Starting phenix.real_space_refine on Thu Jul 2 12:45:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7trq_26101/07_2026/7trq_26101.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trq_26101/07_2026/7trq_26101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7trq_26101/07_2026/7trq_26101.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7trq_26101/07_2026/7trq_26101.cif" model { file = "/net/cci-nas-00/data/ceres_data/7trq_26101/07_2026/7trq_26101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trq_26101/07_2026/7trq_26101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7trq_26101/07_2026/7trq_26101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trq_26101/07_2026/7trq_26101.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 S 65 5.16 5 C 5558 2.51 5 N 1471 2.21 5 O 1626 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8723 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2597 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 419 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1786 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1764 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'IUI': 1, 'IXO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.79, per 1000 atoms: 0.21 Number of scatterers: 8723 At special positions: 0 Unit cell: (92.13, 121.18, 126.99, 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 65 16.00 F 3 9.00 O 1626 8.00 N 1471 7.00 C 5558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " 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: 0.55 Conformation dependent library (CDL) restraints added in 447.6 milliseconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 39.2% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 31 through 60 removed outlier: 4.184A pdb=" N ILE R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA R 36 " --> pdb=" O MET R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 65 through 84 removed outlier: 3.522A pdb=" N TYR R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 removed outlier: 3.512A pdb=" N LEU R 88 " --> pdb=" O PHE R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 136 Processing helix chain 'R' and resid 145 through 176 Proline residue: R 166 - end of helix removed outlier: 5.189A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 191 removed outlier: 3.578A pdb=" N LEU R 190 " --> pdb=" O ILE R 187 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER R 191 " --> pdb=" O GLN R 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 187 through 191' Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 206 through 223 removed outlier: 4.072A pdb=" N ARG R 223 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 426 Proline residue: R 415 - end of helix removed outlier: 3.684A pdb=" N LEU R 421 " --> pdb=" O ASN R 417 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE R 425 " --> pdb=" O LEU R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 453 removed outlier: 3.971A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 457 through 469 removed outlier: 3.566A pdb=" N LYS R 461 " --> pdb=" O ASN R 457 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU R 469 " --> pdb=" O ARG R 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.575A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.645A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 removed outlier: 4.040A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.605A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.668A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.165A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.832A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.849A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.830A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.512A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.657A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.992A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.096A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.004A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.611A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.662A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.993A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.993A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.848A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.592A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.242A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1281 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: 1.27 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1416 1.32 - 1.45: 2599 1.45 - 1.58: 4797 1.58 - 1.72: 0 1.72 - 1.85: 95 Bond restraints: 8907 Sorted by residual: bond pdb=" C10 IXO R 601 " pdb=" N11 IXO R 601 " ideal model delta sigma weight residual 1.270 1.469 -0.199 2.00e-02 2.50e+03 9.89e+01 bond pdb=" C10 IXO R 601 " pdb=" C14 IXO R 601 " ideal model delta sigma weight residual 1.492 1.324 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" C13 IXO R 601 " pdb=" O12 IXO R 601 " ideal model delta sigma weight residual 1.439 1.546 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C05 IXO R 601 " pdb=" C06 IXO R 601 " ideal model delta sigma weight residual 1.450 1.529 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C07 IXO R 601 " pdb=" C08 IXO R 601 " ideal model delta sigma weight residual 1.454 1.528 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 8902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 11698 2.05 - 4.10: 338 4.10 - 6.15: 57 6.15 - 8.20: 8 8.20 - 10.25: 1 Bond angle restraints: 12102 Sorted by residual: angle pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " pdb=" CG TYR B 105 " ideal model delta sigma weight residual 113.90 119.30 -5.40 1.80e+00 3.09e-01 9.00e+00 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.80e+00 angle pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 113.60 119.19 -5.59 1.90e+00 2.77e-01 8.66e+00 angle pdb=" CA TYR R 439 " pdb=" CB TYR R 439 " pdb=" CG TYR R 439 " ideal model delta sigma weight residual 113.90 119.20 -5.30 1.80e+00 3.09e-01 8.66e+00 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 126.55 -10.25 3.50e+00 8.16e-02 8.58e+00 ... (remaining 12097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4886 16.94 - 33.88: 297 33.88 - 50.82: 69 50.82 - 67.75: 8 67.75 - 84.69: 3 Dihedral angle restraints: 5263 sinusoidal: 1982 harmonic: 3281 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PHE A 196 " pdb=" C PHE A 196 " pdb=" N LYS A 197 " pdb=" CA LYS A 197 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE H 32 " pdb=" C PHE H 32 " pdb=" N GLY H 33 " pdb=" CA GLY H 33 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1139 0.067 - 0.134: 206 0.134 - 0.201: 40 0.201 - 0.268: 3 0.268 - 0.335: 1 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CB VAL R 444 " pdb=" CA VAL R 444 " pdb=" CG1 VAL R 444 " pdb=" CG2 VAL R 444 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1386 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N IUI R 602 " -0.005 2.00e-02 2.50e+03 3.15e-02 3.23e+01 pdb=" C IUI R 602 " -0.044 2.00e-02 2.50e+03 pdb=" C1 IUI R 602 " -0.011 2.00e-02 2.50e+03 pdb=" C16 IUI R 602 " 0.077 2.00e-02 2.50e+03 pdb=" C2 IUI R 602 " 0.005 2.00e-02 2.50e+03 pdb=" C3 IUI R 602 " -0.022 2.00e-02 2.50e+03 pdb=" C4 IUI R 602 " -0.020 2.00e-02 2.50e+03 pdb=" C5 IUI R 602 " -0.006 2.00e-02 2.50e+03 pdb=" C6 IUI R 602 " -0.000 2.00e-02 2.50e+03 pdb=" C7 IUI R 602 " 0.058 2.00e-02 2.50e+03 pdb=" N1 IUI R 602 " -0.021 2.00e-02 2.50e+03 pdb=" N3 IUI R 602 " 0.000 2.00e-02 2.50e+03 pdb=" S IUI R 602 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O IUI R 602 " -0.007 2.00e-02 2.50e+03 4.03e-02 2.03e+01 pdb=" C6 IUI R 602 " 0.039 2.00e-02 2.50e+03 pdb=" C7 IUI R 602 " -0.018 2.00e-02 2.50e+03 pdb=" C8 IUI R 602 " 0.049 2.00e-02 2.50e+03 pdb=" N2 IUI R 602 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO B 194 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.044 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2468 2.82 - 3.34: 7677 3.34 - 3.86: 14752 3.86 - 4.38: 17701 4.38 - 4.90: 30427 Nonbonded interactions: 73025 Sorted by model distance: nonbonded pdb=" O ASN R 87 " pdb=" OG1 THR R 90 " model vdw 2.295 3.040 nonbonded pdb=" OE1 GLU B 130 " pdb=" NH1 ARG B 134 " model vdw 2.345 3.120 nonbonded pdb=" O GLU R 395 " pdb=" OG1 THR R 399 " model vdw 2.350 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.359 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.364 3.040 ... (remaining 73020 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 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 : 0.006 0.199 8911 Z= 0.304 Angle : 0.831 10.254 12110 Z= 0.467 Chirality : 0.056 0.335 1389 Planarity : 0.007 0.079 1520 Dihedral : 11.792 84.693 3133 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1113 helix: -0.01 (0.23), residues: 394 sheet: 0.20 (0.29), residues: 291 loop : -0.88 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 98 TYR 0.021 0.002 TYR R 439 PHE 0.029 0.003 PHE B 199 TRP 0.019 0.002 TRP B 169 HIS 0.009 0.002 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.30 ( 8907) covalent geometry : angle 0.83132 / 0.47 (12102) SS BOND : bond 0.00241 / 0.12 ( 4) SS BOND : angle 0.93081 / 0.49 ( 8) hydrogen bonds : bond 0.13599 / 9.40 ( 453) hydrogen bonds : angle 5.83927 / 4.19 ( 1281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8133 (t-100) cc_final: 0.7748 (t-100) REVERT: R 148 MET cc_start: 0.7830 (mmt) cc_final: 0.7545 (mmt) REVERT: R 152 MET cc_start: 0.8152 (mtm) cc_final: 0.7825 (mtp) REVERT: R 400 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7533 (mtm110) REVERT: B 16 ASN cc_start: 0.9207 (m-40) cc_final: 0.8715 (m-40) REVERT: B 17 GLN cc_start: 0.9041 (tt0) cc_final: 0.8678 (tp-100) REVERT: H 73 ASP cc_start: 0.8398 (t0) cc_final: 0.8107 (t0) REVERT: H 87 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8157 (mtt180) REVERT: H 219 LEU cc_start: 0.9253 (tt) cc_final: 0.8919 (tt) REVERT: A 24 ARG cc_start: 0.7696 (ttp-110) cc_final: 0.7296 (mtm-85) REVERT: A 35 LYS cc_start: 0.8542 (mttp) cc_final: 0.8293 (mtpp) REVERT: A 197 LYS cc_start: 0.8841 (mttt) cc_final: 0.8460 (mttm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.7307 time to fit residues: 134.0494 Evaluate side-chains 132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0370 chunk 106 optimal weight: 1.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 117 ASN B 32 GLN B 75 GLN A 294 ASN A 304 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.096018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.061776 restraints weight = 15673.851| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.39 r_work: 0.2645 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8911 Z= 0.137 Angle : 0.531 6.071 12110 Z= 0.289 Chirality : 0.042 0.135 1389 Planarity : 0.004 0.043 1520 Dihedral : 5.082 34.497 1242 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.29 % Allowed : 10.23 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1113 helix: 1.62 (0.25), residues: 397 sheet: 0.55 (0.31), residues: 266 loop : -0.56 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.017 0.001 TYR H 190 PHE 0.013 0.001 PHE A 189 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8907) covalent geometry : angle 0.52887 / 0.29 (12102) SS BOND : bond 0.00458 / 0.22 ( 4) SS BOND : angle 1.71234 / 1.01 ( 8) hydrogen bonds : bond 0.04427 / 3.08 ( 453) hydrogen bonds : angle 4.36497 / 3.14 ( 1281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8272 (t-100) cc_final: 0.7852 (t-100) REVERT: R 148 MET cc_start: 0.7936 (mmt) cc_final: 0.7693 (mmt) REVERT: R 152 MET cc_start: 0.8027 (mtm) cc_final: 0.7735 (mtp) REVERT: R 400 ARG cc_start: 0.8115 (ttp-170) cc_final: 0.7769 (mtm110) REVERT: B 15 LYS cc_start: 0.9172 (mtpp) cc_final: 0.8833 (mtmt) REVERT: B 215 GLU cc_start: 0.8883 (mp0) cc_final: 0.8509 (mp0) REVERT: G 17 GLU cc_start: 0.8928 (tp30) cc_final: 0.8228 (tp30) REVERT: G 20 LYS cc_start: 0.8718 (mttm) cc_final: 0.8485 (tmtt) REVERT: G 21 MET cc_start: 0.8947 (mmm) cc_final: 0.8479 (mmm) REVERT: G 42 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: H 73 ASP cc_start: 0.8611 (t0) cc_final: 0.8228 (t0) REVERT: H 89 GLU cc_start: 0.7940 (pp20) cc_final: 0.7736 (pp20) REVERT: A 24 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7661 (ttp-170) REVERT: A 35 LYS cc_start: 0.8947 (mttp) cc_final: 0.8721 (mtpp) REVERT: A 197 LYS cc_start: 0.9129 (mttt) cc_final: 0.8815 (mttp) REVERT: A 247 MET cc_start: 0.9162 (mtp) cc_final: 0.8873 (mtm) outliers start: 12 outliers final: 3 residues processed: 151 average time/residue: 0.6102 time to fit residues: 96.5095 Evaluate side-chains 139 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 103 optimal weight: 0.0470 chunk 28 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.096916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.063170 restraints weight = 15725.956| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.36 r_work: 0.2705 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8911 Z= 0.127 Angle : 0.506 7.801 12110 Z= 0.273 Chirality : 0.041 0.132 1389 Planarity : 0.003 0.041 1520 Dihedral : 4.558 30.216 1242 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.51 % Allowed : 11.73 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.10 (0.25), residues: 1113 helix: 2.08 (0.26), residues: 399 sheet: 0.54 (0.30), residues: 269 loop : -0.35 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.014 0.001 TYR H 190 PHE 0.011 0.001 PHE B 199 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 8907) covalent geometry : angle 0.50400 / 0.27 (12102) SS BOND : bond 0.00434 / 0.21 ( 4) SS BOND : angle 1.65550 / 0.97 ( 8) hydrogen bonds : bond 0.04078 / 2.85 ( 453) hydrogen bonds : angle 4.14594 / 2.99 ( 1281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8287 (t-100) cc_final: 0.7860 (t-100) REVERT: R 121 MET cc_start: 0.8940 (mmm) cc_final: 0.8731 (mmp) REVERT: R 148 MET cc_start: 0.7985 (mmt) cc_final: 0.7700 (mmt) REVERT: R 152 MET cc_start: 0.8187 (mtm) cc_final: 0.7902 (mtp) REVERT: R 400 ARG cc_start: 0.8138 (ttp-170) cc_final: 0.7797 (mtm110) REVERT: B 15 LYS cc_start: 0.9211 (mtpp) cc_final: 0.8874 (mtmt) REVERT: B 215 GLU cc_start: 0.8881 (mp0) cc_final: 0.8552 (mp0) REVERT: G 17 GLU cc_start: 0.8905 (tp30) cc_final: 0.8072 (tp30) REVERT: G 21 MET cc_start: 0.8986 (mmm) cc_final: 0.8450 (mmm) REVERT: G 42 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: G 58 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8839 (mp0) REVERT: H 89 GLU cc_start: 0.8059 (pp20) cc_final: 0.7787 (pp20) REVERT: A 24 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7758 (ttp-170) REVERT: A 197 LYS cc_start: 0.9191 (mttt) cc_final: 0.8850 (mttp) outliers start: 14 outliers final: 6 residues processed: 148 average time/residue: 0.6168 time to fit residues: 95.6708 Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 93 optimal weight: 0.0030 chunk 15 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.060884 restraints weight = 16018.396| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.36 r_work: 0.2648 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8911 Z= 0.210 Angle : 0.557 8.127 12110 Z= 0.300 Chirality : 0.044 0.134 1389 Planarity : 0.004 0.042 1520 Dihedral : 4.697 31.012 1242 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.05 % Allowed : 12.59 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.25), residues: 1113 helix: 2.17 (0.26), residues: 402 sheet: 0.52 (0.29), residues: 291 loop : -0.20 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 214 TYR 0.013 0.001 TYR R 453 PHE 0.021 0.002 PHE R 84 TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 ( 8907) covalent geometry : angle 0.55582 / 0.30 (12102) SS BOND : bond 0.00379 / 0.19 ( 4) SS BOND : angle 1.74298 / 1.02 ( 8) hydrogen bonds : bond 0.04598 / 3.20 ( 453) hydrogen bonds : angle 4.25391 / 3.07 ( 1281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8397 (t-100) cc_final: 0.7865 (t-100) REVERT: R 148 MET cc_start: 0.7971 (mmt) cc_final: 0.7684 (mmt) REVERT: R 152 MET cc_start: 0.8209 (mtm) cc_final: 0.7942 (mtp) REVERT: R 177 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8200 (pptt) REVERT: R 400 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.7842 (mtm110) REVERT: B 215 GLU cc_start: 0.8886 (mp0) cc_final: 0.8507 (mp0) REVERT: G 17 GLU cc_start: 0.8818 (tp30) cc_final: 0.8079 (tp30) REVERT: G 20 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8378 (tptp) REVERT: G 21 MET cc_start: 0.8994 (mmm) cc_final: 0.8527 (mmm) REVERT: G 24 ASN cc_start: 0.8615 (m110) cc_final: 0.7593 (m-40) REVERT: G 42 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: H 73 ASP cc_start: 0.8552 (t0) cc_final: 0.8264 (t0) REVERT: H 89 GLU cc_start: 0.8201 (pp20) cc_final: 0.7862 (pp20) REVERT: A 24 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7760 (ttp-170) REVERT: A 197 LYS cc_start: 0.9171 (mttt) cc_final: 0.8822 (mttp) REVERT: A 234 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8740 (tt) outliers start: 19 outliers final: 9 residues processed: 142 average time/residue: 0.6174 time to fit residues: 92.0203 Evaluate side-chains 146 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.060942 restraints weight = 16010.008| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.34 r_work: 0.2646 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9165 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 0.030 8911 Z= 0.191 Angle : 0.545 7.725 12110 Z= 0.293 Chirality : 0.043 0.133 1389 Planarity : 0.004 0.042 1520 Dihedral : 4.662 30.705 1242 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.48 % Allowed : 12.49 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.26 (0.25), residues: 1113 helix: 2.25 (0.26), residues: 401 sheet: 0.51 (0.29), residues: 284 loop : -0.23 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.013 0.001 TYR H 190 PHE 0.023 0.002 PHE R 84 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 8907) covalent geometry : angle 0.54345 / 0.29 (12102) SS BOND : bond 0.00321 / 0.16 ( 4) SS BOND : angle 1.71507 / 1.00 ( 8) hydrogen bonds : bond 0.04461 / 3.11 ( 453) hydrogen bonds : angle 4.19289 / 3.02 ( 1281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8424 (t-100) cc_final: 0.7931 (t-100) REVERT: R 148 MET cc_start: 0.8006 (mmt) cc_final: 0.7802 (mmt) REVERT: R 152 MET cc_start: 0.8209 (mtm) cc_final: 0.7926 (mtp) REVERT: R 177 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8240 (pptt) REVERT: R 400 ARG cc_start: 0.8261 (ttp-170) cc_final: 0.7853 (mtm110) REVERT: B 15 LYS cc_start: 0.9203 (mtpp) cc_final: 0.8896 (mtmt) REVERT: B 215 GLU cc_start: 0.8908 (mp0) cc_final: 0.8453 (mp0) REVERT: G 17 GLU cc_start: 0.8827 (tp30) cc_final: 0.8484 (tp30) REVERT: G 20 LYS cc_start: 0.8778 (tmtt) cc_final: 0.8408 (tptt) REVERT: G 24 ASN cc_start: 0.8548 (m110) cc_final: 0.7583 (m-40) REVERT: G 58 GLU cc_start: 0.8637 (mp0) cc_final: 0.8130 (pm20) REVERT: H 73 ASP cc_start: 0.8607 (t0) cc_final: 0.8269 (t0) REVERT: H 87 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7463 (mtt-85) REVERT: H 89 GLU cc_start: 0.8227 (pp20) cc_final: 0.7863 (pp20) REVERT: A 24 ARG cc_start: 0.8290 (ttp-110) cc_final: 0.7795 (ttp-170) outliers start: 23 outliers final: 9 residues processed: 147 average time/residue: 0.6278 time to fit residues: 96.5295 Evaluate side-chains 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.095620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.062169 restraints weight = 15779.025| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.33 r_work: 0.2680 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8911 Z= 0.135 Angle : 0.522 8.533 12110 Z= 0.278 Chirality : 0.041 0.132 1389 Planarity : 0.003 0.042 1520 Dihedral : 4.469 28.232 1242 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.94 % Allowed : 13.56 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.42 (0.25), residues: 1113 helix: 2.39 (0.26), residues: 401 sheet: 0.70 (0.30), residues: 264 loop : -0.22 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.014 0.001 TYR H 190 PHE 0.024 0.001 PHE R 84 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8907) covalent geometry : angle 0.52047 / 0.28 (12102) SS BOND : bond 0.00264 / 0.13 ( 4) SS BOND : angle 1.68155 / 0.98 ( 8) hydrogen bonds : bond 0.04015 / 2.79 ( 453) hydrogen bonds : angle 4.05105 / 2.91 ( 1281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8382 (t-100) cc_final: 0.7954 (t-100) REVERT: R 148 MET cc_start: 0.8006 (mmt) cc_final: 0.7734 (mmt) REVERT: R 152 MET cc_start: 0.8238 (mtm) cc_final: 0.7946 (mtp) REVERT: R 177 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8236 (pptt) REVERT: R 396 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7653 (mtm-85) REVERT: R 400 ARG cc_start: 0.8235 (ttp-170) cc_final: 0.7835 (mtm110) REVERT: B 15 LYS cc_start: 0.9198 (mtpp) cc_final: 0.8896 (mtmt) REVERT: B 215 GLU cc_start: 0.8956 (mp0) cc_final: 0.8487 (mp0) REVERT: G 17 GLU cc_start: 0.8839 (tp30) cc_final: 0.8239 (tp30) REVERT: G 20 LYS cc_start: 0.8785 (tmtt) cc_final: 0.8329 (tptp) REVERT: G 21 MET cc_start: 0.8948 (mmm) cc_final: 0.8492 (mmm) REVERT: G 24 ASN cc_start: 0.8517 (m110) cc_final: 0.7294 (m-40) REVERT: G 58 GLU cc_start: 0.8599 (mp0) cc_final: 0.8302 (pm20) REVERT: H 73 ASP cc_start: 0.8598 (t0) cc_final: 0.8256 (t0) REVERT: H 89 GLU cc_start: 0.8218 (pp20) cc_final: 0.7873 (pp20) REVERT: A 24 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7790 (ttp-170) outliers start: 18 outliers final: 8 residues processed: 142 average time/residue: 0.6249 time to fit residues: 93.1343 Evaluate side-chains 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.095733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.062375 restraints weight = 15980.187| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.34 r_work: 0.2683 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8911 Z= 0.128 Angle : 0.517 8.304 12110 Z= 0.275 Chirality : 0.041 0.130 1389 Planarity : 0.003 0.043 1520 Dihedral : 4.374 26.830 1242 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.83 % Allowed : 13.99 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.47 (0.25), residues: 1113 helix: 2.46 (0.26), residues: 399 sheet: 0.65 (0.30), residues: 266 loop : -0.15 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.014 0.001 TYR H 190 PHE 0.023 0.001 PHE R 84 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8907) covalent geometry : angle 0.51481 / 0.27 (12102) SS BOND : bond 0.00323 / 0.16 ( 4) SS BOND : angle 1.73879 / 1.02 ( 8) hydrogen bonds : bond 0.03897 / 2.71 ( 453) hydrogen bonds : angle 3.99988 / 2.88 ( 1281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8340 (t-100) cc_final: 0.7746 (t-100) REVERT: R 148 MET cc_start: 0.8023 (mmt) cc_final: 0.7748 (mmt) REVERT: R 152 MET cc_start: 0.8232 (mtm) cc_final: 0.7928 (mtp) REVERT: R 177 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8204 (pptt) REVERT: R 400 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7819 (mtm110) REVERT: B 15 LYS cc_start: 0.9194 (mtpp) cc_final: 0.8896 (mtmt) REVERT: B 215 GLU cc_start: 0.8967 (mp0) cc_final: 0.8478 (mp0) REVERT: G 17 GLU cc_start: 0.8844 (tp30) cc_final: 0.8511 (tp30) REVERT: G 24 ASN cc_start: 0.8478 (m110) cc_final: 0.7978 (m-40) REVERT: G 58 GLU cc_start: 0.8745 (mp0) cc_final: 0.8323 (pm20) REVERT: H 76 LYS cc_start: 0.9288 (mtmm) cc_final: 0.9010 (mtmm) REVERT: H 89 GLU cc_start: 0.8240 (pp20) cc_final: 0.7887 (pp20) REVERT: A 24 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7781 (ttp-170) outliers start: 17 outliers final: 8 residues processed: 142 average time/residue: 0.6119 time to fit residues: 90.9551 Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 85 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 106 optimal weight: 0.0980 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.062290 restraints weight = 15873.891| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.31 r_work: 0.2680 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8911 Z= 0.145 Angle : 0.539 8.650 12110 Z= 0.286 Chirality : 0.042 0.130 1389 Planarity : 0.003 0.043 1520 Dihedral : 4.384 26.706 1242 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.61 % Allowed : 14.42 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.47 (0.25), residues: 1113 helix: 2.46 (0.26), residues: 401 sheet: 0.67 (0.30), residues: 266 loop : -0.17 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.013 0.001 TYR H 190 PHE 0.025 0.001 PHE R 84 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8907) covalent geometry : angle 0.53748 / 0.29 (12102) SS BOND : bond 0.00372 / 0.18 ( 4) SS BOND : angle 1.71710 / 1.01 ( 8) hydrogen bonds : bond 0.03982 / 2.75 ( 453) hydrogen bonds : angle 4.01787 / 2.89 ( 1281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8353 (t-100) cc_final: 0.7745 (t-100) REVERT: R 148 MET cc_start: 0.8016 (mmt) cc_final: 0.7742 (mmt) REVERT: R 152 MET cc_start: 0.8209 (mtm) cc_final: 0.7900 (mtp) REVERT: R 177 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8207 (pptt) REVERT: R 400 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7812 (mtm110) REVERT: B 15 LYS cc_start: 0.9202 (mtpp) cc_final: 0.8911 (mtmt) REVERT: B 172 GLU cc_start: 0.8941 (tp30) cc_final: 0.8618 (tp30) REVERT: B 215 GLU cc_start: 0.8957 (mp0) cc_final: 0.8529 (mp0) REVERT: G 17 GLU cc_start: 0.8831 (tp30) cc_final: 0.8110 (tp30) REVERT: G 21 MET cc_start: 0.8937 (mmm) cc_final: 0.8507 (mmm) REVERT: G 58 GLU cc_start: 0.8762 (mp0) cc_final: 0.8356 (pm20) REVERT: H 73 ASP cc_start: 0.8587 (t0) cc_final: 0.8299 (t0) REVERT: H 89 GLU cc_start: 0.8257 (pp20) cc_final: 0.7894 (pp20) REVERT: A 24 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7780 (ttp-170) outliers start: 15 outliers final: 8 residues processed: 139 average time/residue: 0.6723 time to fit residues: 97.9643 Evaluate side-chains 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.095447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.062298 restraints weight = 15857.330| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.32 r_work: 0.2673 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8911 Z= 0.146 Angle : 0.540 8.650 12110 Z= 0.287 Chirality : 0.042 0.130 1389 Planarity : 0.003 0.043 1520 Dihedral : 4.384 26.706 1242 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.97 % Allowed : 15.50 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.47 (0.25), residues: 1113 helix: 2.46 (0.26), residues: 401 sheet: 0.67 (0.30), residues: 266 loop : -0.17 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.013 0.001 TYR H 190 PHE 0.025 0.001 PHE R 84 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8907) covalent geometry : angle 0.53754 / 0.29 (12102) SS BOND : bond 0.01997 / 0.95 ( 4) SS BOND : angle 2.12871 / 1.20 ( 8) hydrogen bonds : bond 0.03982 / 2.75 ( 453) hydrogen bonds : angle 4.01787 / 2.89 ( 1281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8355 (t-100) cc_final: 0.7753 (t-100) REVERT: R 148 MET cc_start: 0.8018 (mmt) cc_final: 0.7746 (mmt) REVERT: R 152 MET cc_start: 0.8213 (mtm) cc_final: 0.7907 (mtp) REVERT: R 177 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8211 (pptt) REVERT: R 400 ARG cc_start: 0.8236 (ttp-170) cc_final: 0.7834 (mtm110) REVERT: B 15 LYS cc_start: 0.9211 (mtpp) cc_final: 0.8921 (mtmt) REVERT: B 172 GLU cc_start: 0.8942 (tp30) cc_final: 0.8622 (tp30) REVERT: B 215 GLU cc_start: 0.8974 (mp0) cc_final: 0.8542 (mp0) REVERT: G 17 GLU cc_start: 0.8865 (tp30) cc_final: 0.8119 (tp30) REVERT: G 21 MET cc_start: 0.8999 (mmm) cc_final: 0.8498 (mmm) REVERT: G 58 GLU cc_start: 0.8774 (mp0) cc_final: 0.8364 (pm20) REVERT: H 73 ASP cc_start: 0.8596 (t0) cc_final: 0.8317 (t0) REVERT: H 89 GLU cc_start: 0.8263 (pp20) cc_final: 0.7900 (pp20) REVERT: A 24 ARG cc_start: 0.8297 (ttp-110) cc_final: 0.7798 (ttp-170) outliers start: 9 outliers final: 8 residues processed: 136 average time/residue: 0.6604 time to fit residues: 94.1028 Evaluate side-chains 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 66 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.063972 restraints weight = 15789.024| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.32 r_work: 0.2715 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8911 Z= 0.107 Angle : 0.537 10.285 12110 Z= 0.285 Chirality : 0.041 0.130 1389 Planarity : 0.003 0.043 1520 Dihedral : 4.186 23.473 1242 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.40 % Allowed : 15.07 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.25), residues: 1113 helix: 2.49 (0.26), residues: 399 sheet: 0.61 (0.29), residues: 276 loop : -0.05 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.015 0.001 TYR H 190 PHE 0.029 0.001 PHE R 84 TRP 0.018 0.001 TRP B 169 HIS 0.003 0.000 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 8907) covalent geometry : angle 0.53600 / 0.28 (12102) SS BOND : bond 0.00239 / 0.12 ( 4) SS BOND : angle 1.62679 / 0.95 ( 8) hydrogen bonds : bond 0.03531 / 2.43 ( 453) hydrogen bonds : angle 3.87437 / 2.79 ( 1281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: R 148 MET cc_start: 0.8027 (mmt) cc_final: 0.7768 (mmt) REVERT: R 152 MET cc_start: 0.8220 (mtm) cc_final: 0.7918 (mtp) REVERT: R 177 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8207 (pptt) REVERT: R 396 ARG cc_start: 0.7568 (mmt90) cc_final: 0.7167 (mpt-90) REVERT: R 400 ARG cc_start: 0.8172 (ttp-170) cc_final: 0.7793 (mtm110) REVERT: B 215 GLU cc_start: 0.8941 (mp0) cc_final: 0.8367 (mp0) REVERT: G 17 GLU cc_start: 0.8846 (tp30) cc_final: 0.8479 (tp30) REVERT: G 20 LYS cc_start: 0.9068 (tptt) cc_final: 0.8409 (mtmt) REVERT: G 58 GLU cc_start: 0.8754 (mp0) cc_final: 0.8384 (pm20) REVERT: H 73 ASP cc_start: 0.8559 (t0) cc_final: 0.8259 (t0) REVERT: H 76 LYS cc_start: 0.9288 (mtmm) cc_final: 0.9076 (mtmm) REVERT: H 87 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7437 (mtt-85) REVERT: H 89 GLU cc_start: 0.8258 (pp20) cc_final: 0.7858 (pp20) REVERT: A 24 ARG cc_start: 0.8295 (ttp-110) cc_final: 0.7796 (ttp-170) outliers start: 13 outliers final: 6 residues processed: 142 average time/residue: 0.6681 time to fit residues: 99.4068 Evaluate side-chains 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 107 optimal weight: 0.0370 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 0.0030 chunk 16 optimal weight: 10.0000 overall best weight: 0.5470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.064407 restraints weight = 15616.395| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.33 r_work: 0.2732 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8911 Z= 0.104 Angle : 0.557 11.845 12110 Z= 0.289 Chirality : 0.040 0.126 1389 Planarity : 0.003 0.043 1520 Dihedral : 4.092 22.813 1242 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 16.47 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.62 (0.25), residues: 1113 helix: 2.52 (0.26), residues: 399 sheet: 0.69 (0.30), residues: 279 loop : 0.02 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.014 0.001 TYR H 190 PHE 0.032 0.001 PHE R 84 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 8907) covalent geometry : angle 0.55523 / 0.29 (12102) SS BOND : bond 0.00287 / 0.14 ( 4) SS BOND : angle 1.58780 / 0.93 ( 8) hydrogen bonds : bond 0.03519 / 2.39 ( 453) hydrogen bonds : angle 3.81034 / 2.74 ( 1281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.03 seconds wall clock time: 61 minutes 21.42 seconds (3681.42 seconds total)