Starting phenix.real_space_refine on Tue Mar 3 20:00:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y15_33557/03_2026/7y15_33557.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y15_33557/03_2026/7y15_33557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y15_33557/03_2026/7y15_33557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y15_33557/03_2026/7y15_33557.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y15_33557/03_2026/7y15_33557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y15_33557/03_2026/7y15_33557.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.087 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 69 5.16 5 C 5428 2.51 5 N 1453 2.21 5 O 1545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8495 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1654 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2053 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 253} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'PLM': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.91, per 1000 atoms: 0.22 Number of scatterers: 8495 At special positions: 0 Unit cell: (122.85, 84.375, 125.55, 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 69 16.00 O 1545 8.00 N 1453 7.00 C 5428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 164 " - pdb=" SG CYS R 175 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 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=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 314.1 milliseconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 37.1% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.599A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.214A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.564A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 329 through 352 removed outlier: 4.588A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.589A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.538A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.504A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 53 Processing helix chain 'R' and resid 61 through 87 removed outlier: 3.781A pdb=" N ILE R 65 " --> pdb=" O PHE R 61 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR R 87 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 129 removed outlier: 3.678A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 140 through 165 removed outlier: 4.497A pdb=" N PHE R 163 " --> pdb=" O LEU R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 209 Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 216 through 234 Processing helix chain 'R' and resid 234 through 245 removed outlier: 4.234A pdb=" N SER R 238 " --> pdb=" O SER R 234 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR R 245 " --> pdb=" O TRP R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 277 Proline residue: R 273 - end of helix Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.182A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.237A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.279A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.703A 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: 4.056A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.964A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.650A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.573A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.587A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.610A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.546A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.973A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.973A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.664A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.605A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1242 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: 1.34 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2712 1.34 - 1.46: 2133 1.46 - 1.58: 3726 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 8671 Sorted by residual: bond pdb=" C1 PLM R 403 " pdb=" C2 PLM R 403 " ideal model delta sigma weight residual 1.542 1.508 0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" C1 PLM R 401 " pdb=" C2 PLM R 401 " ideal model delta sigma weight residual 1.542 1.509 0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" C1 PLM R 402 " pdb=" C2 PLM R 402 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" CA ASP B 205 " pdb=" C ASP B 205 " ideal model delta sigma weight residual 1.523 1.507 0.017 1.80e-02 3.09e+03 8.61e-01 bond pdb=" CB CYS S 96 " pdb=" SG CYS S 96 " ideal model delta sigma weight residual 1.808 1.782 0.026 3.30e-02 9.18e+02 6.15e-01 ... (remaining 8666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 11583 1.97 - 3.93: 136 3.93 - 5.90: 22 5.90 - 7.86: 9 7.86 - 9.83: 1 Bond angle restraints: 11751 Sorted by residual: angle pdb=" CA LEU R 52 " pdb=" CB LEU R 52 " pdb=" CG LEU R 52 " ideal model delta sigma weight residual 116.30 126.13 -9.83 3.50e+00 8.16e-02 7.89e+00 angle pdb=" N LEU B 308 " pdb=" CA LEU B 308 " pdb=" C LEU B 308 " ideal model delta sigma weight residual 114.04 110.76 3.28 1.24e+00 6.50e-01 6.99e+00 angle pdb=" CA TRP R 144 " pdb=" CB TRP R 144 " pdb=" CG TRP R 144 " ideal model delta sigma weight residual 113.60 118.31 -4.71 1.90e+00 2.77e-01 6.15e+00 angle pdb=" O1 PLM R 401 " pdb=" C1 PLM R 401 " pdb=" O2 PLM R 401 " ideal model delta sigma weight residual 126.37 118.94 7.43 3.00e+00 1.11e-01 6.13e+00 angle pdb=" O1 PLM R 402 " pdb=" C1 PLM R 402 " pdb=" O2 PLM R 402 " ideal model delta sigma weight residual 126.37 118.95 7.42 3.00e+00 1.11e-01 6.12e+00 ... (remaining 11746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4450 17.69 - 35.38: 515 35.38 - 53.07: 132 53.07 - 70.76: 29 70.76 - 88.45: 3 Dihedral angle restraints: 5129 sinusoidal: 1910 harmonic: 3219 Sorted by residual: dihedral pdb=" CB CYS R 164 " pdb=" SG CYS R 164 " pdb=" SG CYS R 175 " pdb=" CB CYS R 175 " ideal model delta sinusoidal sigma weight residual -86.00 -29.61 -56.39 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA LEU B 51 " pdb=" C LEU B 51 " pdb=" N ARG B 52 " pdb=" CA ARG B 52 " ideal model delta harmonic sigma weight residual -180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 918 0.032 - 0.064: 294 0.064 - 0.096: 95 0.096 - 0.128: 45 0.128 - 0.160: 5 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA TRP R 144 " pdb=" N TRP R 144 " pdb=" C TRP R 144 " pdb=" CB TRP R 144 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 1354 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 235 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO R 236 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO R 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET R 187 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C MET R 187 " 0.028 2.00e-02 2.50e+03 pdb=" O MET R 187 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY R 188 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 230 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C PHE R 230 " -0.022 2.00e-02 2.50e+03 pdb=" O PHE R 230 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU R 231 " 0.007 2.00e-02 2.50e+03 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1815 2.78 - 3.31: 7720 3.31 - 3.84: 14420 3.84 - 4.37: 17016 4.37 - 4.90: 29915 Nonbonded interactions: 70886 Sorted by model distance: nonbonded pdb=" O THR R 191 " pdb=" OG1 THR R 195 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.282 3.040 nonbonded pdb=" NE ARG B 283 " pdb=" OD1 ASP B 298 " model vdw 2.301 3.120 nonbonded pdb=" OD1 ASP R 72 " pdb=" OG SER R 269 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.309 3.040 ... (remaining 70881 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.590 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8673 Z= 0.119 Angle : 0.563 9.830 11755 Z= 0.277 Chirality : 0.039 0.160 1357 Planarity : 0.003 0.050 1467 Dihedral : 16.240 88.452 3041 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.70 % Allowed : 20.22 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.26), residues: 1093 helix: 2.64 (0.28), residues: 374 sheet: 0.54 (0.32), residues: 255 loop : -0.51 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 148 TYR 0.012 0.001 TYR S 178 PHE 0.015 0.001 PHE R 202 TRP 0.017 0.001 TRP R 144 HIS 0.008 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8671) covalent geometry : angle 0.56328 (11751) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.54644 ( 4) hydrogen bonds : bond 0.13414 ( 436) hydrogen bonds : angle 5.79247 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.234 Fit side-chains REVERT: R 159 LEU cc_start: 0.8101 (tp) cc_final: 0.7819 (tt) outliers start: 24 outliers final: 21 residues processed: 130 average time/residue: 0.5445 time to fit residues: 75.4827 Evaluate side-chains 126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 265 SER Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 340 ASN C 59 ASN R 57 HIS ** R 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.168807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129691 restraints weight = 9272.971| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.95 r_work: 0.3192 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 8673 Z= 0.298 Angle : 0.672 9.208 11755 Z= 0.351 Chirality : 0.047 0.208 1357 Planarity : 0.004 0.054 1467 Dihedral : 7.877 59.708 1264 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.61 % Allowed : 19.55 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1093 helix: 2.32 (0.27), residues: 376 sheet: 0.35 (0.30), residues: 278 loop : -0.67 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 150 TYR 0.022 0.002 TYR S 178 PHE 0.017 0.002 PHE A 196 TRP 0.027 0.002 TRP R 144 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00711 ( 8671) covalent geometry : angle 0.67233 (11751) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.99999 ( 4) hydrogen bonds : bond 0.04606 ( 436) hydrogen bonds : angle 5.05750 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.323 Fit side-chains REVERT: R 79 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7524 (ttp) REVERT: R 174 ARG cc_start: 0.4473 (mtp180) cc_final: 0.4091 (ttp-170) REVERT: R 206 ARG cc_start: 0.7320 (tmm160) cc_final: 0.7025 (ttp-110) REVERT: R 246 TRP cc_start: 0.7170 (OUTLIER) cc_final: 0.6077 (t60) REVERT: R 253 MET cc_start: 0.6457 (pmm) cc_final: 0.6176 (pp-130) outliers start: 41 outliers final: 24 residues processed: 138 average time/residue: 0.5429 time to fit residues: 79.5904 Evaluate side-chains 128 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 79 MET Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS B 237 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134083 restraints weight = 9232.907| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.85 r_work: 0.3271 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8673 Z= 0.124 Angle : 0.512 6.768 11755 Z= 0.269 Chirality : 0.040 0.163 1357 Planarity : 0.003 0.057 1467 Dihedral : 6.722 54.108 1255 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.37 % Allowed : 21.80 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.26), residues: 1093 helix: 2.68 (0.27), residues: 377 sheet: 0.41 (0.30), residues: 272 loop : -0.61 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 103 TYR 0.012 0.001 TYR S 178 PHE 0.015 0.001 PHE R 202 TRP 0.019 0.001 TRP R 144 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8671) covalent geometry : angle 0.51200 (11751) SS BOND : bond 0.00260 ( 2) SS BOND : angle 0.62115 ( 4) hydrogen bonds : bond 0.03459 ( 436) hydrogen bonds : angle 4.61513 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: R 159 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7624 (tt) REVERT: R 174 ARG cc_start: 0.4388 (mtp180) cc_final: 0.3833 (tpp80) REVERT: R 206 ARG cc_start: 0.7274 (tmm160) cc_final: 0.7002 (ttp-110) REVERT: R 246 TRP cc_start: 0.7061 (OUTLIER) cc_final: 0.5985 (t60) outliers start: 30 outliers final: 15 residues processed: 128 average time/residue: 0.5622 time to fit residues: 76.4473 Evaluate side-chains 120 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 86 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.172993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133120 restraints weight = 9349.167| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.94 r_work: 0.3260 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8673 Z= 0.137 Angle : 0.515 7.659 11755 Z= 0.270 Chirality : 0.041 0.163 1357 Planarity : 0.003 0.060 1467 Dihedral : 6.312 54.876 1249 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.48 % Allowed : 22.58 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.26), residues: 1093 helix: 2.76 (0.27), residues: 377 sheet: 0.43 (0.31), residues: 263 loop : -0.65 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 103 TYR 0.014 0.001 TYR S 178 PHE 0.016 0.001 PHE R 202 TRP 0.019 0.001 TRP R 144 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8671) covalent geometry : angle 0.51496 (11751) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.66432 ( 4) hydrogen bonds : bond 0.03412 ( 436) hydrogen bonds : angle 4.52223 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: R 52 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7599 (tt) REVERT: R 159 LEU cc_start: 0.7807 (tp) cc_final: 0.7579 (tt) REVERT: R 174 ARG cc_start: 0.4356 (mtp180) cc_final: 0.3822 (ttp-170) REVERT: R 206 ARG cc_start: 0.7267 (tmm160) cc_final: 0.6996 (ttp-110) REVERT: R 246 TRP cc_start: 0.7052 (OUTLIER) cc_final: 0.5972 (t60) outliers start: 31 outliers final: 17 residues processed: 129 average time/residue: 0.5944 time to fit residues: 81.4166 Evaluate side-chains 122 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.173595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134080 restraints weight = 9272.385| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.00 r_work: 0.3265 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8673 Z= 0.130 Angle : 0.514 8.078 11755 Z= 0.268 Chirality : 0.040 0.162 1357 Planarity : 0.003 0.060 1467 Dihedral : 6.165 55.571 1249 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.82 % Allowed : 23.03 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.26), residues: 1093 helix: 2.76 (0.27), residues: 379 sheet: 0.55 (0.32), residues: 255 loop : -0.67 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 139 TYR 0.013 0.001 TYR S 178 PHE 0.016 0.001 PHE R 202 TRP 0.019 0.001 TRP R 144 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8671) covalent geometry : angle 0.51404 (11751) SS BOND : bond 0.00283 ( 2) SS BOND : angle 0.64444 ( 4) hydrogen bonds : bond 0.03316 ( 436) hydrogen bonds : angle 4.47436 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: R 52 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7558 (tt) REVERT: R 159 LEU cc_start: 0.7823 (tp) cc_final: 0.7597 (tt) REVERT: R 174 ARG cc_start: 0.4349 (mtp180) cc_final: 0.3823 (ttp-170) REVERT: R 206 ARG cc_start: 0.7262 (tmm160) cc_final: 0.6987 (ttp-110) REVERT: R 246 TRP cc_start: 0.7078 (OUTLIER) cc_final: 0.6010 (t60) outliers start: 34 outliers final: 18 residues processed: 131 average time/residue: 0.5624 time to fit residues: 78.3351 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.172796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.132808 restraints weight = 9184.737| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.94 r_work: 0.3224 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8673 Z= 0.150 Angle : 0.526 8.084 11755 Z= 0.275 Chirality : 0.041 0.166 1357 Planarity : 0.003 0.061 1467 Dihedral : 6.171 55.188 1247 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.92 % Allowed : 24.27 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1093 helix: 2.78 (0.27), residues: 378 sheet: 0.53 (0.32), residues: 254 loop : -0.64 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 139 TYR 0.015 0.001 TYR S 178 PHE 0.015 0.001 PHE R 202 TRP 0.020 0.001 TRP R 144 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8671) covalent geometry : angle 0.52621 (11751) SS BOND : bond 0.00294 ( 2) SS BOND : angle 0.65689 ( 4) hydrogen bonds : bond 0.03431 ( 436) hydrogen bonds : angle 4.51466 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: R 47 MET cc_start: 0.7420 (mmm) cc_final: 0.7192 (mmm) REVERT: R 52 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7572 (tt) REVERT: R 159 LEU cc_start: 0.7773 (tp) cc_final: 0.7544 (tt) REVERT: R 174 ARG cc_start: 0.4362 (mtp180) cc_final: 0.3843 (ttp-170) REVERT: R 206 ARG cc_start: 0.7274 (tmm160) cc_final: 0.6992 (ttp-110) REVERT: R 246 TRP cc_start: 0.7090 (OUTLIER) cc_final: 0.6014 (t60) REVERT: R 253 MET cc_start: 0.6482 (pmm) cc_final: 0.6160 (pp-130) outliers start: 26 outliers final: 21 residues processed: 126 average time/residue: 0.6000 time to fit residues: 80.2504 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.176153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136959 restraints weight = 9373.503| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.94 r_work: 0.3311 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8673 Z= 0.096 Angle : 0.491 9.515 11755 Z= 0.254 Chirality : 0.039 0.151 1357 Planarity : 0.003 0.062 1467 Dihedral : 5.691 57.095 1247 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.03 % Allowed : 24.04 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.26), residues: 1093 helix: 2.90 (0.27), residues: 378 sheet: 0.71 (0.32), residues: 253 loop : -0.63 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 139 TYR 0.010 0.001 TYR S 178 PHE 0.015 0.001 PHE R 202 TRP 0.017 0.001 TRP R 144 HIS 0.003 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 8671) covalent geometry : angle 0.49055 (11751) SS BOND : bond 0.00243 ( 2) SS BOND : angle 0.56439 ( 4) hydrogen bonds : bond 0.03007 ( 436) hydrogen bonds : angle 4.31684 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 287 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: C 21 MET cc_start: 0.7918 (mmm) cc_final: 0.7687 (mmm) REVERT: R 47 MET cc_start: 0.7441 (mmm) cc_final: 0.7222 (mmm) REVERT: R 52 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7373 (tt) REVERT: R 246 TRP cc_start: 0.7030 (OUTLIER) cc_final: 0.5982 (t60) REVERT: S 67 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7418 (ptt90) outliers start: 27 outliers final: 19 residues processed: 128 average time/residue: 0.5618 time to fit residues: 76.7465 Evaluate side-chains 125 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 88 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.172503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132592 restraints weight = 9189.848| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.99 r_work: 0.3216 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8673 Z= 0.171 Angle : 0.578 14.509 11755 Z= 0.295 Chirality : 0.042 0.165 1357 Planarity : 0.003 0.062 1467 Dihedral : 6.166 55.700 1246 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.92 % Allowed : 24.61 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.26), residues: 1093 helix: 2.72 (0.27), residues: 378 sheet: 0.58 (0.32), residues: 254 loop : -0.64 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 139 TYR 0.017 0.002 TYR S 178 PHE 0.017 0.002 PHE R 202 TRP 0.020 0.001 TRP R 144 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8671) covalent geometry : angle 0.57841 (11751) SS BOND : bond 0.00307 ( 2) SS BOND : angle 0.76320 ( 4) hydrogen bonds : bond 0.03554 ( 436) hydrogen bonds : angle 4.53882 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 287 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.5780 (m-80) REVERT: R 47 MET cc_start: 0.7419 (mmm) cc_final: 0.7173 (mmm) REVERT: R 206 ARG cc_start: 0.7246 (tmm160) cc_final: 0.6967 (ttp-110) REVERT: R 246 TRP cc_start: 0.7092 (OUTLIER) cc_final: 0.6040 (t60) outliers start: 26 outliers final: 20 residues processed: 127 average time/residue: 0.6490 time to fit residues: 87.2330 Evaluate side-chains 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 101 optimal weight: 4.9990 chunk 58 optimal weight: 0.0570 chunk 82 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.175281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135289 restraints weight = 9225.689| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.99 r_work: 0.3264 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8673 Z= 0.111 Angle : 0.516 10.659 11755 Z= 0.266 Chirality : 0.040 0.155 1357 Planarity : 0.003 0.062 1467 Dihedral : 5.821 57.028 1246 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.81 % Allowed : 24.38 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.26), residues: 1093 helix: 2.78 (0.27), residues: 378 sheet: 0.66 (0.32), residues: 256 loop : -0.60 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 139 TYR 0.012 0.001 TYR S 178 PHE 0.017 0.001 PHE R 202 TRP 0.017 0.001 TRP R 144 HIS 0.003 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8671) covalent geometry : angle 0.51639 (11751) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.60823 ( 4) hydrogen bonds : bond 0.03121 ( 436) hydrogen bonds : angle 4.40211 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 287 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.5842 (m-80) REVERT: R 47 MET cc_start: 0.7351 (mmm) cc_final: 0.7090 (mmm) REVERT: R 79 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7146 (ttm) REVERT: R 206 ARG cc_start: 0.7160 (tmm160) cc_final: 0.6880 (ttp-110) REVERT: R 246 TRP cc_start: 0.7061 (OUTLIER) cc_final: 0.6025 (t60) REVERT: S 67 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7533 (ptt90) outliers start: 25 outliers final: 20 residues processed: 127 average time/residue: 0.6247 time to fit residues: 84.2826 Evaluate side-chains 129 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 79 MET Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 62 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.174179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134112 restraints weight = 9214.413| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.96 r_work: 0.3245 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8673 Z= 0.133 Angle : 0.562 12.072 11755 Z= 0.285 Chirality : 0.041 0.172 1357 Planarity : 0.003 0.062 1467 Dihedral : 5.960 56.721 1246 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.92 % Allowed : 24.72 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 1093 helix: 2.77 (0.27), residues: 378 sheet: 0.64 (0.31), residues: 255 loop : -0.61 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 139 TYR 0.014 0.001 TYR S 178 PHE 0.017 0.001 PHE R 202 TRP 0.018 0.001 TRP R 144 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8671) covalent geometry : angle 0.56148 (11751) SS BOND : bond 0.00259 ( 2) SS BOND : angle 0.62383 ( 4) hydrogen bonds : bond 0.03301 ( 436) hydrogen bonds : angle 4.45080 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 287 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.5858 (m-80) REVERT: C 21 MET cc_start: 0.7853 (mmm) cc_final: 0.7589 (mmm) REVERT: R 47 MET cc_start: 0.7332 (mmm) cc_final: 0.7096 (mmm) REVERT: R 206 ARG cc_start: 0.7176 (tmm160) cc_final: 0.6898 (ttp-110) REVERT: R 246 TRP cc_start: 0.7054 (OUTLIER) cc_final: 0.6014 (t60) outliers start: 26 outliers final: 21 residues processed: 128 average time/residue: 0.6366 time to fit residues: 86.2931 Evaluate side-chains 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.174626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134598 restraints weight = 9248.130| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.98 r_work: 0.3255 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8673 Z= 0.126 Angle : 0.554 11.262 11755 Z= 0.281 Chirality : 0.041 0.181 1357 Planarity : 0.003 0.062 1467 Dihedral : 5.944 56.971 1246 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.70 % Allowed : 24.72 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.26), residues: 1093 helix: 2.78 (0.27), residues: 378 sheet: 0.69 (0.31), residues: 259 loop : -0.59 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 139 TYR 0.013 0.001 TYR S 178 PHE 0.017 0.001 PHE R 202 TRP 0.018 0.001 TRP R 144 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8671) covalent geometry : angle 0.55418 (11751) SS BOND : bond 0.00259 ( 2) SS BOND : angle 0.65002 ( 4) hydrogen bonds : bond 0.03237 ( 436) hydrogen bonds : angle 4.42691 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3300.51 seconds wall clock time: 56 minutes 59.76 seconds (3419.76 seconds total)