutes 7.25 seconds (3427.25 seconds total)