Starting phenix.real_space_refine on Wed Feb 4 02:19:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jcl_61369/02_2026/9jcl_61369.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jcl_61369/02_2026/9jcl_61369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jcl_61369/02_2026/9jcl_61369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jcl_61369/02_2026/9jcl_61369.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jcl_61369/02_2026/9jcl_61369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jcl_61369/02_2026/9jcl_61369.map" } resolution = 2.76 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= -0.002 sd= 0.074 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 54 5.16 5 C 5280 2.51 5 N 1423 2.21 5 O 1541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8300 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1971 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" 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: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 955 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2283 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 11, 'TRANS': 285} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 4, 'HIS:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "R" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'ADP': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.62, per 1000 atoms: 0.20 Number of scatterers: 8300 At special positions: 0 Unit cell: (74.048, 100.672, 135.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 2 15.00 O 1541 8.00 N 1423 7.00 C 5280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 42 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 202 " 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: 1.02 Conformation dependent library (CDL) restraints added in 287.2 milliseconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 42.4% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 270 through 273 removed outlier: 3.903A pdb=" N ARG A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 273' Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.990A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.728A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 47 through 52 Processing helix chain 'R' and resid 52 through 79 removed outlier: 4.045A pdb=" N LEU R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 113 removed outlier: 3.555A pdb=" N TYR R 89 " --> pdb=" O GLY R 85 " (cutoff:3.500A) Proline residue: R 105 - end of helix Processing helix chain 'R' and resid 120 through 155 Processing helix chain 'R' and resid 157 through 161 removed outlier: 4.149A pdb=" N GLY R 161 " --> pdb=" O LYS R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 190 Proline residue: R 185 - end of helix removed outlier: 3.858A pdb=" N PHE R 188 " --> pdb=" O SER R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 226 removed outlier: 3.725A pdb=" N ILE R 216 " --> pdb=" O ARG R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 247 Processing helix chain 'R' and resid 255 through 289 removed outlier: 4.211A pdb=" N ILE R 259 " --> pdb=" O ARG R 255 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 295 through 315 Processing helix chain 'R' and resid 315 through 325 Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 328 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.129A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.717A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.592A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.743A 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: 3.956A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.170A 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: 4.051A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.936A 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: 6.613A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.532A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.604A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.196A 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 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.756A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 192 through 194 458 hydrogen bonds defined for protein. 1320 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: 1.63 Time building geometry restraints manager: 1.28 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: 2684 1.34 - 1.46: 1726 1.46 - 1.58: 3989 1.58 - 1.69: 3 1.69 - 1.81: 75 Bond restraints: 8477 Sorted by residual: bond pdb=" C13 CLR R 602 " pdb=" C17 CLR R 602 " ideal model delta sigma weight residual 1.550 1.523 0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C13 CLR R 602 " pdb=" C14 CLR R 602 " ideal model delta sigma weight residual 1.537 1.511 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C10 CLR R 602 " pdb=" C9 CLR R 602 " ideal model delta sigma weight residual 1.551 1.526 0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.52e+00 bond pdb=" C16 CLR R 602 " pdb=" C17 CLR R 602 " ideal model delta sigma weight residual 1.554 1.531 0.023 2.00e-02 2.50e+03 1.29e+00 ... (remaining 8472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11300 1.71 - 3.41: 174 3.41 - 5.12: 31 5.12 - 6.83: 5 6.83 - 8.54: 2 Bond angle restraints: 11512 Sorted by residual: angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 angle pdb=" N VAL A 224 " pdb=" CA VAL A 224 " pdb=" C VAL A 224 " ideal model delta sigma weight residual 106.21 109.55 -3.34 1.07e+00 8.73e-01 9.73e+00 angle pdb=" O2B ADP R 601 " pdb=" PB ADP R 601 " pdb=" O3B ADP R 601 " ideal model delta sigma weight residual 119.90 111.36 8.54 3.00e+00 1.11e-01 8.10e+00 angle pdb=" O1B ADP R 601 " pdb=" PB ADP R 601 " pdb=" O2B ADP R 601 " ideal model delta sigma weight residual 119.90 111.55 8.35 3.00e+00 1.11e-01 7.75e+00 angle pdb=" N GLY A 52 " pdb=" CA GLY A 52 " pdb=" C GLY A 52 " ideal model delta sigma weight residual 113.18 118.61 -5.43 2.37e+00 1.78e-01 5.25e+00 ... (remaining 11507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4548 17.71 - 35.42: 423 35.42 - 53.12: 76 53.12 - 70.83: 19 70.83 - 88.54: 7 Dihedral angle restraints: 5073 sinusoidal: 1992 harmonic: 3081 Sorted by residual: dihedral pdb=" CB CYS R 42 " pdb=" SG CYS R 42 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual -86.00 -173.98 87.98 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CA SER A 51 " pdb=" C SER A 51 " pdb=" N GLY A 52 " pdb=" CA GLY A 52 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 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 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 960 0.042 - 0.085: 261 0.085 - 0.127: 75 0.127 - 0.169: 8 0.169 - 0.211: 2 Chirality restraints: 1306 Sorted by residual: chirality pdb=" C13 CLR R 602 " pdb=" C12 CLR R 602 " pdb=" C14 CLR R 602 " pdb=" C17 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C10 CLR R 602 " pdb=" C1 CLR R 602 " pdb=" C5 CLR R 602 " pdb=" C9 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.85 -2.66 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.48 0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 1303 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 81 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO R 82 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 82 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 82 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 252 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO R 253 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 253 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 253 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 228 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO R 229 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 229 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 229 " -0.028 5.00e-02 4.00e+02 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 111 2.63 - 3.20: 7609 3.20 - 3.77: 13807 3.77 - 4.33: 19910 4.33 - 4.90: 32178 Nonbonded interactions: 73615 Sorted by model distance: nonbonded pdb=" OH TYR R 110 " pdb=" O1B ADP R 601 " model vdw 2.067 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.167 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.207 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.228 3.040 ... (remaining 73610 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.380 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 0.043 8479 Z= 0.155 Angle : 0.566 8.536 11516 Z= 0.299 Chirality : 0.042 0.211 1306 Planarity : 0.004 0.065 1457 Dihedral : 14.303 88.539 3083 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.36 % Allowed : 9.43 % Favored : 89.20 % 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 are not related in a simple way. whole: 1.14 (0.27), residues: 1045 helix: 2.48 (0.25), residues: 405 sheet: -0.53 (0.32), residues: 234 loop : -0.14 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 128 TYR 0.011 0.001 TYR A 37 PHE 0.014 0.001 PHE R 131 TRP 0.015 0.002 TRP B 99 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8477) covalent geometry : angle 0.56644 (11512) SS BOND : bond 0.00061 ( 2) SS BOND : angle 0.23150 ( 4) hydrogen bonds : bond 0.12111 ( 458) hydrogen bonds : angle 5.85430 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6985 (mm-30) REVERT: A 29 GLN cc_start: 0.8335 (tp40) cc_final: 0.8125 (tp-100) REVERT: B 277 SER cc_start: 0.9077 (m) cc_final: 0.8812 (t) REVERT: R 216 ILE cc_start: 0.8629 (mt) cc_final: 0.8399 (mm) REVERT: R 233 ILE cc_start: 0.8131 (tt) cc_final: 0.7900 (mt) REVERT: R 242 ARG cc_start: 0.8106 (tmm-80) cc_final: 0.7893 (ttp-170) outliers start: 12 outliers final: 13 residues processed: 206 average time/residue: 0.4975 time to fit residues: 108.7291 Evaluate side-chains 150 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 282 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 50 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN B 16 ASN B 88 ASN B 155 ASN B 237 ASN N 120 GLN R 134 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.169770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133733 restraints weight = 8776.904| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.49 r_work: 0.3246 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8479 Z= 0.140 Angle : 0.563 6.818 11516 Z= 0.294 Chirality : 0.042 0.145 1306 Planarity : 0.004 0.056 1457 Dihedral : 6.475 69.718 1252 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.32 % Allowed : 15.00 % 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: 1.31 (0.27), residues: 1045 helix: 2.67 (0.25), residues: 407 sheet: -0.19 (0.32), residues: 224 loop : -0.32 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.014 0.001 TYR R 53 PHE 0.017 0.001 PHE R 131 TRP 0.013 0.002 TRP B 99 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8477) covalent geometry : angle 0.56258 (11512) SS BOND : bond 0.00043 ( 2) SS BOND : angle 0.32131 ( 4) hydrogen bonds : bond 0.04082 ( 458) hydrogen bonds : angle 4.99312 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7291 (mm-30) REVERT: A 29 GLN cc_start: 0.8372 (tp40) cc_final: 0.8171 (tp-100) REVERT: A 283 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8361 (mttm) REVERT: A 289 GLU cc_start: 0.8057 (tt0) cc_final: 0.7718 (mt-10) REVERT: A 304 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7437 (mp0) REVERT: A 334 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7830 (tp30) REVERT: B 186 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: B 277 SER cc_start: 0.8943 (m) cc_final: 0.8692 (t) REVERT: R 128 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8168 (mmt180) REVERT: R 204 ASP cc_start: 0.7736 (t70) cc_final: 0.6984 (p0) REVERT: R 216 ILE cc_start: 0.8577 (mt) cc_final: 0.8352 (mm) REVERT: R 233 ILE cc_start: 0.8048 (tt) cc_final: 0.7714 (mt) REVERT: R 242 ARG cc_start: 0.8180 (tmm-80) cc_final: 0.7947 (ttp-170) outliers start: 38 outliers final: 17 residues processed: 172 average time/residue: 0.4956 time to fit residues: 90.7174 Evaluate side-chains 142 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 128 ARG Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 221 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN B 237 ASN N 35 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.165256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129521 restraints weight = 8779.972| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.54 r_work: 0.3235 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8479 Z= 0.171 Angle : 0.574 6.735 11516 Z= 0.298 Chirality : 0.042 0.148 1306 Planarity : 0.005 0.058 1457 Dihedral : 6.028 70.351 1242 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.57 % Allowed : 16.36 % Favored : 78.07 % 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: 1.19 (0.27), residues: 1045 helix: 2.62 (0.25), residues: 407 sheet: -0.30 (0.32), residues: 224 loop : -0.42 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.014 0.002 TYR R 53 PHE 0.015 0.002 PHE R 131 TRP 0.016 0.002 TRP B 99 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8477) covalent geometry : angle 0.57399 (11512) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.18070 ( 4) hydrogen bonds : bond 0.04121 ( 458) hydrogen bonds : angle 4.96591 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7230 (mm-30) REVERT: A 283 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8484 (mttm) REVERT: A 289 GLU cc_start: 0.8074 (tt0) cc_final: 0.7758 (mt-10) REVERT: A 304 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7330 (pm20) REVERT: A 334 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7859 (tp30) REVERT: B 186 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: B 258 ASP cc_start: 0.7994 (t70) cc_final: 0.7757 (t0) REVERT: B 266 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7701 (t70) REVERT: B 277 SER cc_start: 0.9019 (m) cc_final: 0.8773 (t) REVERT: B 314 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8618 (ptt180) REVERT: B 336 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8969 (mp) REVERT: R 57 VAL cc_start: 0.8336 (t) cc_final: 0.8122 (t) REVERT: R 75 MET cc_start: 0.7687 (mmm) cc_final: 0.7476 (mmm) REVERT: R 128 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7890 (mmt180) REVERT: R 204 ASP cc_start: 0.7722 (t70) cc_final: 0.6811 (p0) REVERT: R 216 ILE cc_start: 0.8581 (mt) cc_final: 0.8342 (mm) REVERT: R 233 ILE cc_start: 0.8040 (tt) cc_final: 0.7784 (mt) outliers start: 49 outliers final: 23 residues processed: 162 average time/residue: 0.4976 time to fit residues: 86.0235 Evaluate side-chains 147 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 128 ARG Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 221 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 35 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 382 ASN N 35 ASN N 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.166110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.129313 restraints weight = 8983.317| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.56 r_work: 0.3189 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8479 Z= 0.172 Angle : 0.573 6.459 11516 Z= 0.297 Chirality : 0.043 0.149 1306 Planarity : 0.004 0.056 1457 Dihedral : 5.996 70.357 1242 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.57 % Allowed : 16.48 % Favored : 77.95 % 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: 1.11 (0.26), residues: 1045 helix: 2.57 (0.25), residues: 410 sheet: -0.39 (0.31), residues: 224 loop : -0.47 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.012 0.001 TYR R 100 PHE 0.016 0.002 PHE B 151 TRP 0.015 0.002 TRP B 99 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8477) covalent geometry : angle 0.57285 (11512) SS BOND : bond 0.00082 ( 2) SS BOND : angle 0.09221 ( 4) hydrogen bonds : bond 0.04064 ( 458) hydrogen bonds : angle 4.95666 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7237 (mm-30) REVERT: A 40 THR cc_start: 0.8752 (t) cc_final: 0.8538 (t) REVERT: A 289 GLU cc_start: 0.8171 (tt0) cc_final: 0.7821 (mt-10) REVERT: A 304 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7379 (mp0) REVERT: A 307 ARG cc_start: 0.8198 (mpp-170) cc_final: 0.7782 (ptp-110) REVERT: B 186 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: B 258 ASP cc_start: 0.8122 (t70) cc_final: 0.7882 (t0) REVERT: B 266 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7798 (t70) REVERT: B 277 SER cc_start: 0.9062 (m) cc_final: 0.8834 (t) REVERT: B 314 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8646 (ptt180) REVERT: R 212 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7416 (mtp-110) REVERT: R 216 ILE cc_start: 0.8570 (mt) cc_final: 0.8325 (mm) REVERT: R 233 ILE cc_start: 0.8102 (tt) cc_final: 0.7818 (mt) REVERT: R 282 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8465 (mtp) outliers start: 49 outliers final: 24 residues processed: 160 average time/residue: 0.4524 time to fit residues: 77.4124 Evaluate side-chains 143 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 212 ARG Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 282 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 31 GLN A 35 GLN A 220 HIS A 284 GLN A 382 ASN N 35 ASN N 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.166172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.130558 restraints weight = 8894.568| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.58 r_work: 0.3197 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8479 Z= 0.178 Angle : 0.574 6.544 11516 Z= 0.298 Chirality : 0.043 0.177 1306 Planarity : 0.004 0.056 1457 Dihedral : 6.026 70.735 1242 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.91 % Allowed : 17.16 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.02 (0.26), residues: 1045 helix: 2.42 (0.25), residues: 416 sheet: -0.41 (0.31), residues: 224 loop : -0.48 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.012 0.001 TYR R 100 PHE 0.016 0.002 PHE R 131 TRP 0.015 0.002 TRP B 99 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8477) covalent geometry : angle 0.57408 (11512) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.05437 ( 4) hydrogen bonds : bond 0.04086 ( 458) hydrogen bonds : angle 4.96063 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 119 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7351 (mtpt) REVERT: A 220 HIS cc_start: 0.8652 (t-170) cc_final: 0.8446 (t-90) REVERT: A 304 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7298 (mp0) REVERT: A 307 ARG cc_start: 0.8188 (mpp-170) cc_final: 0.7780 (ptp-110) REVERT: B 43 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8458 (mt) REVERT: B 186 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7316 (m-30) REVERT: B 258 ASP cc_start: 0.8130 (t70) cc_final: 0.7926 (t0) REVERT: B 266 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7732 (t70) REVERT: B 277 SER cc_start: 0.9039 (m) cc_final: 0.8816 (t) REVERT: B 314 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8635 (ptt180) REVERT: R 59 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7912 (pp) REVERT: R 90 MET cc_start: 0.8338 (mmt) cc_final: 0.8121 (mmt) REVERT: R 204 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7444 (t0) REVERT: R 212 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7396 (mtp-110) REVERT: R 216 ILE cc_start: 0.8556 (mt) cc_final: 0.8297 (mm) REVERT: R 233 ILE cc_start: 0.8079 (tt) cc_final: 0.7798 (mt) REVERT: R 282 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8445 (mtp) outliers start: 52 outliers final: 25 residues processed: 155 average time/residue: 0.5489 time to fit residues: 90.0543 Evaluate side-chains 151 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 204 ASP Chi-restraints excluded: chain R residue 212 ARG Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 282 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 4.9990 chunk 62 optimal weight: 0.0870 chunk 73 optimal weight: 0.0170 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 0.0370 chunk 45 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 overall best weight: 0.1874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 35 GLN A 284 GLN A 382 ASN N 35 ASN N 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.175128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.139342 restraints weight = 8746.232| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.50 r_work: 0.3297 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8479 Z= 0.103 Angle : 0.514 7.474 11516 Z= 0.265 Chirality : 0.040 0.139 1306 Planarity : 0.004 0.057 1457 Dihedral : 5.692 76.678 1242 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.41 % Allowed : 20.23 % Favored : 76.36 % 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: 1.23 (0.27), residues: 1045 helix: 2.63 (0.25), residues: 416 sheet: -0.22 (0.31), residues: 221 loop : -0.46 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.014 0.001 TYR R 100 PHE 0.014 0.001 PHE A 222 TRP 0.017 0.002 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8477) covalent geometry : angle 0.51387 (11512) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.12872 ( 4) hydrogen bonds : bond 0.03443 ( 458) hydrogen bonds : angle 4.67240 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.320 Fit side-chains REVERT: A 27 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7246 (tp30) REVERT: A 304 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7179 (pm20) REVERT: A 334 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7802 (tp30) REVERT: B 22 ARG cc_start: 0.6471 (mtt180) cc_final: 0.6261 (mtt180) REVERT: B 258 ASP cc_start: 0.8077 (t70) cc_final: 0.7872 (t0) REVERT: R 57 VAL cc_start: 0.8200 (t) cc_final: 0.7985 (t) REVERT: R 108 ILE cc_start: 0.7470 (mt) cc_final: 0.7163 (mp) REVERT: R 128 ARG cc_start: 0.8537 (mmt-90) cc_final: 0.8142 (mmt90) REVERT: R 216 ILE cc_start: 0.8553 (mt) cc_final: 0.8290 (mm) outliers start: 30 outliers final: 16 residues processed: 160 average time/residue: 0.4927 time to fit residues: 83.6362 Evaluate side-chains 140 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 192 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 284 GLN A 382 ASN B 237 ASN B 266 HIS B 268 ASN N 35 ASN N 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.170358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133123 restraints weight = 8817.153| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.52 r_work: 0.3312 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8479 Z= 0.134 Angle : 0.552 9.890 11516 Z= 0.281 Chirality : 0.042 0.145 1306 Planarity : 0.004 0.059 1457 Dihedral : 5.751 75.364 1242 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.41 % Allowed : 21.36 % Favored : 75.23 % 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: 1.25 (0.27), residues: 1045 helix: 2.59 (0.25), residues: 415 sheet: -0.17 (0.32), residues: 226 loop : -0.41 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.020 0.001 TYR N 95 PHE 0.014 0.001 PHE R 131 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8477) covalent geometry : angle 0.55202 (11512) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.10652 ( 4) hydrogen bonds : bond 0.03701 ( 458) hydrogen bonds : angle 4.73798 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.312 Fit side-chains REVERT: A 27 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7281 (tp30) REVERT: A 40 THR cc_start: 0.8671 (t) cc_final: 0.8457 (t) REVERT: A 304 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7423 (pt0) REVERT: B 186 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: B 258 ASP cc_start: 0.8079 (t70) cc_final: 0.7864 (t0) REVERT: R 57 VAL cc_start: 0.8233 (t) cc_final: 0.8003 (t) REVERT: R 212 ARG cc_start: 0.7880 (mtp-110) cc_final: 0.7286 (tpt170) REVERT: R 216 ILE cc_start: 0.8556 (mt) cc_final: 0.8293 (mm) outliers start: 30 outliers final: 19 residues processed: 144 average time/residue: 0.5852 time to fit residues: 89.3899 Evaluate side-chains 140 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 186 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 284 GLN N 35 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.169274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133812 restraints weight = 8765.322| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.52 r_work: 0.3228 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8479 Z= 0.151 Angle : 0.570 9.521 11516 Z= 0.292 Chirality : 0.042 0.143 1306 Planarity : 0.004 0.059 1457 Dihedral : 5.818 74.935 1241 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.07 % Allowed : 21.59 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.16 (0.26), residues: 1045 helix: 2.50 (0.25), residues: 415 sheet: -0.26 (0.31), residues: 222 loop : -0.42 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.013 0.001 TYR N 95 PHE 0.014 0.001 PHE R 131 TRP 0.013 0.002 TRP B 169 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8477) covalent geometry : angle 0.56965 (11512) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.11907 ( 4) hydrogen bonds : bond 0.03793 ( 458) hydrogen bonds : angle 4.84275 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.336 Fit side-chains REVERT: A 40 THR cc_start: 0.8741 (t) cc_final: 0.8529 (t) REVERT: A 304 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7507 (pt0) REVERT: B 186 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: B 258 ASP cc_start: 0.8111 (t70) cc_final: 0.7889 (t0) REVERT: B 314 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8568 (ptt180) REVERT: R 212 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.7323 (tpt170) REVERT: R 216 ILE cc_start: 0.8586 (mt) cc_final: 0.8329 (mm) REVERT: R 233 ILE cc_start: 0.8093 (tt) cc_final: 0.7778 (mt) outliers start: 27 outliers final: 20 residues processed: 145 average time/residue: 0.5361 time to fit residues: 82.3773 Evaluate side-chains 138 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 194 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.0970 chunk 49 optimal weight: 0.0270 chunk 18 optimal weight: 0.8980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 284 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.172439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137402 restraints weight = 8821.521| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.52 r_work: 0.3271 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8479 Z= 0.115 Angle : 0.548 12.286 11516 Z= 0.280 Chirality : 0.041 0.168 1306 Planarity : 0.004 0.056 1457 Dihedral : 5.740 77.069 1241 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.95 % Allowed : 21.70 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.21 (0.26), residues: 1045 helix: 2.54 (0.25), residues: 415 sheet: -0.17 (0.32), residues: 220 loop : -0.44 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.012 0.001 TYR R 100 PHE 0.014 0.001 PHE R 131 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8477) covalent geometry : angle 0.54770 (11512) SS BOND : bond 0.00103 ( 2) SS BOND : angle 0.19410 ( 4) hydrogen bonds : bond 0.03528 ( 458) hydrogen bonds : angle 4.73797 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.227 Fit side-chains REVERT: A 40 THR cc_start: 0.8626 (t) cc_final: 0.8410 (t) REVERT: A 289 GLU cc_start: 0.8126 (tt0) cc_final: 0.7919 (mm-30) REVERT: A 304 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7451 (mp0) REVERT: A 348 TYR cc_start: 0.8525 (t80) cc_final: 0.8306 (t80) REVERT: B 186 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6988 (m-30) REVERT: G 22 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6361 (mt-10) REVERT: R 176 TRP cc_start: 0.8314 (m100) cc_final: 0.7990 (m100) REVERT: R 212 ARG cc_start: 0.7880 (mtp-110) cc_final: 0.7297 (tpt170) REVERT: R 216 ILE cc_start: 0.8548 (mt) cc_final: 0.8283 (mm) REVERT: R 219 MET cc_start: 0.8630 (tpp) cc_final: 0.7674 (mpp) REVERT: R 282 MET cc_start: 0.7987 (mtm) cc_final: 0.7084 (tpt) outliers start: 26 outliers final: 18 residues processed: 144 average time/residue: 0.4959 time to fit residues: 75.8940 Evaluate side-chains 135 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 71 optimal weight: 0.0060 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 284 GLN N 35 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.171401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136032 restraints weight = 8731.177| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.52 r_work: 0.3252 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8479 Z= 0.127 Angle : 0.551 9.183 11516 Z= 0.283 Chirality : 0.042 0.202 1306 Planarity : 0.004 0.056 1457 Dihedral : 5.775 76.510 1241 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.73 % Allowed : 22.05 % Favored : 75.23 % 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: 1.22 (0.27), residues: 1045 helix: 2.54 (0.25), residues: 415 sheet: -0.17 (0.31), residues: 226 loop : -0.41 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 128 TYR 0.013 0.001 TYR N 95 PHE 0.015 0.001 PHE A 208 TRP 0.013 0.002 TRP B 169 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8477) covalent geometry : angle 0.55082 (11512) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.29616 ( 4) hydrogen bonds : bond 0.03640 ( 458) hydrogen bonds : angle 4.77633 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 40 THR cc_start: 0.8655 (t) cc_final: 0.8445 (t) REVERT: A 289 GLU cc_start: 0.8126 (tt0) cc_final: 0.7920 (mm-30) REVERT: A 304 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7448 (mp0) REVERT: B 186 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7000 (m-30) REVERT: G 22 GLU cc_start: 0.6613 (mt-10) cc_final: 0.6397 (mt-10) REVERT: R 75 MET cc_start: 0.7383 (mmm) cc_final: 0.7136 (mmm) REVERT: R 176 TRP cc_start: 0.8295 (m100) cc_final: 0.7969 (m100) REVERT: R 212 ARG cc_start: 0.7898 (mtp-110) cc_final: 0.7297 (tpt170) REVERT: R 216 ILE cc_start: 0.8546 (mt) cc_final: 0.8279 (mm) REVERT: R 219 MET cc_start: 0.8613 (tpp) cc_final: 0.7671 (mpp) REVERT: R 282 MET cc_start: 0.7927 (mtm) cc_final: 0.7049 (tpt) outliers start: 24 outliers final: 19 residues processed: 140 average time/residue: 0.5233 time to fit residues: 78.0462 Evaluate side-chains 136 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 49 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 284 GLN B 237 ASN N 35 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.172618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.137330 restraints weight = 8748.012| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.54 r_work: 0.3314 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8479 Z= 0.124 Angle : 0.558 11.311 11516 Z= 0.285 Chirality : 0.042 0.201 1306 Planarity : 0.004 0.057 1457 Dihedral : 5.769 76.553 1241 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.61 % Allowed : 22.39 % Favored : 75.00 % 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: 1.22 (0.26), residues: 1045 helix: 2.53 (0.25), residues: 415 sheet: -0.15 (0.31), residues: 226 loop : -0.42 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 128 TYR 0.016 0.001 TYR N 95 PHE 0.013 0.001 PHE R 131 TRP 0.013 0.002 TRP B 169 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8477) covalent geometry : angle 0.55841 (11512) SS BOND : bond 0.00102 ( 2) SS BOND : angle 0.34705 ( 4) hydrogen bonds : bond 0.03595 ( 458) hydrogen bonds : angle 4.76831 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.91 seconds wall clock time: 52 minutes 16.38 seconds (3136.38 seconds total)