Starting phenix.real_space_refine on Wed Sep 17 10:44:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfz_61445/09_2025/9jfz_61445.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfz_61445/09_2025/9jfz_61445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jfz_61445/09_2025/9jfz_61445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfz_61445/09_2025/9jfz_61445.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jfz_61445/09_2025/9jfz_61445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfz_61445/09_2025/9jfz_61445.map" } resolution = 2.9 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5200 2.51 5 N 1424 2.21 5 O 1522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8198 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1924 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2575 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 420 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 2324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2324 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 280} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 2.00, per 1000 atoms: 0.24 Number of scatterers: 8198 At special positions: 0 Unit cell: (93.12, 90.24, 139.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1522 8.00 N 1424 7.00 C 5200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.07 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " 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: 0.61 Conformation dependent library (CDL) restraints added in 327.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 40.0% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 4.272A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.726A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.789A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 238' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.169A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.559A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (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 34 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.756A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'R' and resid 18 through 48 removed outlier: 4.303A pdb=" N SER R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 50 through 76 removed outlier: 4.328A pdb=" N VAL R 54 " --> pdb=" O ASN R 50 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 120 removed outlier: 3.523A pdb=" N CYS R 90 " --> pdb=" O GLY R 86 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE R 95 " --> pdb=" O LYS R 91 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 150 Processing helix chain 'R' and resid 157 through 163 removed outlier: 3.557A pdb=" N TYR R 163 " --> pdb=" O ARG R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 188 Processing helix chain 'R' and resid 190 through 210 Processing helix chain 'R' and resid 215 through 254 removed outlier: 4.148A pdb=" N VAL R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 258 through 264 Processing helix chain 'R' and resid 265 through 275 Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.362A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.940A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.105A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.090A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.012A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.199A 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: 7.102A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.490A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.896A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.110A 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 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.333A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA N 92 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1143 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: 1.20 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2693 1.34 - 1.46: 1718 1.46 - 1.58: 3898 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8379 Sorted by residual: bond pdb=" N PHE R 77 " pdb=" CA PHE R 77 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.03e+00 bond pdb=" N VAL R 15 " pdb=" CA VAL R 15 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.09e-02 8.42e+03 8.91e+00 bond pdb=" N LEU R 78 " pdb=" CA LEU R 78 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.96e+00 bond pdb=" N TYR R 76 " pdb=" CA TYR R 76 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.35e-02 5.49e+03 5.26e+00 bond pdb=" N ARG R 202 " pdb=" CA ARG R 202 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.84e+00 ... (remaining 8374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 11145 2.06 - 4.13: 196 4.13 - 6.19: 24 6.19 - 8.25: 5 8.25 - 10.32: 5 Bond angle restraints: 11375 Sorted by residual: angle pdb=" C ASP R 16 " pdb=" CA ASP R 16 " pdb=" CB ASP R 16 " ideal model delta sigma weight residual 111.74 101.93 9.81 1.37e+00 5.33e-01 5.13e+01 angle pdb=" C CYS R 168 " pdb=" CA CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sigma weight residual 116.54 110.32 6.22 1.15e+00 7.56e-01 2.92e+01 angle pdb=" N LEU R 78 " pdb=" CA LEU R 78 " pdb=" C LEU R 78 " ideal model delta sigma weight residual 110.80 100.70 10.10 2.13e+00 2.20e-01 2.25e+01 angle pdb=" N VAL R 15 " pdb=" CA VAL R 15 " pdb=" C VAL R 15 " ideal model delta sigma weight residual 113.43 109.21 4.22 1.09e+00 8.42e-01 1.50e+01 angle pdb=" N TYR R 76 " pdb=" CA TYR R 76 " pdb=" C TYR R 76 " ideal model delta sigma weight residual 113.01 108.63 4.38 1.20e+00 6.94e-01 1.33e+01 ... (remaining 11370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 4283 16.40 - 32.80: 471 32.80 - 49.20: 147 49.20 - 65.60: 49 65.60 - 82.00: 8 Dihedral angle restraints: 4958 sinusoidal: 1906 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual -86.00 -154.71 68.71 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -141.79 55.79 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 39.25 53.75 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 4955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1100 0.065 - 0.129: 166 0.129 - 0.194: 4 0.194 - 0.258: 0 0.258 - 0.323: 2 Chirality restraints: 1272 Sorted by residual: chirality pdb=" CA LEU R 78 " pdb=" N LEU R 78 " pdb=" C LEU R 78 " pdb=" CB LEU R 78 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ASP R 16 " pdb=" N ASP R 16 " pdb=" C ASP R 16 " pdb=" CB ASP R 16 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA VAL R 15 " pdb=" N VAL R 15 " pdb=" C VAL R 15 " pdb=" CB VAL R 15 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 1269 not shown) Planarity restraints: 1462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " 0.101 5.00e-02 4.00e+02 1.51e-01 3.67e+01 pdb=" N PRO N 88 " -0.262 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " 0.084 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " -0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO C 53 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 48 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C GLN R 48 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN R 48 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG R 49 " 0.015 2.00e-02 2.50e+03 ... (remaining 1459 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 717 2.74 - 3.28: 7829 3.28 - 3.82: 13041 3.82 - 4.36: 14808 4.36 - 4.90: 26535 Nonbonded interactions: 62930 Sorted by model distance: nonbonded pdb=" N GLU R 157 " pdb=" OE1 GLU R 157 " model vdw 2.203 3.120 nonbonded pdb=" CG1 VAL A 247 " pdb=" OD1 ASN A 282 " model vdw 2.218 3.460 nonbonded pdb=" N GLU R 51 " pdb=" OE1 GLU R 51 " model vdw 2.228 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASN R 290 " pdb=" N ALA R 293 " model vdw 2.256 3.120 ... (remaining 62925 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: 2.070 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 0.053 8383 Z= 0.177 Angle : 0.695 13.728 11383 Z= 0.392 Chirality : 0.044 0.323 1272 Planarity : 0.007 0.151 1462 Dihedral : 16.113 81.996 2976 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.57 % Allowed : 25.72 % Favored : 73.71 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.26), residues: 1037 helix: 1.70 (0.27), residues: 393 sheet: 0.41 (0.34), residues: 223 loop : -1.58 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.020 0.002 TYR N 60 PHE 0.026 0.002 PHE R 172 TRP 0.014 0.001 TRP R 177 HIS 0.005 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8379) covalent geometry : angle 0.67271 (11375) SS BOND : bond 0.01906 ( 4) SS BOND : angle 6.55238 ( 8) hydrogen bonds : bond 0.13626 ( 395) hydrogen bonds : angle 5.30091 ( 1143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 171 time to evaluate : 0.306 Fit side-chains REVERT: A 38 ARG cc_start: 0.6629 (ttp80) cc_final: 0.6421 (tpp80) REVERT: A 209 GLU cc_start: 0.7574 (tp30) cc_final: 0.7336 (tp30) REVERT: A 273 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6876 (mtp180) REVERT: A 282 ASN cc_start: 0.7670 (m110) cc_final: 0.7338 (m110) REVERT: A 297 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7864 (mtpt) REVERT: A 368 ASP cc_start: 0.7491 (m-30) cc_final: 0.7157 (m-30) REVERT: B 59 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7780 (t80) REVERT: B 78 LYS cc_start: 0.8524 (tttp) cc_final: 0.8276 (tttt) REVERT: B 111 TYR cc_start: 0.8174 (m-80) cc_final: 0.7847 (m-80) outliers start: 5 outliers final: 4 residues processed: 174 average time/residue: 0.5720 time to fit residues: 105.5426 Evaluate side-chains 159 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 105 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.0010 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.0670 chunk 38 optimal weight: 0.0670 chunk 61 optimal weight: 0.9990 overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 176 GLN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.129144 restraints weight = 11593.734| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.08 r_work: 0.3583 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8383 Z= 0.124 Angle : 0.546 8.176 11383 Z= 0.294 Chirality : 0.041 0.142 1272 Planarity : 0.005 0.106 1462 Dihedral : 5.072 56.834 1153 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.56 % Allowed : 23.65 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.26), residues: 1037 helix: 2.05 (0.27), residues: 404 sheet: 0.33 (0.34), residues: 233 loop : -1.59 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 98 TYR 0.016 0.001 TYR R 251 PHE 0.017 0.001 PHE R 167 TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8379) covalent geometry : angle 0.54577 (11375) SS BOND : bond 0.00143 ( 4) SS BOND : angle 1.02617 ( 8) hydrogen bonds : bond 0.04623 ( 395) hydrogen bonds : angle 4.21688 ( 1143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.324 Fit side-chains REVERT: A 34 LYS cc_start: 0.7687 (ttmm) cc_final: 0.7440 (tttm) REVERT: A 36 VAL cc_start: 0.8042 (t) cc_final: 0.7815 (t) REVERT: A 38 ARG cc_start: 0.7275 (ttp80) cc_final: 0.7009 (ttp80) REVERT: A 273 ARG cc_start: 0.7491 (mtp180) cc_final: 0.7209 (mtp180) REVERT: A 368 ASP cc_start: 0.7641 (m-30) cc_final: 0.7356 (m-30) REVERT: B 136 SER cc_start: 0.7838 (t) cc_final: 0.7565 (m) REVERT: C 37 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6995 (tt) REVERT: R 225 LEU cc_start: 0.6781 (tp) cc_final: 0.6530 (tp) outliers start: 31 outliers final: 9 residues processed: 167 average time/residue: 0.5596 time to fit residues: 99.2595 Evaluate side-chains 150 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 187 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.0070 chunk 83 optimal weight: 0.1980 chunk 63 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 237 ASN B 239 ASN B 340 ASN N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128433 restraints weight = 11547.485| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.07 r_work: 0.3576 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8383 Z= 0.127 Angle : 0.539 8.973 11383 Z= 0.288 Chirality : 0.041 0.144 1272 Planarity : 0.005 0.083 1462 Dihedral : 4.538 56.127 1149 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.44 % Allowed : 24.45 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.26), residues: 1037 helix: 2.22 (0.27), residues: 404 sheet: 0.26 (0.33), residues: 242 loop : -1.64 (0.27), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.018 0.002 TYR R 268 PHE 0.015 0.002 PHE R 167 TRP 0.011 0.001 TRP B 82 HIS 0.008 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8379) covalent geometry : angle 0.53842 (11375) SS BOND : bond 0.00208 ( 4) SS BOND : angle 1.03899 ( 8) hydrogen bonds : bond 0.04633 ( 395) hydrogen bonds : angle 4.10718 ( 1143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 260 LEU cc_start: 0.8018 (mt) cc_final: 0.7686 (mt) REVERT: A 289 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6829 (tm-30) REVERT: A 368 ASP cc_start: 0.7619 (m-30) cc_final: 0.7263 (m-30) REVERT: B 136 SER cc_start: 0.7882 (t) cc_final: 0.7605 (p) REVERT: C 37 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6979 (tt) REVERT: R 16 ASP cc_start: 0.4982 (OUTLIER) cc_final: 0.4657 (p0) REVERT: R 102 TYR cc_start: 0.7943 (m-80) cc_final: 0.7601 (m-80) REVERT: R 225 LEU cc_start: 0.6844 (tp) cc_final: 0.6610 (tp) outliers start: 30 outliers final: 13 residues processed: 170 average time/residue: 0.5839 time to fit residues: 105.1514 Evaluate side-chains 159 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.0270 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 237 ASN B 239 ASN R 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.145693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127052 restraints weight = 11731.984| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.09 r_work: 0.3526 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8383 Z= 0.150 Angle : 0.563 8.236 11383 Z= 0.302 Chirality : 0.042 0.144 1272 Planarity : 0.005 0.074 1462 Dihedral : 4.654 55.127 1149 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.67 % Allowed : 25.26 % Favored : 71.07 % 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 aren not related in a simple way. whole: 0.45 (0.26), residues: 1037 helix: 2.12 (0.26), residues: 404 sheet: 0.30 (0.34), residues: 230 loop : -1.67 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.018 0.002 TYR R 102 PHE 0.016 0.002 PHE R 169 TRP 0.012 0.001 TRP B 82 HIS 0.008 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8379) covalent geometry : angle 0.56285 (11375) SS BOND : bond 0.00168 ( 4) SS BOND : angle 1.03396 ( 8) hydrogen bonds : bond 0.05061 ( 395) hydrogen bonds : angle 4.21534 ( 1143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.374 Fit side-chains REVERT: A 38 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7137 (tpp80) REVERT: A 209 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: A 260 LEU cc_start: 0.8033 (mt) cc_final: 0.7710 (mt) REVERT: A 289 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6841 (tm-30) REVERT: A 333 ASP cc_start: 0.5573 (OUTLIER) cc_final: 0.5359 (m-30) REVERT: A 368 ASP cc_start: 0.7681 (m-30) cc_final: 0.7255 (m-30) REVERT: A 371 ASP cc_start: 0.8201 (t0) cc_final: 0.7842 (t70) REVERT: B 127 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7589 (mmtt) REVERT: B 136 SER cc_start: 0.7873 (t) cc_final: 0.7606 (p) REVERT: C 37 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6995 (tt) REVERT: R 163 TYR cc_start: 0.5732 (OUTLIER) cc_final: 0.5489 (t80) REVERT: R 225 LEU cc_start: 0.6945 (tp) cc_final: 0.6712 (tp) outliers start: 32 outliers final: 14 residues processed: 169 average time/residue: 0.5776 time to fit residues: 103.5047 Evaluate side-chains 167 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 233 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 0.0030 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 367 ASN B 155 ASN B 176 GLN B 239 ASN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124886 restraints weight = 11639.367| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.07 r_work: 0.3522 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8383 Z= 0.208 Angle : 0.627 8.097 11383 Z= 0.337 Chirality : 0.045 0.149 1272 Planarity : 0.005 0.069 1462 Dihedral : 4.954 53.630 1149 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.36 % Allowed : 24.45 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 1037 helix: 1.82 (0.26), residues: 404 sheet: 0.32 (0.34), residues: 229 loop : -1.69 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.019 0.002 TYR R 102 PHE 0.021 0.002 PHE R 169 TRP 0.012 0.002 TRP B 82 HIS 0.008 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 8379) covalent geometry : angle 0.62681 (11375) SS BOND : bond 0.00217 ( 4) SS BOND : angle 1.19106 ( 8) hydrogen bonds : bond 0.06082 ( 395) hydrogen bonds : angle 4.45751 ( 1143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.315 Fit side-chains REVERT: A 209 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: A 255 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7469 (mtp180) REVERT: A 289 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6944 (tm-30) REVERT: A 333 ASP cc_start: 0.5531 (OUTLIER) cc_final: 0.5310 (m-30) REVERT: A 368 ASP cc_start: 0.7671 (m-30) cc_final: 0.7167 (m-30) REVERT: A 371 ASP cc_start: 0.8207 (t0) cc_final: 0.7915 (t70) REVERT: B 127 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7607 (mmtt) REVERT: B 136 SER cc_start: 0.7922 (t) cc_final: 0.7698 (p) REVERT: B 186 ASP cc_start: 0.7640 (m-30) cc_final: 0.7313 (m-30) REVERT: B 188 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8024 (mmp) REVERT: C 37 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7030 (tt) REVERT: R 163 TYR cc_start: 0.5807 (OUTLIER) cc_final: 0.5578 (t80) REVERT: R 225 LEU cc_start: 0.7031 (tp) cc_final: 0.6791 (tp) outliers start: 38 outliers final: 15 residues processed: 171 average time/residue: 0.6309 time to fit residues: 114.2006 Evaluate side-chains 170 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 233 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 67 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 62 optimal weight: 0.0770 chunk 40 optimal weight: 0.8980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 176 GLN B 239 ASN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.146254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.127715 restraints weight = 11579.922| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.07 r_work: 0.3553 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8383 Z= 0.127 Angle : 0.536 7.866 11383 Z= 0.289 Chirality : 0.042 0.143 1272 Planarity : 0.004 0.063 1462 Dihedral : 4.677 51.825 1149 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.67 % Allowed : 25.72 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.26), residues: 1037 helix: 2.00 (0.27), residues: 404 sheet: 0.34 (0.34), residues: 230 loop : -1.73 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.017 0.001 TYR N 60 PHE 0.015 0.001 PHE R 169 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8379) covalent geometry : angle 0.53602 (11375) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.84035 ( 8) hydrogen bonds : bond 0.04620 ( 395) hydrogen bonds : angle 4.12532 ( 1143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.313 Fit side-chains REVERT: A 34 LYS cc_start: 0.7635 (tttm) cc_final: 0.7298 (tttm) REVERT: A 36 VAL cc_start: 0.8126 (t) cc_final: 0.7899 (p) REVERT: A 38 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7274 (tpp80) REVERT: A 209 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: A 260 LEU cc_start: 0.7965 (mt) cc_final: 0.7625 (mt) REVERT: A 273 ARG cc_start: 0.7530 (mtp180) cc_final: 0.7252 (mtm110) REVERT: A 289 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6855 (tm-30) REVERT: A 368 ASP cc_start: 0.7680 (m-30) cc_final: 0.7230 (m-30) REVERT: A 378 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7948 (mt) REVERT: B 127 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7651 (mmtt) REVERT: B 136 SER cc_start: 0.7931 (t) cc_final: 0.7666 (p) REVERT: B 155 ASN cc_start: 0.7679 (t0) cc_final: 0.7119 (t0) REVERT: B 186 ASP cc_start: 0.7577 (m-30) cc_final: 0.7225 (m-30) REVERT: C 37 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7007 (tt) REVERT: R 102 TYR cc_start: 0.7973 (m-80) cc_final: 0.7582 (m-80) REVERT: R 163 TYR cc_start: 0.5715 (OUTLIER) cc_final: 0.5469 (t80) outliers start: 32 outliers final: 15 residues processed: 171 average time/residue: 0.5937 time to fit residues: 107.6703 Evaluate side-chains 166 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 187 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN B 176 GLN B 239 ASN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.144157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125625 restraints weight = 11677.616| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.07 r_work: 0.3521 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8383 Z= 0.184 Angle : 0.609 10.313 11383 Z= 0.325 Chirality : 0.044 0.147 1272 Planarity : 0.005 0.063 1462 Dihedral : 4.817 50.866 1147 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.56 % Allowed : 25.72 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.26), residues: 1037 helix: 1.84 (0.27), residues: 404 sheet: 0.36 (0.34), residues: 230 loop : -1.73 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.018 0.002 TYR R 268 PHE 0.018 0.002 PHE R 169 TRP 0.011 0.002 TRP B 82 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 8379) covalent geometry : angle 0.60883 (11375) SS BOND : bond 0.00197 ( 4) SS BOND : angle 1.07551 ( 8) hydrogen bonds : bond 0.05635 ( 395) hydrogen bonds : angle 4.31570 ( 1143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.298 Fit side-chains REVERT: A 27 GLU cc_start: 0.7554 (tp30) cc_final: 0.6831 (mp0) REVERT: A 209 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: A 260 LEU cc_start: 0.8076 (mt) cc_final: 0.7763 (mt) REVERT: A 289 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6927 (tm-30) REVERT: A 368 ASP cc_start: 0.7702 (m-30) cc_final: 0.7235 (m-30) REVERT: A 371 ASP cc_start: 0.8241 (t0) cc_final: 0.7982 (t70) REVERT: B 127 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7663 (mmtt) REVERT: B 136 SER cc_start: 0.7947 (t) cc_final: 0.7700 (p) REVERT: B 186 ASP cc_start: 0.7602 (m-30) cc_final: 0.7277 (m-30) REVERT: B 188 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8007 (mmp) REVERT: C 37 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7100 (tt) REVERT: N 83 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7287 (mtp) REVERT: R 102 TYR cc_start: 0.8041 (m-80) cc_final: 0.7508 (m-80) REVERT: R 163 TYR cc_start: 0.5914 (OUTLIER) cc_final: 0.5570 (t80) outliers start: 31 outliers final: 15 residues processed: 168 average time/residue: 0.6463 time to fit residues: 114.8054 Evaluate side-chains 169 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 239 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.144539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.126116 restraints weight = 11635.217| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.04 r_work: 0.3541 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8383 Z= 0.150 Angle : 0.570 9.422 11383 Z= 0.305 Chirality : 0.042 0.144 1272 Planarity : 0.005 0.059 1462 Dihedral : 4.736 49.973 1147 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.67 % Allowed : 25.72 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.26), residues: 1037 helix: 1.93 (0.27), residues: 404 sheet: 0.39 (0.34), residues: 230 loop : -1.71 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 337 TYR 0.017 0.002 TYR R 268 PHE 0.015 0.002 PHE R 169 TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8379) covalent geometry : angle 0.56988 (11375) SS BOND : bond 0.00155 ( 4) SS BOND : angle 0.89662 ( 8) hydrogen bonds : bond 0.05071 ( 395) hydrogen bonds : angle 4.19037 ( 1143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.324 Fit side-chains REVERT: A 27 GLU cc_start: 0.7571 (tp30) cc_final: 0.6868 (mp0) REVERT: A 36 VAL cc_start: 0.8178 (t) cc_final: 0.7976 (p) REVERT: A 209 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: A 260 LEU cc_start: 0.8065 (mt) cc_final: 0.7741 (mt) REVERT: A 273 ARG cc_start: 0.7511 (mtp180) cc_final: 0.7233 (mtm110) REVERT: A 289 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6897 (tm-30) REVERT: A 368 ASP cc_start: 0.7699 (m-30) cc_final: 0.7229 (m-30) REVERT: A 371 ASP cc_start: 0.8244 (t0) cc_final: 0.7962 (t70) REVERT: B 127 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7654 (mmtt) REVERT: B 136 SER cc_start: 0.7925 (t) cc_final: 0.7671 (p) REVERT: B 186 ASP cc_start: 0.7573 (m-30) cc_final: 0.7250 (m-30) REVERT: B 188 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8007 (mmp) REVERT: C 37 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7042 (tt) REVERT: N 83 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7288 (mtp) REVERT: R 163 TYR cc_start: 0.5794 (OUTLIER) cc_final: 0.5498 (t80) outliers start: 32 outliers final: 15 residues processed: 167 average time/residue: 0.6116 time to fit residues: 108.1778 Evaluate side-chains 168 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 0.0670 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 155 ASN B 239 ASN N 31 ASN R 85 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.145375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126802 restraints weight = 11560.887| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.07 r_work: 0.3540 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8383 Z= 0.146 Angle : 0.569 9.414 11383 Z= 0.304 Chirality : 0.042 0.144 1272 Planarity : 0.005 0.059 1462 Dihedral : 4.706 49.465 1147 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.53 % Allowed : 26.75 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.26), residues: 1037 helix: 1.99 (0.27), residues: 404 sheet: 0.31 (0.34), residues: 239 loop : -1.66 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 337 TYR 0.017 0.002 TYR R 268 PHE 0.014 0.002 PHE R 169 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8379) covalent geometry : angle 0.56909 (11375) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.90870 ( 8) hydrogen bonds : bond 0.05012 ( 395) hydrogen bonds : angle 4.17786 ( 1143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.239 Fit side-chains REVERT: A 27 GLU cc_start: 0.7574 (tp30) cc_final: 0.6878 (mp0) REVERT: A 36 VAL cc_start: 0.8152 (t) cc_final: 0.7950 (p) REVERT: A 209 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: A 260 LEU cc_start: 0.8037 (mt) cc_final: 0.7707 (mt) REVERT: A 273 ARG cc_start: 0.7514 (mtp180) cc_final: 0.7222 (mtm110) REVERT: A 289 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 337 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7242 (ttp80) REVERT: A 368 ASP cc_start: 0.7691 (m-30) cc_final: 0.7249 (m-30) REVERT: A 371 ASP cc_start: 0.8244 (t0) cc_final: 0.7933 (t70) REVERT: B 127 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7646 (mmtt) REVERT: B 136 SER cc_start: 0.7936 (t) cc_final: 0.7681 (p) REVERT: B 186 ASP cc_start: 0.7601 (m-30) cc_final: 0.7274 (m-30) REVERT: B 188 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8007 (mmp) REVERT: C 37 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7021 (tt) REVERT: N 83 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7271 (mtp) REVERT: R 163 TYR cc_start: 0.5868 (OUTLIER) cc_final: 0.5554 (t80) REVERT: R 225 LEU cc_start: 0.6998 (tp) cc_final: 0.6780 (tp) outliers start: 22 outliers final: 14 residues processed: 161 average time/residue: 0.6257 time to fit residues: 106.6514 Evaluate side-chains 170 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 163 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 91 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 49 optimal weight: 0.0070 chunk 56 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.145994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127274 restraints weight = 11628.202| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.08 r_work: 0.3547 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8383 Z= 0.136 Angle : 0.558 9.254 11383 Z= 0.298 Chirality : 0.042 0.151 1272 Planarity : 0.005 0.058 1462 Dihedral : 4.656 49.492 1147 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.30 % Allowed : 27.10 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.26), residues: 1037 helix: 2.03 (0.27), residues: 404 sheet: 0.31 (0.34), residues: 239 loop : -1.66 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.018 0.002 TYR R 268 PHE 0.012 0.001 PHE R 169 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8379) covalent geometry : angle 0.55739 (11375) SS BOND : bond 0.00123 ( 4) SS BOND : angle 0.88048 ( 8) hydrogen bonds : bond 0.04759 ( 395) hydrogen bonds : angle 4.11910 ( 1143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.272 Fit side-chains REVERT: A 27 GLU cc_start: 0.7595 (tp30) cc_final: 0.6907 (mp0) REVERT: A 36 VAL cc_start: 0.8141 (t) cc_final: 0.7916 (p) REVERT: A 209 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6452 (mp0) REVERT: A 260 LEU cc_start: 0.8014 (mt) cc_final: 0.7689 (mt) REVERT: A 273 ARG cc_start: 0.7517 (mtp180) cc_final: 0.7223 (mtm110) REVERT: A 289 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6863 (tm-30) REVERT: A 337 ARG cc_start: 0.7514 (ttp80) cc_final: 0.7310 (ttp80) REVERT: A 368 ASP cc_start: 0.7674 (m-30) cc_final: 0.7219 (m-30) REVERT: B 127 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7652 (mmtt) REVERT: B 136 SER cc_start: 0.7938 (t) cc_final: 0.7680 (p) REVERT: B 186 ASP cc_start: 0.7581 (m-30) cc_final: 0.7263 (m-30) REVERT: B 188 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8013 (mmp) REVERT: C 37 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7022 (tt) REVERT: N 83 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7257 (mtp) REVERT: R 65 LEU cc_start: 0.8254 (mt) cc_final: 0.8007 (mm) REVERT: R 163 TYR cc_start: 0.5829 (OUTLIER) cc_final: 0.5518 (t80) REVERT: R 225 LEU cc_start: 0.6993 (tp) cc_final: 0.6754 (tp) outliers start: 20 outliers final: 13 residues processed: 159 average time/residue: 0.6304 time to fit residues: 105.9325 Evaluate side-chains 168 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 163 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 239 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.143350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124886 restraints weight = 11647.116| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.06 r_work: 0.3533 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8383 Z= 0.189 Angle : 0.621 9.477 11383 Z= 0.330 Chirality : 0.044 0.174 1272 Planarity : 0.005 0.059 1462 Dihedral : 4.862 49.337 1147 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.76 % Allowed : 27.32 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.26), residues: 1037 helix: 1.81 (0.26), residues: 404 sheet: 0.42 (0.34), residues: 234 loop : -1.70 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.017 0.002 TYR R 268 PHE 0.018 0.002 PHE R 169 TRP 0.011 0.002 TRP B 82 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 8379) covalent geometry : angle 0.62080 (11375) SS BOND : bond 0.00172 ( 4) SS BOND : angle 1.02122 ( 8) hydrogen bonds : bond 0.05690 ( 395) hydrogen bonds : angle 4.33711 ( 1143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3375.48 seconds wall clock time: 58 minutes 16.51 seconds (3496.51 seconds total)