Starting phenix.real_space_refine on Fri Sep 11 08:15:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eja_31157/09_2026/7eja_31157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eja_31157/09_2026/7eja_31157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eja_31157/09_2026/7eja_31157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eja_31157/09_2026/7eja_31157.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7eja_31157/09_2026/7eja_31157.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eja_31157/09_2026/7eja_31157.cif" model { file = "/net/cci-nas-00/data/ceres_data/7eja_31157/09_2026/7eja_31157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eja_31157/09_2026/7eja_31157.cif" } resolution = 3.6 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= -0.007 sd= 0.192 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5487 2.51 5 N 1458 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8584 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1632 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 198} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2541 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2193 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1785 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CZX': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 1.55, per 1000 atoms: 0.18 Number of scatterers: 8584 At special positions: 0 Unit cell: (88.4, 120.7, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1581 8.00 N 1458 7.00 C 5487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 372.7 milliseconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 34.7% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.682A pdb=" N ARG A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.207A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 4.170A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 245 through 256 removed outlier: 4.213A pdb=" N MET A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.100A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 329 through 350 removed outlier: 4.482A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.591A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.802A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'R' and resid 47 through 74 Processing helix chain 'R' and resid 83 through 108 removed outlier: 4.473A pdb=" N LEU R 87 " --> pdb=" O GLN R 83 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 120 through 151 Processing helix chain 'R' and resid 152 through 157 Processing helix chain 'R' and resid 158 through 160 No H-bonds generated for 'chain 'R' and resid 158 through 160' Processing helix chain 'R' and resid 161 through 181 Processing helix chain 'R' and resid 208 through 242 removed outlier: 3.683A pdb=" N ILE R 213 " --> pdb=" O LYS R 209 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER R 214 " --> pdb=" O TRP R 210 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ALA R 222 " --> pdb=" O GLY R 218 " (cutoff:3.500A) Proline residue: R 223 - end of helix Processing helix chain 'R' and resid 376 through 411 removed outlier: 3.698A pdb=" N ASN R 382 " --> pdb=" O ARG R 378 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE R 398 " --> pdb=" O VAL R 394 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL R 399 " --> pdb=" O ILE R 395 " (cutoff:3.500A) Proline residue: R 404 - end of helix Processing helix chain 'R' and resid 422 through 443 removed outlier: 3.775A pdb=" N GLY R 430 " --> pdb=" O PHE R 426 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR R 431 " --> pdb=" O PHE R 427 " (cutoff:3.500A) Proline residue: R 438 - end of helix removed outlier: 3.543A pdb=" N TYR R 441 " --> pdb=" O ASN R 437 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 457 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.762A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.862A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 201 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.967A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.931A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.306A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.615A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.679A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.599A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.804A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.464A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.847A pdb=" N GLU H 234 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU H 162 " --> pdb=" O TYR H 178 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR H 178 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU H 176 " --> pdb=" O TRP H 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 143 through 148 removed outlier: 3.952A pdb=" N PHE H 200 " --> pdb=" O CYS H 147 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1035 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: 1.25 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 - 1.31: 1385 1.31 - 1.44: 2457 1.44 - 1.56: 4847 1.56 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8768 Sorted by residual: bond pdb=" N ILE R 123 " pdb=" CA ILE R 123 " ideal model delta sigma weight residual 1.461 1.396 0.065 1.17e-02 7.31e+03 3.07e+01 bond pdb=" N ASN A 346 " pdb=" CA ASN A 346 " ideal model delta sigma weight residual 1.459 1.400 0.060 1.20e-02 6.94e+03 2.47e+01 bond pdb=" CA TYR R 156 " pdb=" C TYR R 156 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.29e-02 6.01e+03 2.45e+01 bond pdb=" CA ASN A 346 " pdb=" C ASN A 346 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.26e-02 6.30e+03 2.30e+01 bond pdb=" N PRO R 438 " pdb=" CD PRO R 438 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.22e+01 ... (remaining 8763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 11697 2.88 - 5.76: 148 5.76 - 8.64: 27 8.64 - 11.53: 6 11.53 - 14.41: 3 Bond angle restraints: 11881 Sorted by residual: angle pdb=" N ARG R 378 " pdb=" CA ARG R 378 " pdb=" C ARG R 378 " ideal model delta sigma weight residual 111.28 121.19 -9.91 1.09e+00 8.42e-01 8.27e+01 angle pdb=" N LYS A 211 " pdb=" CA LYS A 211 " pdb=" C LYS A 211 " ideal model delta sigma weight residual 111.14 119.75 -8.61 1.08e+00 8.57e-01 6.36e+01 angle pdb=" N HIS A 214 " pdb=" CA HIS A 214 " pdb=" C HIS A 214 " ideal model delta sigma weight residual 111.28 119.83 -8.55 1.09e+00 8.42e-01 6.16e+01 angle pdb=" N LYS R 159 " pdb=" CA LYS R 159 " pdb=" C LYS R 159 " ideal model delta sigma weight residual 113.15 122.41 -9.26 1.19e+00 7.06e-01 6.06e+01 angle pdb=" N CYS R 121 " pdb=" CA CYS R 121 " pdb=" C CYS R 121 " ideal model delta sigma weight residual 112.90 103.56 9.34 1.31e+00 5.83e-01 5.08e+01 ... (remaining 11876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4741 17.69 - 35.39: 349 35.39 - 53.08: 70 53.08 - 70.78: 7 70.78 - 88.47: 7 Dihedral angle restraints: 5174 sinusoidal: 1996 harmonic: 3178 Sorted by residual: dihedral pdb=" N ILE R 123 " pdb=" C ILE R 123 " pdb=" CA ILE R 123 " pdb=" CB ILE R 123 " ideal model delta harmonic sigma weight residual 123.40 109.48 13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" C PHE A 216 " pdb=" N PHE A 216 " pdb=" CA PHE A 216 " pdb=" CB PHE A 216 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" CA ILE G 25 " pdb=" C ILE G 25 " pdb=" N ASP G 26 " pdb=" CA ASP G 26 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 5171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1292 0.110 - 0.219: 39 0.219 - 0.329: 12 0.329 - 0.438: 4 0.438 - 0.548: 2 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA PHE A 216 " pdb=" N PHE A 216 " pdb=" C PHE A 216 " pdb=" CB PHE A 216 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" CA GLU A 217 " pdb=" N GLU A 217 " pdb=" C GLU A 217 " pdb=" CB GLU A 217 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA LYS R 159 " pdb=" N LYS R 159 " pdb=" C LYS R 159 " pdb=" CB LYS R 159 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 1346 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 161 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO R 162 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 162 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 162 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 183 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C THR A 183 " -0.034 2.00e-02 2.50e+03 pdb=" O THR A 183 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 184 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 282 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A 283 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.026 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 68 2.49 - 3.10: 6396 3.10 - 3.70: 13194 3.70 - 4.30: 17548 4.30 - 4.90: 28824 Nonbonded interactions: 66030 Sorted by model distance: nonbonded pdb=" OE1 GLN R 83 " pdb=" NH2 ARG R 160 " model vdw 1.893 3.120 nonbonded pdb=" O PHE A 224 " pdb=" N PHE A 268 " model vdw 1.959 3.120 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.175 3.040 nonbonded pdb=" OG SER H 192 " pdb=" OG1 THR H 203 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.224 3.040 ... (remaining 66025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.090 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.005 0.103 8772 Z= 0.305 Angle : 0.850 14.408 11887 Z= 0.537 Chirality : 0.059 0.548 1349 Planarity : 0.004 0.055 1496 Dihedral : 13.050 88.469 3113 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.11 % Allowed : 0.75 % Favored : 99.14 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.43 (0.26), residues: 1075 helix: 1.20 (0.28), residues: 341 sheet: -0.37 (0.33), residues: 263 loop : -1.32 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 202 TYR 0.013 0.001 TYR R 156 PHE 0.022 0.001 PHE R 398 TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.28 ( 8768) covalent geometry : angle 0.84981 / 0.54 (11881) SS BOND : bond 0.00262 / 0.13 ( 3) SS BOND : angle 0.57853 / 0.22 ( 6) hydrogen bonds : bond 0.17853 / 12.34 ( 361) hydrogen bonds : angle 7.31004 / 4.97 ( 1035) Misc. bond : bond 0.10299 / 5.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8705 (mmm-85) REVERT: B 36 ASN cc_start: 0.8672 (m-40) cc_final: 0.8362 (p0) REVERT: B 255 LEU cc_start: 0.9382 (pt) cc_final: 0.9117 (mm) REVERT: B 261 LEU cc_start: 0.9371 (mt) cc_final: 0.9168 (mt) REVERT: B 280 LYS cc_start: 0.9349 (tptp) cc_final: 0.9026 (tptp) REVERT: B 292 PHE cc_start: 0.7801 (m-10) cc_final: 0.7482 (m-10) REVERT: G 21 MET cc_start: 0.8107 (mmp) cc_final: 0.7294 (mtm) REVERT: G 32 LYS cc_start: 0.9511 (ptpp) cc_final: 0.9293 (ptmm) REVERT: G 42 GLU cc_start: 0.8135 (tp30) cc_final: 0.7530 (mt-10) REVERT: G 58 GLU cc_start: 0.8998 (mp0) cc_final: 0.8428 (mp0) REVERT: R 53 CYS cc_start: 0.9179 (m) cc_final: 0.8880 (p) REVERT: R 57 LEU cc_start: 0.9416 (tp) cc_final: 0.9184 (tp) REVERT: R 109 GLU cc_start: 0.8887 (tp30) cc_final: 0.8314 (tm-30) REVERT: R 450 ARG cc_start: 0.9489 (mtm110) cc_final: 0.9217 (mtm-85) REVERT: H 46 GLU cc_start: 0.8579 (pt0) cc_final: 0.8189 (pm20) REVERT: H 90 ASP cc_start: 0.8059 (m-30) cc_final: 0.7532 (m-30) REVERT: H 137 VAL cc_start: 0.7359 (m) cc_final: 0.7129 (m) REVERT: H 180 MET cc_start: 0.8772 (ppp) cc_final: 0.8274 (ppp) REVERT: H 210 GLU cc_start: 0.8971 (mp0) cc_final: 0.8577 (mp0) REVERT: H 211 ASP cc_start: 0.7848 (m-30) cc_final: 0.7330 (m-30) REVERT: H 218 MET cc_start: 0.8712 (tmm) cc_final: 0.8146 (tmm) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.1001 time to fit residues: 31.1672 Evaluate side-chains 152 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 256 ASN A 333 GLN B 266 HIS ** R 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 433 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.091204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.066888 restraints weight = 31853.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068915 restraints weight = 17290.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070282 restraints weight = 11862.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071162 restraints weight = 9307.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.071634 restraints weight = 8017.435| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8772 Z= 0.206 Angle : 0.734 10.284 11887 Z= 0.383 Chirality : 0.046 0.183 1349 Planarity : 0.004 0.054 1496 Dihedral : 4.668 19.728 1185 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.15 % Allowed : 12.90 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.33 (0.26), residues: 1075 helix: 1.36 (0.28), residues: 341 sheet: -0.39 (0.32), residues: 275 loop : -1.31 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 168 TYR 0.026 0.002 TYR R 156 PHE 0.028 0.002 PHE R 387 TRP 0.015 0.001 TRP B 169 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 ( 8768) covalent geometry : angle 0.73391 / 0.38 (11881) SS BOND : bond 0.00545 / 0.28 ( 3) SS BOND : angle 0.60474 / 0.23 ( 6) hydrogen bonds : bond 0.04725 / 3.09 ( 361) hydrogen bonds : angle 5.13632 / 3.53 ( 1035) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8591 (tm-30) REVERT: A 354 TYR cc_start: 0.8676 (p90) cc_final: 0.8337 (p90) REVERT: B 12 GLU cc_start: 0.9310 (pt0) cc_final: 0.8983 (pm20) REVERT: B 36 ASN cc_start: 0.8616 (m-40) cc_final: 0.8316 (p0) REVERT: B 292 PHE cc_start: 0.8142 (m-10) cc_final: 0.7710 (m-10) REVERT: G 42 GLU cc_start: 0.8190 (tp30) cc_final: 0.7586 (mt-10) REVERT: G 58 GLU cc_start: 0.9089 (mp0) cc_final: 0.8502 (mp0) REVERT: R 53 CYS cc_start: 0.9081 (m) cc_final: 0.8858 (m) REVERT: R 94 ASP cc_start: 0.8252 (t70) cc_final: 0.7465 (t70) REVERT: R 95 ILE cc_start: 0.9703 (mm) cc_final: 0.9489 (mm) REVERT: R 109 GLU cc_start: 0.8831 (tp30) cc_final: 0.8201 (tm-30) REVERT: R 381 GLN cc_start: 0.9020 (pt0) cc_final: 0.8537 (pt0) REVERT: R 446 HIS cc_start: 0.9017 (OUTLIER) cc_final: 0.8643 (t70) REVERT: R 447 ASP cc_start: 0.9341 (p0) cc_final: 0.9117 (p0) REVERT: H 180 MET cc_start: 0.8841 (ppp) cc_final: 0.8384 (ppp) REVERT: H 218 MET cc_start: 0.8603 (tmm) cc_final: 0.8302 (tmm) outliers start: 20 outliers final: 14 residues processed: 192 average time/residue: 0.0978 time to fit residues: 25.9038 Evaluate side-chains 161 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 433 ASN Chi-restraints excluded: chain R residue 446 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 176 GLN ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.090874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066933 restraints weight = 31742.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.068984 restraints weight = 17266.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.070345 restraints weight = 11818.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.071137 restraints weight = 9279.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.071773 restraints weight = 8032.893| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8772 Z= 0.193 Angle : 0.736 11.834 11887 Z= 0.376 Chirality : 0.045 0.144 1349 Planarity : 0.004 0.050 1496 Dihedral : 4.658 20.025 1185 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.23 % Allowed : 16.56 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.33 (0.26), residues: 1075 helix: 1.40 (0.28), residues: 340 sheet: -0.36 (0.32), residues: 271 loop : -1.35 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 378 TYR 0.026 0.002 TYR R 409 PHE 0.021 0.001 PHE R 387 TRP 0.011 0.001 TRP B 169 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 8768) covalent geometry : angle 0.73558 / 0.38 (11881) SS BOND : bond 0.00429 / 0.22 ( 3) SS BOND : angle 0.65540 / 0.25 ( 6) hydrogen bonds : bond 0.04455 / 2.90 ( 361) hydrogen bonds : angle 4.80231 / 3.29 ( 1035) Misc. bond : bond 0.00076 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8598 (tm-30) REVERT: A 354 TYR cc_start: 0.8718 (p90) cc_final: 0.8302 (p90) REVERT: B 12 GLU cc_start: 0.9303 (pt0) cc_final: 0.8971 (pm20) REVERT: B 36 ASN cc_start: 0.8574 (m-40) cc_final: 0.8274 (p0) REVERT: B 232 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8470 (tt) REVERT: B 292 PHE cc_start: 0.8227 (m-10) cc_final: 0.7830 (m-10) REVERT: G 21 MET cc_start: 0.8428 (mmm) cc_final: 0.7406 (mtm) REVERT: G 38 MET cc_start: 0.6558 (ptp) cc_final: 0.5867 (ptt) REVERT: G 42 GLU cc_start: 0.8188 (tp30) cc_final: 0.7612 (mt-10) REVERT: G 58 GLU cc_start: 0.9142 (mp0) cc_final: 0.8568 (mp0) REVERT: R 49 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7196 (pt) REVERT: R 53 CYS cc_start: 0.9094 (m) cc_final: 0.8882 (m) REVERT: R 94 ASP cc_start: 0.8128 (t70) cc_final: 0.7340 (t70) REVERT: R 109 GLU cc_start: 0.8781 (tp30) cc_final: 0.8174 (tm-30) REVERT: R 446 HIS cc_start: 0.9001 (OUTLIER) cc_final: 0.8672 (t70) REVERT: H 180 MET cc_start: 0.8831 (ppp) cc_final: 0.8382 (ppp) REVERT: H 218 MET cc_start: 0.8650 (tmm) cc_final: 0.8434 (tmm) outliers start: 30 outliers final: 21 residues processed: 182 average time/residue: 0.0890 time to fit residues: 22.6649 Evaluate side-chains 166 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN R 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.092833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068887 restraints weight = 31803.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.070985 restraints weight = 17110.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072383 restraints weight = 11629.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073199 restraints weight = 9103.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073860 restraints weight = 7884.128| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8772 Z= 0.133 Angle : 0.701 11.965 11887 Z= 0.352 Chirality : 0.043 0.155 1349 Planarity : 0.004 0.051 1496 Dihedral : 4.496 20.908 1185 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.90 % Allowed : 17.74 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.18 (0.26), residues: 1075 helix: 1.61 (0.28), residues: 336 sheet: -0.18 (0.34), residues: 250 loop : -1.34 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 168 TYR 0.027 0.001 TYR R 409 PHE 0.022 0.001 PHE R 387 TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8768) covalent geometry : angle 0.70094 / 0.35 (11881) SS BOND : bond 0.00345 / 0.17 ( 3) SS BOND : angle 0.56592 / 0.23 ( 6) hydrogen bonds : bond 0.03877 / 2.53 ( 361) hydrogen bonds : angle 4.51974 / 3.10 ( 1035) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8636 (tm-30) REVERT: A 354 TYR cc_start: 0.8733 (p90) cc_final: 0.8341 (p90) REVERT: B 12 GLU cc_start: 0.9308 (pt0) cc_final: 0.8965 (pm20) REVERT: B 36 ASN cc_start: 0.8515 (m-40) cc_final: 0.8179 (p0) REVERT: B 292 PHE cc_start: 0.8155 (m-10) cc_final: 0.7749 (m-10) REVERT: G 21 MET cc_start: 0.8570 (mmm) cc_final: 0.7687 (mtm) REVERT: G 38 MET cc_start: 0.6593 (ptp) cc_final: 0.6334 (ptt) REVERT: G 42 GLU cc_start: 0.8123 (tp30) cc_final: 0.7641 (mt-10) REVERT: G 58 GLU cc_start: 0.9134 (mp0) cc_final: 0.8570 (mp0) REVERT: R 53 CYS cc_start: 0.9040 (m) cc_final: 0.8740 (p) REVERT: R 94 ASP cc_start: 0.8117 (t70) cc_final: 0.7272 (t70) REVERT: R 95 ILE cc_start: 0.9672 (mm) cc_final: 0.9405 (mm) REVERT: R 109 GLU cc_start: 0.8638 (tp30) cc_final: 0.8117 (tm-30) REVERT: R 204 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8684 (tm-30) REVERT: R 446 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8719 (t70) REVERT: H 34 MET cc_start: 0.8576 (tpp) cc_final: 0.8290 (tpp) outliers start: 27 outliers final: 15 residues processed: 179 average time/residue: 0.0841 time to fit residues: 20.7996 Evaluate side-chains 155 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.092253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.068284 restraints weight = 31429.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070353 restraints weight = 16895.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.071728 restraints weight = 11512.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072630 restraints weight = 9016.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.073165 restraints weight = 7743.791| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8772 Z= 0.151 Angle : 0.722 12.459 11887 Z= 0.359 Chirality : 0.044 0.242 1349 Planarity : 0.004 0.049 1496 Dihedral : 4.476 22.017 1185 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.80 % Allowed : 19.35 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.19 (0.26), residues: 1075 helix: 1.61 (0.28), residues: 340 sheet: -0.26 (0.33), residues: 260 loop : -1.33 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.016 0.001 TYR R 156 PHE 0.020 0.001 PHE R 387 TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 8768) covalent geometry : angle 0.72213 / 0.36 (11881) SS BOND : bond 0.00303 / 0.15 ( 3) SS BOND : angle 0.62879 / 0.23 ( 6) hydrogen bonds : bond 0.03814 / 2.49 ( 361) hydrogen bonds : angle 4.48928 / 3.08 ( 1035) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8751 (p90) cc_final: 0.8340 (p90) REVERT: B 12 GLU cc_start: 0.9296 (pt0) cc_final: 0.8964 (pm20) REVERT: B 36 ASN cc_start: 0.8503 (m-40) cc_final: 0.8189 (p0) REVERT: B 130 GLU cc_start: 0.8982 (mp0) cc_final: 0.8698 (mp0) REVERT: B 292 PHE cc_start: 0.8223 (m-10) cc_final: 0.7838 (m-10) REVERT: G 38 MET cc_start: 0.6638 (ptp) cc_final: 0.6391 (ptt) REVERT: G 42 GLU cc_start: 0.8137 (tp30) cc_final: 0.7664 (mt-10) REVERT: G 58 GLU cc_start: 0.9132 (mp0) cc_final: 0.8574 (mp0) REVERT: R 53 CYS cc_start: 0.8987 (m) cc_final: 0.8714 (p) REVERT: R 94 ASP cc_start: 0.8128 (t70) cc_final: 0.7258 (t70) REVERT: R 95 ILE cc_start: 0.9679 (mm) cc_final: 0.9402 (mm) REVERT: R 109 GLU cc_start: 0.8650 (tp30) cc_final: 0.8186 (tm-30) REVERT: H 148 ARG cc_start: 0.8819 (tpp-160) cc_final: 0.8368 (mmm160) REVERT: H 218 MET cc_start: 0.8729 (tmm) cc_final: 0.8471 (ppp) outliers start: 26 outliers final: 17 residues processed: 170 average time/residue: 0.0817 time to fit residues: 19.5633 Evaluate side-chains 156 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 454 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 0.9980 chunk 98 optimal weight: 40.0000 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.093409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069441 restraints weight = 31388.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071554 restraints weight = 16920.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072898 restraints weight = 11528.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.073859 restraints weight = 9069.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074362 restraints weight = 7777.435| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8772 Z= 0.127 Angle : 0.729 13.237 11887 Z= 0.356 Chirality : 0.043 0.167 1349 Planarity : 0.004 0.050 1496 Dihedral : 4.398 20.645 1185 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.90 % Allowed : 20.32 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.21 (0.26), residues: 1075 helix: 1.55 (0.29), residues: 342 sheet: -0.27 (0.34), residues: 250 loop : -1.31 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 168 TYR 0.015 0.001 TYR R 156 PHE 0.023 0.001 PHE R 387 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8768) covalent geometry : angle 0.72891 / 0.36 (11881) SS BOND : bond 0.00254 / 0.13 ( 3) SS BOND : angle 0.46329 / 0.15 ( 6) hydrogen bonds : bond 0.03560 / 2.34 ( 361) hydrogen bonds : angle 4.34359 / 2.99 ( 1035) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8747 (p90) cc_final: 0.8281 (p90) REVERT: B 12 GLU cc_start: 0.9297 (pt0) cc_final: 0.8972 (pm20) REVERT: B 36 ASN cc_start: 0.8561 (m-40) cc_final: 0.8182 (p0) REVERT: B 59 TYR cc_start: 0.8402 (m-80) cc_final: 0.7829 (m-80) REVERT: B 100 VAL cc_start: 0.9319 (t) cc_final: 0.9113 (p) REVERT: B 130 GLU cc_start: 0.8941 (mp0) cc_final: 0.8645 (mp0) REVERT: B 175 GLN cc_start: 0.8289 (mp10) cc_final: 0.8018 (mp10) REVERT: B 220 GLN cc_start: 0.8745 (mp10) cc_final: 0.8527 (mp10) REVERT: B 283 ARG cc_start: 0.7386 (ttt180) cc_final: 0.6826 (ttt90) REVERT: B 292 PHE cc_start: 0.8157 (m-10) cc_final: 0.7765 (m-10) REVERT: G 21 MET cc_start: 0.8372 (mmm) cc_final: 0.7426 (mtm) REVERT: G 24 ASN cc_start: 0.7703 (t0) cc_final: 0.7168 (m-40) REVERT: G 38 MET cc_start: 0.6689 (ptp) cc_final: 0.6003 (ptt) REVERT: G 42 GLU cc_start: 0.8080 (tp30) cc_final: 0.7497 (mt-10) REVERT: G 58 GLU cc_start: 0.9116 (mp0) cc_final: 0.8575 (mp0) REVERT: R 53 CYS cc_start: 0.9010 (m) cc_final: 0.8730 (p) REVERT: R 79 LEU cc_start: 0.8764 (tp) cc_final: 0.8554 (tp) REVERT: R 109 GLU cc_start: 0.8645 (tp30) cc_final: 0.8256 (tm-30) REVERT: R 111 MET cc_start: 0.8518 (mtm) cc_final: 0.8223 (ptp) REVERT: H 34 MET cc_start: 0.8594 (tpp) cc_final: 0.8340 (tpp) REVERT: H 148 ARG cc_start: 0.8832 (tpp-160) cc_final: 0.8392 (mmm160) REVERT: H 160 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8036 (p) REVERT: H 190 ARG cc_start: 0.5931 (OUTLIER) cc_final: 0.5668 (ptm160) REVERT: H 234 GLU cc_start: 0.6690 (pm20) cc_final: 0.6354 (pp20) outliers start: 27 outliers final: 17 residues processed: 186 average time/residue: 0.0901 time to fit residues: 22.9376 Evaluate side-chains 167 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 82 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.1194 > 50:) chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.094921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.070571 restraints weight = 31707.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.072729 restraints weight = 17005.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.074157 restraints weight = 11528.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.075110 restraints weight = 9029.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.075610 restraints weight = 7728.462| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8772 Z= 0.125 Angle : 0.748 14.022 11887 Z= 0.364 Chirality : 0.044 0.335 1349 Planarity : 0.004 0.058 1496 Dihedral : 4.294 20.583 1185 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.47 % Allowed : 21.61 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.16 (0.26), residues: 1075 helix: 1.54 (0.29), residues: 340 sheet: -0.18 (0.34), residues: 250 loop : -1.28 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 87 TYR 0.015 0.001 TYR R 156 PHE 0.019 0.001 PHE R 387 TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8768) covalent geometry : angle 0.74815 / 0.36 (11881) SS BOND : bond 0.00186 / 0.09 ( 3) SS BOND : angle 0.45834 / 0.15 ( 6) hydrogen bonds : bond 0.03413 / 2.24 ( 361) hydrogen bonds : angle 4.37440 / 3.02 ( 1035) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8743 (p90) cc_final: 0.8279 (p90) REVERT: B 12 GLU cc_start: 0.9298 (pt0) cc_final: 0.8975 (pm20) REVERT: B 283 ARG cc_start: 0.7412 (ttt180) cc_final: 0.6741 (ttt90) REVERT: B 292 PHE cc_start: 0.8131 (m-10) cc_final: 0.7751 (m-10) REVERT: G 21 MET cc_start: 0.8455 (mmm) cc_final: 0.7558 (mtm) REVERT: G 24 ASN cc_start: 0.7723 (t0) cc_final: 0.7200 (m-40) REVERT: G 38 MET cc_start: 0.6621 (ptp) cc_final: 0.5986 (ptt) REVERT: G 42 GLU cc_start: 0.8064 (tp30) cc_final: 0.7493 (mt-10) REVERT: G 58 GLU cc_start: 0.9084 (mp0) cc_final: 0.8553 (mp0) REVERT: R 53 CYS cc_start: 0.9016 (m) cc_final: 0.8732 (p) REVERT: R 94 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7381 (t70) REVERT: R 109 GLU cc_start: 0.8637 (tp30) cc_final: 0.8243 (tm-30) REVERT: R 111 MET cc_start: 0.8595 (mtm) cc_final: 0.8274 (ptp) REVERT: H 148 ARG cc_start: 0.8788 (tpp-160) cc_final: 0.8413 (mmm160) REVERT: H 160 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8193 (p) REVERT: H 218 MET cc_start: 0.8620 (tmm) cc_final: 0.8368 (ppp) outliers start: 23 outliers final: 18 residues processed: 177 average time/residue: 0.0868 time to fit residues: 21.3569 Evaluate side-chains 165 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 100 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 138 HIS ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.093778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069842 restraints weight = 30885.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.071937 restraints weight = 16686.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073349 restraints weight = 11361.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.074269 restraints weight = 8894.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.074677 restraints weight = 7625.111| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8772 Z= 0.138 Angle : 0.768 15.361 11887 Z= 0.371 Chirality : 0.043 0.185 1349 Planarity : 0.004 0.076 1496 Dihedral : 4.297 20.284 1185 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.58 % Allowed : 22.69 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.19 (0.26), residues: 1075 helix: 1.51 (0.29), residues: 340 sheet: -0.20 (0.35), residues: 246 loop : -1.26 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.014 0.001 TYR R 156 PHE 0.031 0.001 PHE R 387 TRP 0.012 0.001 TRP B 169 HIS 0.008 0.001 HIS R 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8768) covalent geometry : angle 0.76792 / 0.37 (11881) SS BOND : bond 0.00251 / 0.13 ( 3) SS BOND : angle 0.48979 / 0.17 ( 6) hydrogen bonds : bond 0.03476 / 2.27 ( 361) hydrogen bonds : angle 4.38646 / 3.03 ( 1035) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8679 (p90) cc_final: 0.8138 (p90) REVERT: B 12 GLU cc_start: 0.9295 (pt0) cc_final: 0.8967 (pm20) REVERT: B 292 PHE cc_start: 0.8214 (m-10) cc_final: 0.7838 (m-10) REVERT: G 21 MET cc_start: 0.8510 (mmm) cc_final: 0.7596 (mtm) REVERT: G 24 ASN cc_start: 0.7702 (t0) cc_final: 0.7164 (m-40) REVERT: G 38 MET cc_start: 0.6687 (ptp) cc_final: 0.6055 (ptt) REVERT: G 42 GLU cc_start: 0.8053 (tp30) cc_final: 0.7484 (mt-10) REVERT: G 58 GLU cc_start: 0.9082 (mp0) cc_final: 0.8542 (mp0) REVERT: R 53 CYS cc_start: 0.8997 (m) cc_final: 0.8722 (p) REVERT: R 94 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7430 (t70) REVERT: R 109 GLU cc_start: 0.8601 (tp30) cc_final: 0.8225 (tm-30) REVERT: R 111 MET cc_start: 0.8550 (mtm) cc_final: 0.8226 (ptp) REVERT: H 34 MET cc_start: 0.8616 (tpp) cc_final: 0.8362 (tpp) REVERT: H 148 ARG cc_start: 0.8790 (tpp-160) cc_final: 0.8432 (mmm160) REVERT: H 218 MET cc_start: 0.8673 (tmm) cc_final: 0.8430 (ppp) outliers start: 24 outliers final: 18 residues processed: 165 average time/residue: 0.0992 time to fit residues: 22.4054 Evaluate side-chains 161 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 76 optimal weight: 0.0470 chunk 99 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.0670 chunk 65 optimal weight: 7.9990 overall best weight: 1.1818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.094326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070172 restraints weight = 31076.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.072293 restraints weight = 16801.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.073719 restraints weight = 11443.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.074532 restraints weight = 8961.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.075196 restraints weight = 7747.906| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8772 Z= 0.133 Angle : 0.792 14.512 11887 Z= 0.382 Chirality : 0.044 0.193 1349 Planarity : 0.004 0.067 1496 Dihedral : 4.260 20.266 1185 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.37 % Allowed : 22.69 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.20 (0.26), residues: 1075 helix: 1.46 (0.29), residues: 340 sheet: -0.12 (0.35), residues: 244 loop : -1.30 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.015 0.001 TYR R 156 PHE 0.033 0.001 PHE R 387 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS R 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8768) covalent geometry : angle 0.79228 / 0.38 (11881) SS BOND : bond 0.00229 / 0.11 ( 3) SS BOND : angle 0.47304 / 0.16 ( 6) hydrogen bonds : bond 0.03398 / 2.24 ( 361) hydrogen bonds : angle 4.36672 / 3.01 ( 1035) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 TYR cc_start: 0.8043 (m-80) cc_final: 0.7771 (m-80) REVERT: A 354 TYR cc_start: 0.8666 (p90) cc_final: 0.8154 (p90) REVERT: B 12 GLU cc_start: 0.9289 (pt0) cc_final: 0.8960 (pm20) REVERT: B 78 LYS cc_start: 0.9575 (mmmm) cc_final: 0.9059 (mmmm) REVERT: B 188 MET cc_start: 0.8829 (mtm) cc_final: 0.8595 (ptm) REVERT: B 283 ARG cc_start: 0.7324 (ttt180) cc_final: 0.6844 (ttt90) REVERT: B 292 PHE cc_start: 0.8172 (m-10) cc_final: 0.7761 (m-10) REVERT: G 21 MET cc_start: 0.8511 (mmm) cc_final: 0.7575 (mtm) REVERT: G 24 ASN cc_start: 0.7699 (t0) cc_final: 0.7161 (m-40) REVERT: G 38 MET cc_start: 0.6630 (ptp) cc_final: 0.6008 (ptt) REVERT: G 42 GLU cc_start: 0.8035 (tp30) cc_final: 0.7475 (mt-10) REVERT: G 58 GLU cc_start: 0.9082 (mp0) cc_final: 0.8534 (mp0) REVERT: R 53 CYS cc_start: 0.8965 (m) cc_final: 0.8700 (p) REVERT: R 94 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7456 (t70) REVERT: R 109 GLU cc_start: 0.8613 (tp30) cc_final: 0.8227 (tm-30) REVERT: H 34 MET cc_start: 0.8615 (tpp) cc_final: 0.8366 (tpp) REVERT: H 148 ARG cc_start: 0.8782 (tpp-160) cc_final: 0.8424 (mmm160) REVERT: H 218 MET cc_start: 0.8624 (tmm) cc_final: 0.8401 (ppp) outliers start: 22 outliers final: 17 residues processed: 165 average time/residue: 0.1005 time to fit residues: 22.6819 Evaluate side-chains 163 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 29 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.094493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070333 restraints weight = 31562.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.072471 restraints weight = 17129.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073834 restraints weight = 11661.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074820 restraints weight = 9162.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.075326 restraints weight = 7851.056| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8772 Z= 0.135 Angle : 0.803 15.239 11887 Z= 0.387 Chirality : 0.044 0.209 1349 Planarity : 0.004 0.063 1496 Dihedral : 4.269 21.368 1185 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.58 % Allowed : 22.47 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.19 (0.27), residues: 1075 helix: 1.46 (0.29), residues: 340 sheet: -0.10 (0.35), residues: 247 loop : -1.29 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.014 0.001 TYR R 156 PHE 0.034 0.001 PHE R 387 TRP 0.011 0.001 TRP B 169 HIS 0.017 0.001 HIS R 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8768) covalent geometry : angle 0.80309 / 0.39 (11881) SS BOND : bond 0.00229 / 0.11 ( 3) SS BOND : angle 0.50247 / 0.17 ( 6) hydrogen bonds : bond 0.03490 / 2.25 ( 361) hydrogen bonds : angle 4.38049 / 3.04 ( 1035) Misc. bond : bond 0.00037 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8643 (p90) cc_final: 0.8146 (p90) REVERT: B 12 GLU cc_start: 0.9281 (pt0) cc_final: 0.8964 (pm20) REVERT: B 283 ARG cc_start: 0.7302 (ttt180) cc_final: 0.6824 (ttt90) REVERT: B 292 PHE cc_start: 0.8159 (m-10) cc_final: 0.7751 (m-10) REVERT: G 21 MET cc_start: 0.8482 (mmm) cc_final: 0.7570 (mtm) REVERT: G 24 ASN cc_start: 0.7713 (t0) cc_final: 0.7170 (m-40) REVERT: G 38 MET cc_start: 0.6627 (ptp) cc_final: 0.6411 (ptt) REVERT: G 42 GLU cc_start: 0.8033 (tp30) cc_final: 0.7592 (mt-10) REVERT: G 58 GLU cc_start: 0.9088 (mp0) cc_final: 0.8591 (mp0) REVERT: R 53 CYS cc_start: 0.8979 (m) cc_final: 0.8704 (p) REVERT: R 94 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7473 (t70) REVERT: R 109 GLU cc_start: 0.8612 (tp30) cc_final: 0.8231 (tm-30) REVERT: H 34 MET cc_start: 0.8611 (tpp) cc_final: 0.8365 (tpp) REVERT: H 148 ARG cc_start: 0.8774 (tpp-160) cc_final: 0.8411 (mmm160) REVERT: H 218 MET cc_start: 0.8667 (tmm) cc_final: 0.8430 (ppp) REVERT: H 232 LYS cc_start: 0.8129 (mppt) cc_final: 0.7656 (pptt) REVERT: H 234 GLU cc_start: 0.6848 (pm20) cc_final: 0.6638 (pm20) outliers start: 24 outliers final: 21 residues processed: 162 average time/residue: 0.0926 time to fit residues: 21.0103 Evaluate side-chains 165 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 0.1980 chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 103 optimal weight: 0.0670 chunk 22 optimal weight: 30.0000 chunk 78 optimal weight: 4.9990 chunk 29 optimal weight: 0.0470 chunk 50 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.2618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.094547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070308 restraints weight = 31316.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.072458 restraints weight = 17058.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.073873 restraints weight = 11630.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074790 restraints weight = 9116.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.075336 restraints weight = 7824.430| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8772 Z= 0.136 Angle : 0.807 17.372 11887 Z= 0.389 Chirality : 0.044 0.205 1349 Planarity : 0.004 0.054 1496 Dihedral : 4.258 21.570 1185 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.26 % Allowed : 23.33 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.23 (0.26), residues: 1075 helix: 1.44 (0.29), residues: 340 sheet: -0.15 (0.35), residues: 242 loop : -1.30 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.014 0.001 TYR R 156 PHE 0.031 0.001 PHE R 387 TRP 0.011 0.001 TRP B 169 HIS 0.011 0.001 HIS R 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 8768) covalent geometry : angle 0.80732 / 0.39 (11881) SS BOND : bond 0.00239 / 0.12 ( 3) SS BOND : angle 0.52685 / 0.18 ( 6) hydrogen bonds : bond 0.03475 / 2.26 ( 361) hydrogen bonds : angle 4.37196 / 3.05 ( 1035) Misc. bond : bond 0.00037 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1760.24 seconds wall clock time: 31 minutes 10.21 seconds (1870.21 seconds total)