Starting phenix.real_space_refine on Tue Mar 3 21:14:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7trq_26101/03_2026/7trq_26101.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trq_26101/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7trq_26101/03_2026/7trq_26101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trq_26101/03_2026/7trq_26101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7trq_26101/03_2026/7trq_26101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trq_26101/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 1.97, per 1000 atoms: 0.23 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: 0.67 Conformation dependent library (CDL) restraints added in 324.9 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: 0.28 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: 1.41 Time building geometry restraints manager: 0.93 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: 4888 16.94 - 33.88: 299 33.88 - 50.82: 69 50.82 - 67.75: 8 67.75 - 84.69: 3 Dihedral angle restraints: 5267 sinusoidal: 1986 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 5264 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.210 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:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 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 : 11.802 84.693 3137 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 covalent geometry : bond 0.00640 ( 8907) covalent geometry : angle 0.83132 (12102) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.93081 ( 8) hydrogen bonds : bond 0.13599 ( 453) hydrogen bonds : angle 5.83927 ( 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 : 0.346 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: 0.8754 time to fit residues: 160.4844 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 : 0.290 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.096005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.061617 restraints weight = 15669.523| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.43 r_work: 0.2638 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8911 Z= 0.137 Angle : 0.538 5.884 12110 Z= 0.293 Chirality : 0.042 0.135 1389 Planarity : 0.004 0.043 1520 Dihedral : 5.253 35.759 1246 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.29 % Allowed : 10.44 % Favored : 88.27 % 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: 0.68 (0.25), residues: 1113 helix: 1.56 (0.25), residues: 397 sheet: 0.52 (0.30), residues: 279 loop : -0.57 (0.28), residues: 437 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 0.014 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 covalent geometry : bond 0.00302 ( 8907) covalent geometry : angle 0.53581 (12102) SS BOND : bond 0.00230 ( 4) SS BOND : angle 1.97867 ( 8) hydrogen bonds : bond 0.04601 ( 453) hydrogen bonds : angle 4.42293 ( 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 154 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8272 (t-100) cc_final: 0.7890 (t-100) REVERT: R 148 MET cc_start: 0.7900 (mmt) cc_final: 0.7655 (mmt) REVERT: R 152 MET cc_start: 0.7965 (mtm) cc_final: 0.7689 (mtp) REVERT: R 400 ARG cc_start: 0.8081 (ttp-170) cc_final: 0.7733 (mtm110) REVERT: B 15 LYS cc_start: 0.9160 (mtpp) cc_final: 0.8817 (mtmt) REVERT: B 172 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8560 (tp30) REVERT: B 215 GLU cc_start: 0.8837 (mp0) cc_final: 0.8486 (mp0) REVERT: G 17 GLU cc_start: 0.8898 (tp30) cc_final: 0.8646 (tp30) REVERT: G 20 LYS cc_start: 0.8702 (mttm) cc_final: 0.8459 (tmtt) REVERT: G 42 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: H 73 ASP cc_start: 0.8581 (t0) cc_final: 0.8198 (t0) REVERT: A 24 ARG cc_start: 0.8103 (ttp-110) cc_final: 0.7628 (ttp-170) REVERT: A 35 LYS cc_start: 0.8910 (mttp) cc_final: 0.8668 (mtpp) REVERT: A 197 LYS cc_start: 0.9116 (mttt) cc_final: 0.8775 (mttp) REVERT: A 247 MET cc_start: 0.9129 (mtp) cc_final: 0.8841 (mtm) outliers start: 12 outliers final: 3 residues processed: 147 average time/residue: 0.8694 time to fit residues: 133.4941 Evaluate side-chains 138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 9.9990 chunk 15 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.059054 restraints weight = 15527.629| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.37 r_work: 0.2582 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 8911 Z= 0.241 Angle : 0.585 7.885 12110 Z= 0.315 Chirality : 0.045 0.137 1389 Planarity : 0.004 0.042 1520 Dihedral : 5.038 34.290 1246 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.61 % Allowed : 11.95 % Favored : 86.44 % 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: 1.03 (0.25), residues: 1113 helix: 1.92 (0.26), residues: 396 sheet: 0.53 (0.29), residues: 290 loop : -0.32 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 38 TYR 0.016 0.001 TYR R 453 PHE 0.015 0.002 PHE B 151 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 8907) covalent geometry : angle 0.58311 (12102) SS BOND : bond 0.00314 ( 4) SS BOND : angle 1.83096 ( 8) hydrogen bonds : bond 0.04976 ( 453) hydrogen bonds : angle 4.44399 ( 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 152 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8361 (t-100) cc_final: 0.7906 (t-100) REVERT: R 148 MET cc_start: 0.7884 (mmt) cc_final: 0.7602 (mmt) REVERT: R 152 MET cc_start: 0.7988 (mtm) cc_final: 0.7719 (mtp) REVERT: R 400 ARG cc_start: 0.8118 (ttp-170) cc_final: 0.7739 (mtm110) REVERT: B 15 LYS cc_start: 0.9165 (mtpp) cc_final: 0.8816 (mtmt) REVERT: B 19 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8244 (ttp80) REVERT: B 215 GLU cc_start: 0.8826 (mp0) cc_final: 0.8440 (mp0) REVERT: G 17 GLU cc_start: 0.8930 (tp30) cc_final: 0.8193 (tp30) REVERT: G 20 LYS cc_start: 0.8738 (mttm) cc_final: 0.8495 (tmtt) REVERT: G 21 MET cc_start: 0.8999 (mmm) cc_final: 0.8468 (mmm) REVERT: G 42 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: G 58 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8779 (mp0) REVERT: H 220 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 24 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7667 (ttp-170) REVERT: A 35 LYS cc_start: 0.9017 (mttp) cc_final: 0.8751 (mtpp) REVERT: A 197 LYS cc_start: 0.9155 (mttt) cc_final: 0.8789 (mttp) REVERT: A 234 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8688 (tt) outliers start: 15 outliers final: 6 residues processed: 145 average time/residue: 0.8220 time to fit residues: 124.7468 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 : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 chunk 85 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 chunk 73 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.059181 restraints weight = 15751.435| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.37 r_work: 0.2583 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 8911 Z= 0.254 Angle : 0.591 7.891 12110 Z= 0.318 Chirality : 0.045 0.137 1389 Planarity : 0.004 0.042 1520 Dihedral : 5.038 34.290 1246 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.86 % Allowed : 13.35 % Favored : 85.79 % 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: 1.03 (0.25), residues: 1113 helix: 1.92 (0.26), residues: 396 sheet: 0.53 (0.29), residues: 290 loop : -0.32 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 38 TYR 0.016 0.001 TYR R 453 PHE 0.015 0.002 PHE B 151 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 8907) covalent geometry : angle 0.58329 (12102) SS BOND : bond 0.07396 ( 4) SS BOND : angle 3.74184 ( 8) hydrogen bonds : bond 0.04976 ( 453) hydrogen bonds : angle 4.44399 ( 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 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8364 (t-100) cc_final: 0.7912 (t-100) REVERT: R 148 MET cc_start: 0.7888 (mmt) cc_final: 0.7605 (mmt) REVERT: R 152 MET cc_start: 0.7995 (mtm) cc_final: 0.7724 (mtp) REVERT: R 400 ARG cc_start: 0.8134 (ttp-170) cc_final: 0.7743 (mtm110) REVERT: B 15 LYS cc_start: 0.9166 (mtpp) cc_final: 0.8824 (mtmt) REVERT: B 215 GLU cc_start: 0.8835 (mp0) cc_final: 0.8440 (mp0) REVERT: G 17 GLU cc_start: 0.8928 (tp30) cc_final: 0.8187 (tp30) REVERT: G 20 LYS cc_start: 0.8732 (mttm) cc_final: 0.8498 (tmtt) REVERT: G 21 MET cc_start: 0.8988 (mmm) cc_final: 0.8459 (mmm) REVERT: G 42 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: G 58 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8776 (mp0) REVERT: A 24 ARG cc_start: 0.8171 (ttp-110) cc_final: 0.7658 (ttp-170) REVERT: A 35 LYS cc_start: 0.9018 (mttp) cc_final: 0.8753 (mtpp) REVERT: A 197 LYS cc_start: 0.9159 (mttt) cc_final: 0.8789 (mttp) REVERT: A 234 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8687 (tt) outliers start: 8 outliers final: 6 residues processed: 137 average time/residue: 0.8547 time to fit residues: 122.4662 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 : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 48 THR 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: 0.1980 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.093641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.059193 restraints weight = 15718.366| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.37 r_work: 0.2582 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 8911 Z= 0.254 Angle : 0.591 7.891 12110 Z= 0.318 Chirality : 0.045 0.137 1389 Planarity : 0.004 0.042 1520 Dihedral : 5.038 34.290 1246 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.86 % Allowed : 13.46 % Favored : 85.68 % 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: 1.03 (0.25), residues: 1113 helix: 1.92 (0.26), residues: 396 sheet: 0.53 (0.29), residues: 290 loop : -0.32 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 38 TYR 0.016 0.001 TYR R 453 PHE 0.015 0.002 PHE B 151 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 8907) covalent geometry : angle 0.58329 (12102) SS BOND : bond 0.07396 ( 4) SS BOND : angle 3.74184 ( 8) hydrogen bonds : bond 0.04976 ( 453) hydrogen bonds : angle 4.44399 ( 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 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8363 (t-100) cc_final: 0.7910 (t-100) REVERT: R 148 MET cc_start: 0.7890 (mmt) cc_final: 0.7607 (mmt) REVERT: R 152 MET cc_start: 0.7991 (mtm) cc_final: 0.7720 (mtp) REVERT: R 400 ARG cc_start: 0.8137 (ttp-170) cc_final: 0.7745 (mtm110) REVERT: B 15 LYS cc_start: 0.9164 (mtpp) cc_final: 0.8821 (mtmt) REVERT: B 215 GLU cc_start: 0.8834 (mp0) cc_final: 0.8438 (mp0) REVERT: G 17 GLU cc_start: 0.8930 (tp30) cc_final: 0.8190 (tp30) REVERT: G 20 LYS cc_start: 0.8736 (mttm) cc_final: 0.8501 (tmtt) REVERT: G 21 MET cc_start: 0.8992 (mmm) cc_final: 0.8465 (mmm) REVERT: G 42 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: G 58 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8780 (mp0) REVERT: A 24 ARG cc_start: 0.8173 (ttp-110) cc_final: 0.7660 (ttp-170) REVERT: A 35 LYS cc_start: 0.9017 (mttp) cc_final: 0.8751 (mtpp) REVERT: A 197 LYS cc_start: 0.9158 (mttt) cc_final: 0.8788 (mttp) REVERT: A 234 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8687 (tt) outliers start: 8 outliers final: 6 residues processed: 137 average time/residue: 0.8309 time to fit residues: 119.0566 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 : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.093641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.059221 restraints weight = 15544.948| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.36 r_work: 0.2583 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 8911 Z= 0.254 Angle : 0.591 7.891 12110 Z= 0.318 Chirality : 0.045 0.137 1389 Planarity : 0.004 0.042 1520 Dihedral : 5.038 34.290 1246 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.86 % Allowed : 13.46 % Favored : 85.68 % 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: 1.03 (0.25), residues: 1113 helix: 1.92 (0.26), residues: 396 sheet: 0.53 (0.29), residues: 290 loop : -0.32 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 38 TYR 0.016 0.001 TYR R 453 PHE 0.015 0.002 PHE B 151 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 8907) covalent geometry : angle 0.58329 (12102) SS BOND : bond 0.07396 ( 4) SS BOND : angle 3.74184 ( 8) hydrogen bonds : bond 0.04976 ( 453) hydrogen bonds : angle 4.44399 ( 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 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8362 (t-100) cc_final: 0.7910 (t-100) REVERT: R 148 MET cc_start: 0.7890 (mmt) cc_final: 0.7607 (mmt) REVERT: R 152 MET cc_start: 0.7994 (mtm) cc_final: 0.7723 (mtp) REVERT: R 400 ARG cc_start: 0.8136 (ttp-170) cc_final: 0.7744 (mtm110) REVERT: B 15 LYS cc_start: 0.9167 (mtpp) cc_final: 0.8825 (mtmt) REVERT: B 215 GLU cc_start: 0.8836 (mp0) cc_final: 0.8440 (mp0) REVERT: G 17 GLU cc_start: 0.8930 (tp30) cc_final: 0.8191 (tp30) REVERT: G 20 LYS cc_start: 0.8739 (mttm) cc_final: 0.8504 (tmtt) REVERT: G 21 MET cc_start: 0.8992 (mmm) cc_final: 0.8466 (mmm) REVERT: G 42 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: G 58 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8778 (mp0) REVERT: A 24 ARG cc_start: 0.8172 (ttp-110) cc_final: 0.7659 (ttp-170) REVERT: A 35 LYS cc_start: 0.9016 (mttp) cc_final: 0.8750 (mtpp) REVERT: A 197 LYS cc_start: 0.9157 (mttt) cc_final: 0.8787 (mttp) REVERT: A 234 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8689 (tt) outliers start: 8 outliers final: 6 residues processed: 137 average time/residue: 0.8147 time to fit residues: 116.6310 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 : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.095079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.060741 restraints weight = 15634.709| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.40 r_work: 0.2618 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8911 Z= 0.128 Angle : 0.550 9.767 12110 Z= 0.293 Chirality : 0.042 0.132 1389 Planarity : 0.004 0.041 1520 Dihedral : 4.815 31.813 1246 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.40 % Allowed : 13.02 % Favored : 85.58 % 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: 1.18 (0.25), residues: 1113 helix: 2.19 (0.26), residues: 396 sheet: 0.54 (0.30), residues: 277 loop : -0.32 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.017 0.001 TYR H 190 PHE 0.029 0.001 PHE R 84 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8907) covalent geometry : angle 0.54835 (12102) SS BOND : bond 0.00274 ( 4) SS BOND : angle 1.64249 ( 8) hydrogen bonds : bond 0.04239 ( 453) hydrogen bonds : angle 4.25337 ( 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 147 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8310 (t-100) cc_final: 0.7806 (t-100) REVERT: R 121 MET cc_start: 0.8764 (mmm) cc_final: 0.8556 (mmp) REVERT: R 148 MET cc_start: 0.7843 (mmt) cc_final: 0.7552 (mmt) REVERT: R 152 MET cc_start: 0.7946 (mtm) cc_final: 0.7646 (mtp) REVERT: R 400 ARG cc_start: 0.8099 (ttp-170) cc_final: 0.7721 (mtm110) REVERT: B 15 LYS cc_start: 0.9161 (mtpp) cc_final: 0.8802 (mtmt) REVERT: B 215 GLU cc_start: 0.8867 (mp0) cc_final: 0.8433 (mp0) REVERT: G 17 GLU cc_start: 0.8907 (tp30) cc_final: 0.8529 (tp30) REVERT: G 20 LYS cc_start: 0.8697 (mttm) cc_final: 0.8470 (tmtt) REVERT: G 42 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: G 57 SER cc_start: 0.9249 (p) cc_final: 0.9030 (p) REVERT: G 58 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8783 (mp0) REVERT: H 73 ASP cc_start: 0.8521 (t0) cc_final: 0.8178 (t0) REVERT: H 76 LYS cc_start: 0.9272 (mtmm) cc_final: 0.9026 (mtmm) REVERT: A 24 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7616 (ttp-170) REVERT: A 35 LYS cc_start: 0.8924 (mttp) cc_final: 0.8668 (mtpp) REVERT: A 197 LYS cc_start: 0.9131 (mttt) cc_final: 0.8754 (mttp) outliers start: 13 outliers final: 6 residues processed: 139 average time/residue: 0.8450 time to fit residues: 122.5932 Evaluate side-chains 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS 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 A residue 33 GLU 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: 4.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.060841 restraints weight = 15538.157| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.40 r_work: 0.2617 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8911 Z= 0.133 Angle : 0.552 9.768 12110 Z= 0.294 Chirality : 0.042 0.132 1389 Planarity : 0.004 0.041 1520 Dihedral : 4.822 31.813 1246 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.75 % Allowed : 13.46 % Favored : 85.79 % 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: 1.18 (0.25), residues: 1113 helix: 2.19 (0.26), residues: 396 sheet: 0.54 (0.30), residues: 277 loop : -0.32 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.017 0.001 TYR H 190 PHE 0.029 0.001 PHE R 84 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8907) covalent geometry : angle 0.54838 (12102) SS BOND : bond 0.03176 ( 4) SS BOND : angle 2.37422 ( 8) hydrogen bonds : bond 0.04240 ( 453) hydrogen bonds : angle 4.25337 ( 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 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8313 (t-100) cc_final: 0.7810 (t-100) REVERT: R 121 MET cc_start: 0.8777 (mmm) cc_final: 0.8570 (mmp) REVERT: R 148 MET cc_start: 0.7842 (mmt) cc_final: 0.7554 (mmt) REVERT: R 152 MET cc_start: 0.7945 (mtm) cc_final: 0.7646 (mtp) REVERT: R 400 ARG cc_start: 0.8099 (ttp-170) cc_final: 0.7722 (mtm110) REVERT: B 15 LYS cc_start: 0.9166 (mtpp) cc_final: 0.8807 (mtmt) REVERT: B 215 GLU cc_start: 0.8883 (mp0) cc_final: 0.8442 (mp0) REVERT: G 17 GLU cc_start: 0.8903 (tp30) cc_final: 0.8524 (tp30) REVERT: G 20 LYS cc_start: 0.8702 (mttm) cc_final: 0.8473 (tmtt) REVERT: G 42 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: G 57 SER cc_start: 0.9250 (p) cc_final: 0.9031 (p) REVERT: G 58 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8780 (mp0) REVERT: H 73 ASP cc_start: 0.8522 (t0) cc_final: 0.8178 (t0) REVERT: H 76 LYS cc_start: 0.9272 (mtmm) cc_final: 0.9026 (mtmm) REVERT: A 24 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7617 (ttp-170) REVERT: A 35 LYS cc_start: 0.8920 (mttp) cc_final: 0.8662 (mtpp) REVERT: A 197 LYS cc_start: 0.9134 (mttt) cc_final: 0.8757 (mttp) outliers start: 7 outliers final: 6 residues processed: 137 average time/residue: 0.7870 time to fit residues: 112.6605 Evaluate side-chains 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS 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 A residue 33 GLU 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: 2.9990 chunk 101 optimal weight: 0.0570 chunk 27 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.060867 restraints weight = 15512.150| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.39 r_work: 0.2620 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8911 Z= 0.133 Angle : 0.551 9.769 12110 Z= 0.293 Chirality : 0.042 0.132 1389 Planarity : 0.004 0.041 1520 Dihedral : 4.907 41.431 1246 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.75 % Allowed : 13.46 % Favored : 85.79 % 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: 1.18 (0.25), residues: 1113 helix: 2.19 (0.26), residues: 396 sheet: 0.54 (0.30), residues: 277 loop : -0.32 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.017 0.001 TYR H 190 PHE 0.028 0.001 PHE R 84 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8907) covalent geometry : angle 0.54791 (12102) SS BOND : bond 0.03091 ( 4) SS BOND : angle 2.37296 ( 8) hydrogen bonds : bond 0.04240 ( 453) hydrogen bonds : angle 4.25339 ( 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 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8312 (t-100) cc_final: 0.7808 (t-100) REVERT: R 121 MET cc_start: 0.8773 (mmm) cc_final: 0.8565 (mmp) REVERT: R 148 MET cc_start: 0.7841 (mmt) cc_final: 0.7553 (mmt) REVERT: R 152 MET cc_start: 0.7941 (mtm) cc_final: 0.7643 (mtp) REVERT: R 400 ARG cc_start: 0.8101 (ttp-170) cc_final: 0.7725 (mtm110) REVERT: B 15 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8804 (mtmt) REVERT: B 215 GLU cc_start: 0.8884 (mp0) cc_final: 0.8443 (mp0) REVERT: G 17 GLU cc_start: 0.8904 (tp30) cc_final: 0.8526 (tp30) REVERT: G 20 LYS cc_start: 0.8701 (mttm) cc_final: 0.8471 (tmtt) REVERT: G 42 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: G 57 SER cc_start: 0.9251 (p) cc_final: 0.9032 (p) REVERT: G 58 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8782 (mp0) REVERT: H 73 ASP cc_start: 0.8523 (t0) cc_final: 0.8181 (t0) REVERT: H 76 LYS cc_start: 0.9273 (mtmm) cc_final: 0.9027 (mtmm) REVERT: A 24 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7614 (ttp-170) REVERT: A 35 LYS cc_start: 0.8921 (mttp) cc_final: 0.8663 (mtpp) REVERT: A 197 LYS cc_start: 0.9133 (mttt) cc_final: 0.8755 (mttp) outliers start: 7 outliers final: 6 residues processed: 137 average time/residue: 0.8645 time to fit residues: 123.8462 Evaluate side-chains 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS 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 A residue 33 GLU 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: 0.1980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.064261 restraints weight = 15808.634| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.33 r_work: 0.2725 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8911 Z= 0.111 Angle : 0.544 12.356 12110 Z= 0.286 Chirality : 0.041 0.130 1389 Planarity : 0.003 0.041 1520 Dihedral : 4.328 26.602 1246 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.86 % Allowed : 13.46 % Favored : 85.68 % 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: 1.30 (0.25), residues: 1113 helix: 2.21 (0.26), residues: 400 sheet: 0.66 (0.30), residues: 269 loop : -0.21 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.017 0.001 TYR H 190 PHE 0.036 0.001 PHE R 84 TRP 0.019 0.001 TRP B 169 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8907) covalent geometry : angle 0.54182 (12102) SS BOND : bond 0.00354 ( 4) SS BOND : angle 1.76243 ( 8) hydrogen bonds : bond 0.03681 ( 453) hydrogen bonds : angle 4.02115 ( 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 152 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8310 (t-100) cc_final: 0.7764 (t-100) REVERT: R 148 MET cc_start: 0.7983 (mmt) cc_final: 0.7713 (mmt) REVERT: R 152 MET cc_start: 0.8183 (mtm) cc_final: 0.7921 (mtp) REVERT: R 400 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7819 (mtm110) REVERT: B 215 GLU cc_start: 0.8873 (mp0) cc_final: 0.8522 (mp0) REVERT: G 17 GLU cc_start: 0.8890 (tp30) cc_final: 0.8445 (tp30) REVERT: H 73 ASP cc_start: 0.8549 (t0) cc_final: 0.8238 (t0) REVERT: A 24 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7768 (ttp-170) REVERT: A 197 LYS cc_start: 0.9146 (mttt) cc_final: 0.8807 (mttp) outliers start: 8 outliers final: 5 residues processed: 146 average time/residue: 0.7690 time to fit residues: 117.3631 Evaluate side-chains 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 33 GLU 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: 5.9990 chunk 56 optimal weight: 0.8980 chunk 93 optimal weight: 0.0670 chunk 45 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.0370 chunk 98 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.064258 restraints weight = 15587.884| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.31 r_work: 0.2723 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8911 Z= 0.112 Angle : 0.562 9.359 12110 Z= 0.294 Chirality : 0.041 0.130 1389 Planarity : 0.003 0.041 1520 Dihedral : 4.312 26.118 1246 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.86 % Allowed : 14.53 % Favored : 84.61 % 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: 1.32 (0.25), residues: 1113 helix: 2.25 (0.26), residues: 400 sheet: 0.68 (0.30), residues: 269 loop : -0.23 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.017 0.001 TYR H 190 PHE 0.037 0.001 PHE R 84 TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8907) covalent geometry : angle 0.56035 (12102) SS BOND : bond 0.00217 ( 4) SS BOND : angle 1.70027 ( 8) hydrogen bonds : bond 0.03660 ( 453) hydrogen bonds : angle 4.01236 ( 1281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4467.92 seconds wall clock time: 76 minutes 31.59 seconds (4591.59 seconds total)