Starting phenix.real_space_refine on Sat Dec 28 12:10:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y15_33557/12_2024/7y15_33557.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y15_33557/12_2024/7y15_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y15_33557/12_2024/7y15_33557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y15_33557/12_2024/7y15_33557.map" model { file = "/net/cci-nas-00/data/ceres_data/7y15_33557/12_2024/7y15_33557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y15_33557/12_2024/7y15_33557.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} 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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} 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: 5.52, per 1000 atoms: 0.65 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: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.10 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: 2.87 Time building geometry restraints manager: 2.62 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: 2.000 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.060 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.590 ------------------------------------------------------------------------------- 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 8671 Z= 0.170 Angle : 0.563 9.830 11751 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 : 7.87 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.001 TRP R 144 HIS 0.008 0.001 HIS B 183 PHE 0.015 0.001 PHE R 202 TYR 0.012 0.001 TYR S 178 ARG 0.004 0.000 ARG S 148 *********************** 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 : 0.877 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: 1.2051 time to fit residues: 167.6422 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 : 1.011 ------------------------------------------------------------------------------- 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 91 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 259 GLN B 340 ASN C 59 ASN S 130 GLN S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8671 Z= 0.186 Angle : 0.502 7.472 11751 Z= 0.266 Chirality : 0.040 0.158 1357 Planarity : 0.003 0.057 1467 Dihedral : 6.964 59.958 1264 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.15 % Allowed : 19.21 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1093 helix: 2.77 (0.27), residues: 377 sheet: 0.64 (0.31), residues: 252 loop : -0.51 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 144 HIS 0.005 0.001 HIS B 183 PHE 0.014 0.001 PHE R 202 TYR 0.012 0.001 TYR S 178 ARG 0.003 0.000 ARG A 208 *********************** 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 133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.931 Fit side-chains REVERT: B 259 GLN cc_start: 0.8073 (pt0) cc_final: 0.7862 (pt0) outliers start: 28 outliers final: 14 residues processed: 123 average time/residue: 1.1627 time to fit residues: 153.0126 Evaluate side-chains 113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN 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 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 237 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 0.0570 overall best weight: 1.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 88 ASN S 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8671 Z= 0.264 Angle : 0.545 11.254 11751 Z= 0.283 Chirality : 0.042 0.171 1357 Planarity : 0.003 0.057 1467 Dihedral : 6.616 57.872 1249 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.82 % Allowed : 19.66 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1093 helix: 2.76 (0.27), residues: 377 sheet: 0.46 (0.31), residues: 260 loop : -0.54 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 144 HIS 0.003 0.001 HIS A 188 PHE 0.015 0.002 PHE R 202 TYR 0.016 0.001 TYR S 178 ARG 0.003 0.000 ARG B 150 *********************** 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: 34 poor density : 104 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: R 246 TRP cc_start: 0.6809 (OUTLIER) cc_final: 0.5792 (t60) outliers start: 34 outliers final: 19 residues processed: 127 average time/residue: 1.1827 time to fit residues: 160.9685 Evaluate side-chains 120 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG 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 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 175 CYS 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 R residue 265 SER Chi-restraints excluded: chain R residue 267 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 0.0010 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8671 Z= 0.167 Angle : 0.499 7.976 11751 Z= 0.258 Chirality : 0.040 0.154 1357 Planarity : 0.003 0.060 1467 Dihedral : 6.130 56.667 1249 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.15 % Allowed : 20.67 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1093 helix: 2.84 (0.27), residues: 379 sheet: 0.53 (0.31), residues: 260 loop : -0.55 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 144 HIS 0.003 0.001 HIS A 188 PHE 0.014 0.001 PHE R 202 TYR 0.012 0.001 TYR S 178 ARG 0.002 0.000 ARG B 49 *********************** 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 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: C 21 MET cc_start: 0.7887 (mmm) cc_final: 0.7684 (mmm) REVERT: R 246 TRP cc_start: 0.6757 (OUTLIER) cc_final: 0.5749 (t60) outliers start: 28 outliers final: 15 residues processed: 124 average time/residue: 1.1834 time to fit residues: 157.1095 Evaluate side-chains 117 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8671 Z= 0.306 Angle : 0.569 8.535 11751 Z= 0.295 Chirality : 0.042 0.175 1357 Planarity : 0.004 0.060 1467 Dihedral : 6.628 56.499 1249 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.71 % Allowed : 20.67 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1093 helix: 2.73 (0.27), residues: 379 sheet: 0.45 (0.32), residues: 254 loop : -0.59 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 144 HIS 0.004 0.001 HIS A 188 PHE 0.016 0.002 PHE R 202 TYR 0.018 0.002 TYR S 178 ARG 0.003 0.000 ARG B 150 *********************** 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 138 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: R 174 ARG cc_start: 0.4391 (mtp180) cc_final: 0.3961 (ttp-170) REVERT: R 246 TRP cc_start: 0.6825 (OUTLIER) cc_final: 0.5822 (t60) outliers start: 33 outliers final: 22 residues processed: 131 average time/residue: 1.2851 time to fit residues: 179.2011 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 : 1.044 ------------------------------------------------------------------------------- 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 37 ILE 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 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 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 175 CYS Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain R residue 265 SER Chi-restraints excluded: chain R residue 267 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8671 Z= 0.156 Angle : 0.495 8.295 11751 Z= 0.257 Chirality : 0.039 0.156 1357 Planarity : 0.003 0.061 1467 Dihedral : 5.990 56.384 1249 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.92 % Allowed : 22.92 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1093 helix: 2.87 (0.27), residues: 379 sheet: 0.60 (0.32), residues: 256 loop : -0.53 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 144 HIS 0.003 0.000 HIS A 188 PHE 0.015 0.001 PHE R 202 TYR 0.011 0.001 TYR S 178 ARG 0.005 0.000 ARG R 206 *********************** 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 129 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: R 246 TRP cc_start: 0.6761 (OUTLIER) cc_final: 0.5790 (t60) REVERT: S 67 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7529 (ptt90) outliers start: 26 outliers final: 18 residues processed: 123 average time/residue: 1.2284 time to fit residues: 161.6979 Evaluate side-chains 119 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 65 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 35 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain R residue 267 VAL 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 11 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 chunk 104 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8671 Z= 0.159 Angle : 0.507 10.434 11751 Z= 0.260 Chirality : 0.039 0.150 1357 Planarity : 0.003 0.062 1467 Dihedral : 5.738 57.222 1247 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.47 % Allowed : 23.26 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 1093 helix: 2.91 (0.27), residues: 378 sheet: 0.70 (0.32), residues: 252 loop : -0.54 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 144 HIS 0.003 0.001 HIS A 188 PHE 0.015 0.001 PHE R 202 TYR 0.012 0.001 TYR S 178 ARG 0.004 0.000 ARG R 206 *********************** 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 123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: C 21 MET cc_start: 0.7809 (mmm) cc_final: 0.7555 (mmm) REVERT: R 246 TRP cc_start: 0.6758 (OUTLIER) cc_final: 0.5789 (t60) REVERT: S 67 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7534 (ptt90) outliers start: 22 outliers final: 17 residues processed: 120 average time/residue: 1.1893 time to fit residues: 152.6240 Evaluate side-chains 118 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 175 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 246 TRP Chi-restraints excluded: chain R residue 265 SER 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 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.0050 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8671 Z= 0.133 Angle : 0.492 8.995 11751 Z= 0.252 Chirality : 0.039 0.149 1357 Planarity : 0.003 0.063 1467 Dihedral : 5.458 58.334 1246 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.25 % Allowed : 23.48 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 1093 helix: 2.94 (0.27), residues: 378 sheet: 0.73 (0.32), residues: 253 loop : -0.52 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 144 HIS 0.003 0.000 HIS A 188 PHE 0.015 0.001 PHE R 202 TYR 0.010 0.001 TYR S 178 ARG 0.003 0.000 ARG R 206 *********************** 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 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: C 21 MET cc_start: 0.7851 (mmm) cc_final: 0.7634 (mmm) REVERT: R 253 MET cc_start: 0.6350 (pmm) cc_final: 0.5901 (pp-130) REVERT: S 46 GLU cc_start: 0.7974 (tt0) cc_final: 0.7753 (pt0) REVERT: S 67 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7390 (ptt90) outliers start: 20 outliers final: 16 residues processed: 121 average time/residue: 1.2256 time to fit residues: 158.1064 Evaluate side-chains 121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 175 CYS Chi-restraints excluded: chain R residue 265 SER 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 90 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8671 Z= 0.166 Angle : 0.525 9.367 11751 Z= 0.269 Chirality : 0.040 0.172 1357 Planarity : 0.003 0.063 1467 Dihedral : 5.492 57.869 1245 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.13 % Allowed : 23.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 1093 helix: 2.86 (0.27), residues: 378 sheet: 0.69 (0.31), residues: 259 loop : -0.50 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 144 HIS 0.003 0.001 HIS A 188 PHE 0.017 0.001 PHE A 274 TYR 0.012 0.001 TYR S 178 ARG 0.003 0.000 ARG R 206 *********************** 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 123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: R 253 MET cc_start: 0.6332 (pmm) cc_final: 0.5913 (pp-130) REVERT: S 46 GLU cc_start: 0.8007 (tt0) cc_final: 0.7784 (pt0) REVERT: S 67 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7589 (ptt90) outliers start: 19 outliers final: 16 residues processed: 120 average time/residue: 1.2049 time to fit residues: 154.4280 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 : 0.924 ------------------------------------------------------------------------------- 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 65 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 175 CYS Chi-restraints excluded: chain R residue 235 LEU 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 102 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8671 Z= 0.158 Angle : 0.521 9.622 11751 Z= 0.268 Chirality : 0.040 0.175 1357 Planarity : 0.003 0.063 1467 Dihedral : 5.426 58.137 1245 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.02 % Allowed : 24.72 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.26), residues: 1093 helix: 2.86 (0.27), residues: 378 sheet: 0.70 (0.32), residues: 258 loop : -0.47 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.003 0.000 HIS A 188 PHE 0.017 0.001 PHE R 77 TYR 0.011 0.001 TYR S 178 ARG 0.003 0.000 ARG R 206 ********************** 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 125 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: R 253 MET cc_start: 0.6303 (pmm) cc_final: 0.5889 (pp-130) REVERT: S 46 GLU cc_start: 0.7995 (tt0) cc_final: 0.7784 (pt0) REVERT: S 67 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7513 (ptt90) outliers start: 18 outliers final: 17 residues processed: 121 average time/residue: 1.1871 time to fit residues: 153.6275 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 65 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 175 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 265 SER 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 91 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.173489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133403 restraints weight = 9085.388| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.90 r_work: 0.3267 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8671 Z= 0.253 Angle : 0.575 10.407 11751 Z= 0.295 Chirality : 0.041 0.158 1357 Planarity : 0.004 0.062 1467 Dihedral : 5.899 56.083 1245 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.36 % Allowed : 24.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1093 helix: 2.77 (0.27), residues: 379 sheet: 0.57 (0.32), residues: 259 loop : -0.49 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 144 HIS 0.004 0.001 HIS A 188 PHE 0.018 0.002 PHE R 77 TYR 0.016 0.001 TYR S 178 ARG 0.004 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3279.58 seconds wall clock time: 59 minutes 49.38 seconds (3589.38 seconds total)