Starting phenix.real_space_refine on Mon Apr 28 22:50:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zce_39927/04_2025/8zce_39927.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zce_39927/04_2025/8zce_39927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zce_39927/04_2025/8zce_39927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zce_39927/04_2025/8zce_39927.map" model { file = "/net/cci-nas-00/data/ceres_data/8zce_39927/04_2025/8zce_39927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zce_39927/04_2025/8zce_39927.cif" } resolution = 3.1 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 251 atoms to isotropic. 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 50 5.16 5 C 5054 2.51 5 N 1375 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7963 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1797 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 3 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2508 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 395 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 947 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2316 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 12, 'TRANS': 282} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 5.12, per 1000 atoms: 0.64 Number of scatterers: 7963 At special positions: 0 Unit cell: (84.24, 94.64, 132.08, 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 50 16.00 O 1484 8.00 N 1375 7.00 C 5054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 258 " 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: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 40.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.747A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 61 removed outlier: 3.744A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.865A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.287A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.983A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 11 through 25 removed outlier: 3.599A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 4.424A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 17 Processing helix chain 'R' and resid 18 through 48 removed outlier: 3.712A pdb=" N LEU R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 79 removed outlier: 3.891A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 98 removed outlier: 4.042A pdb=" N PHE R 95 " --> pdb=" O LYS R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 120 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 150 through 155 removed outlier: 3.983A pdb=" N PHE R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 150 through 155' Processing helix chain 'R' and resid 175 through 188 Processing helix chain 'R' and resid 190 through 211 Processing helix chain 'R' and resid 215 through 254 removed outlier: 4.052A pdb=" N VAL R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 259 through 276 removed outlier: 4.087A pdb=" N ARG R 263 " --> pdb=" O GLY R 259 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 301 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.719A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.670A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.798A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.408A 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: 4.248A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.843A 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 153 removed outlier: 3.759A pdb=" N LEU B 152 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.714A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.648A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.589A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.518A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.825A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN N 39 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR N 95 " --> pdb=" O VAL N 37 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 17 through 19 Processing sheet with id=AB3, first strand: chain 'R' and resid 159 through 160 392 hydrogen bonds defined for protein. 1122 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: 2.21 Time building geometry restraints manager: 2.35 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: 2628 1.34 - 1.46: 1991 1.46 - 1.58: 3453 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 8139 Sorted by residual: bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.457 1.496 -0.039 9.30e-03 1.16e+04 1.78e+01 bond pdb=" CA GLN N 39 " pdb=" CB GLN N 39 " ideal model delta sigma weight residual 1.528 1.577 -0.049 1.51e-02 4.39e+03 1.05e+01 bond pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.35e-02 5.49e+03 6.30e+00 bond pdb=" C LEU R 70 " pdb=" N PRO R 71 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.37e+00 bond pdb=" C ILE B 270 " pdb=" O ILE B 270 " ideal model delta sigma weight residual 1.232 1.251 -0.019 1.30e-02 5.92e+03 2.24e+00 ... (remaining 8134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 10844 2.00 - 3.99: 197 3.99 - 5.99: 21 5.99 - 7.99: 9 7.99 - 9.98: 1 Bond angle restraints: 11072 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 106.56 6.64 9.60e-01 1.09e+00 4.78e+01 angle pdb=" CB LYS A 271 " pdb=" CG LYS A 271 " pdb=" CD LYS A 271 " ideal model delta sigma weight residual 111.30 103.69 7.61 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA PRO R 173 " pdb=" N PRO R 173 " pdb=" CD PRO R 173 " ideal model delta sigma weight residual 112.00 107.62 4.38 1.40e+00 5.10e-01 9.79e+00 angle pdb=" CD LYS A 271 " pdb=" CE LYS A 271 " pdb=" NZ LYS A 271 " ideal model delta sigma weight residual 111.90 101.92 9.98 3.20e+00 9.77e-02 9.74e+00 angle pdb=" N ILE A 308 " pdb=" CA ILE A 308 " pdb=" C ILE A 308 " ideal model delta sigma weight residual 111.62 109.17 2.45 7.90e-01 1.60e+00 9.65e+00 ... (remaining 11067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.26: 4052 13.26 - 26.52: 451 26.52 - 39.77: 176 39.77 - 53.03: 62 53.03 - 66.29: 37 Dihedral angle restraints: 4778 sinusoidal: 1755 harmonic: 3023 Sorted by residual: dihedral pdb=" CB CYS R 9 " pdb=" SG CYS R 9 " pdb=" SG CYS R 258 " pdb=" CB CYS R 258 " ideal model delta sinusoidal sigma weight residual -86.00 -123.42 37.42 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N PRO R 173 " pdb=" CA PRO R 173 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CG ARG R 216 " pdb=" CD ARG R 216 " pdb=" NE ARG R 216 " pdb=" CZ ARG R 216 " ideal model delta sinusoidal sigma weight residual -90.00 -36.73 -53.27 2 1.50e+01 4.44e-03 1.37e+01 ... (remaining 4775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 937 0.045 - 0.091: 252 0.091 - 0.136: 62 0.136 - 0.182: 2 0.182 - 0.227: 1 Chirality restraints: 1254 Sorted by residual: chirality pdb=" CA ILE B 270 " pdb=" N ILE B 270 " pdb=" C ILE B 270 " pdb=" CB ILE B 270 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LYS A 271 " pdb=" N LYS A 271 " pdb=" C LYS A 271 " pdb=" CB LYS A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CB ILE B 18 " pdb=" CA ILE B 18 " pdb=" CG1 ILE B 18 " pdb=" CG2 ILE B 18 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.09e-01 ... (remaining 1251 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 172 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO R 173 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO R 173 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 173 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS N 99 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO N 100 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO N 100 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO N 100 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 99 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.36e+00 pdb=" C THR R 99 " -0.040 2.00e-02 2.50e+03 pdb=" O THR R 99 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN R 100 " 0.013 2.00e-02 2.50e+03 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 169 2.68 - 3.23: 7972 3.23 - 3.79: 13355 3.79 - 4.34: 17856 4.34 - 4.90: 29087 Nonbonded interactions: 68439 Sorted by model distance: nonbonded pdb=" OG SER R 13 " pdb=" OG SER R 266 " model vdw 2.122 3.040 nonbonded pdb=" O ALA R 267 " pdb=" OG SER R 271 " model vdw 2.135 3.040 nonbonded pdb=" NH1 ARG N 67 " pdb=" O SER N 85 " model vdw 2.174 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.217 3.040 nonbonded pdb=" OE2 GLU B 226 " pdb=" OH TYR N 32 " model vdw 2.244 3.040 ... (remaining 68434 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.770 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 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 : 0.004 0.065 8140 Z= 0.192 Angle : 0.661 9.985 11074 Z= 0.374 Chirality : 0.043 0.227 1254 Planarity : 0.005 0.103 1425 Dihedral : 15.439 66.291 2821 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.36 % Allowed : 24.09 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.26), residues: 1023 helix: 1.37 (0.26), residues: 389 sheet: -0.36 (0.40), residues: 188 loop : -1.69 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.006 0.001 HIS B 54 PHE 0.031 0.002 PHE R 169 TYR 0.026 0.002 TYR N 115 ARG 0.012 0.001 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.16431 ( 392) hydrogen bonds : angle 6.23893 ( 1122) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.48289 ( 2) covalent geometry : bond 0.00394 ( 8139) covalent geometry : angle 0.66133 (11072) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 ASP cc_start: 0.6773 (t0) cc_final: 0.6531 (t0) REVERT: R 102 TYR cc_start: 0.7506 (m-80) cc_final: 0.7222 (m-80) REVERT: R 155 HIS cc_start: 0.6212 (m90) cc_final: 0.5843 (m90) REVERT: R 169 PHE cc_start: 0.6048 (t80) cc_final: 0.5505 (t80) outliers start: 3 outliers final: 2 residues processed: 130 average time/residue: 0.2643 time to fit residues: 43.9983 Evaluate side-chains 128 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 9 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN A 362 HIS ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.167014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.150346 restraints weight = 10961.853| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.80 r_work: 0.3871 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8140 Z= 0.187 Angle : 0.605 7.187 11074 Z= 0.324 Chirality : 0.043 0.132 1254 Planarity : 0.005 0.067 1425 Dihedral : 4.863 49.806 1127 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.41 % Allowed : 20.92 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.26), residues: 1023 helix: 1.55 (0.26), residues: 390 sheet: -0.60 (0.37), residues: 200 loop : -1.67 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.006 0.001 HIS B 54 PHE 0.021 0.002 PHE R 107 TYR 0.017 0.002 TYR R 76 ARG 0.007 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 392) hydrogen bonds : angle 4.93691 ( 1122) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.55372 ( 2) covalent geometry : bond 0.00422 ( 8139) covalent geometry : angle 0.60467 (11072) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.6636 (pp30) cc_final: 0.6433 (pp30) REVERT: A 270 LEU cc_start: 0.8205 (mt) cc_final: 0.7795 (mp) REVERT: A 299 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5270 (pp20) REVERT: A 384 GLN cc_start: 0.6944 (tt0) cc_final: 0.6727 (tt0) REVERT: B 188 MET cc_start: 0.7728 (mmt) cc_final: 0.7522 (mmm) REVERT: B 212 ASP cc_start: 0.6852 (t70) cc_final: 0.6589 (t0) REVERT: B 234 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: B 262 MET cc_start: 0.7637 (tpt) cc_final: 0.7433 (tpt) REVERT: B 314 ARG cc_start: 0.7190 (ttt90) cc_final: 0.6921 (ttt90) REVERT: R 155 HIS cc_start: 0.6492 (m90) cc_final: 0.5846 (m90) REVERT: R 169 PHE cc_start: 0.6367 (t80) cc_final: 0.5723 (t80) REVERT: R 223 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7826 (ttmm) REVERT: R 277 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7200 (mt) outliers start: 28 outliers final: 14 residues processed: 151 average time/residue: 0.2379 time to fit residues: 46.9974 Evaluate side-chains 149 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 9 CYS Chi-restraints excluded: chain R residue 89 SER Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 84 optimal weight: 0.0170 chunk 55 optimal weight: 0.0000 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.3220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 HIS ** 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 = 0.4185 r_free = 0.4185 target = 0.169203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.152385 restraints weight = 11173.780| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.84 r_work: 0.3898 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8140 Z= 0.124 Angle : 0.538 6.732 11074 Z= 0.288 Chirality : 0.041 0.142 1254 Planarity : 0.004 0.064 1425 Dihedral : 4.554 50.896 1125 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.65 % Allowed : 19.10 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.26), residues: 1023 helix: 1.84 (0.26), residues: 390 sheet: -0.42 (0.37), residues: 198 loop : -1.61 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS B 54 PHE 0.015 0.002 PHE R 93 TYR 0.016 0.001 TYR N 115 ARG 0.008 0.001 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 392) hydrogen bonds : angle 4.64258 ( 1122) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.63968 ( 2) covalent geometry : bond 0.00268 ( 8139) covalent geometry : angle 0.53756 (11072) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.6638 (pp30) cc_final: 0.6397 (pp30) REVERT: A 20 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6475 (mmp-170) REVERT: A 270 LEU cc_start: 0.8272 (mt) cc_final: 0.8066 (mt) REVERT: A 299 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5298 (pp20) REVERT: B 125 ASN cc_start: 0.7576 (t0) cc_final: 0.7296 (t0) REVERT: B 212 ASP cc_start: 0.6705 (t70) cc_final: 0.6434 (t0) REVERT: B 234 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: B 262 MET cc_start: 0.7434 (tpt) cc_final: 0.7103 (tpt) REVERT: B 314 ARG cc_start: 0.7206 (ttt90) cc_final: 0.6914 (ttt90) REVERT: N 80 TYR cc_start: 0.7702 (m-80) cc_final: 0.7441 (m-80) REVERT: R 66 TYR cc_start: 0.7267 (t80) cc_final: 0.7064 (t80) REVERT: R 155 HIS cc_start: 0.6470 (m90) cc_final: 0.5824 (m90) REVERT: R 169 PHE cc_start: 0.6199 (t80) cc_final: 0.5451 (t80) REVERT: R 223 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7777 (ttmm) outliers start: 30 outliers final: 15 residues processed: 163 average time/residue: 0.2334 time to fit residues: 49.8529 Evaluate side-chains 151 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 9 CYS Chi-restraints excluded: chain R residue 89 SER Chi-restraints excluded: chain R residue 264 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 12 optimal weight: 0.0980 chunk 4 optimal weight: 0.0170 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 100 optimal weight: 0.0370 chunk 67 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.169588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.152841 restraints weight = 11016.491| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.83 r_work: 0.3909 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8140 Z= 0.113 Angle : 0.516 6.756 11074 Z= 0.275 Chirality : 0.041 0.136 1254 Planarity : 0.004 0.065 1425 Dihedral : 4.389 49.565 1125 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.77 % Allowed : 19.95 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.26), residues: 1023 helix: 2.02 (0.27), residues: 391 sheet: -0.44 (0.36), residues: 198 loop : -1.57 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS B 54 PHE 0.015 0.001 PHE A 212 TYR 0.015 0.001 TYR N 115 ARG 0.009 0.001 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 392) hydrogen bonds : angle 4.42690 ( 1122) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.58205 ( 2) covalent geometry : bond 0.00241 ( 8139) covalent geometry : angle 0.51561 (11072) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.6611 (pp30) cc_final: 0.6369 (pp30) REVERT: A 20 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6467 (mmp-170) REVERT: A 227 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7254 (mm-40) REVERT: A 299 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5288 (pp20) REVERT: B 125 ASN cc_start: 0.7487 (t0) cc_final: 0.7246 (t0) REVERT: B 212 ASP cc_start: 0.6638 (t70) cc_final: 0.6352 (t0) REVERT: B 234 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: B 262 MET cc_start: 0.7395 (tpt) cc_final: 0.7149 (tpt) REVERT: B 314 ARG cc_start: 0.7224 (ttt90) cc_final: 0.6943 (ttt90) REVERT: C 15 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7361 (tm) REVERT: N 80 TYR cc_start: 0.7643 (m-80) cc_final: 0.7383 (m-80) REVERT: R 155 HIS cc_start: 0.6514 (m90) cc_final: 0.5949 (m90) REVERT: R 159 PHE cc_start: 0.8032 (m-80) cc_final: 0.7268 (m-80) REVERT: R 169 PHE cc_start: 0.6084 (t80) cc_final: 0.5373 (t80) REVERT: R 223 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7784 (ttmm) REVERT: R 277 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7204 (mt) outliers start: 31 outliers final: 20 residues processed: 167 average time/residue: 0.2241 time to fit residues: 48.8744 Evaluate side-chains 163 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 9 CYS Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 0.0980 chunk 59 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS B 340 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.168699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.151896 restraints weight = 10975.226| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.83 r_work: 0.3895 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8140 Z= 0.131 Angle : 0.528 6.805 11074 Z= 0.281 Chirality : 0.041 0.133 1254 Planarity : 0.004 0.064 1425 Dihedral : 4.395 48.069 1125 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.26 % Allowed : 20.07 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.26), residues: 1023 helix: 1.98 (0.26), residues: 391 sheet: -0.58 (0.35), residues: 205 loop : -1.52 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.002 PHE A 212 TYR 0.016 0.001 TYR R 76 ARG 0.008 0.001 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 392) hydrogen bonds : angle 4.41902 ( 1122) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.66444 ( 2) covalent geometry : bond 0.00290 ( 8139) covalent geometry : angle 0.52846 (11072) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.6608 (pp30) cc_final: 0.6359 (pp30) REVERT: A 20 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6470 (mmp-170) REVERT: A 299 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5304 (pp20) REVERT: B 125 ASN cc_start: 0.7451 (t0) cc_final: 0.7222 (t0) REVERT: B 212 ASP cc_start: 0.6604 (t70) cc_final: 0.6305 (t0) REVERT: B 234 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: B 255 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6797 (mt) REVERT: B 283 ARG cc_start: 0.7351 (tpt-90) cc_final: 0.7138 (tpt-90) REVERT: B 314 ARG cc_start: 0.7284 (ttt90) cc_final: 0.7048 (ttt90) REVERT: C 15 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7396 (tm) REVERT: N 80 TYR cc_start: 0.7644 (m-80) cc_final: 0.7378 (m-80) REVERT: R 155 HIS cc_start: 0.6516 (m90) cc_final: 0.5972 (m90) REVERT: R 169 PHE cc_start: 0.6112 (t80) cc_final: 0.5436 (t80) REVERT: R 223 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7788 (ttmm) REVERT: R 277 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7208 (mt) outliers start: 35 outliers final: 23 residues processed: 163 average time/residue: 0.2769 time to fit residues: 60.5892 Evaluate side-chains 163 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 9 CYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 96 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.168654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.151847 restraints weight = 10902.566| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.83 r_work: 0.3897 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8140 Z= 0.127 Angle : 0.525 6.826 11074 Z= 0.279 Chirality : 0.041 0.140 1254 Planarity : 0.004 0.063 1425 Dihedral : 4.358 47.618 1125 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.87 % Allowed : 20.19 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.26), residues: 1023 helix: 2.02 (0.26), residues: 391 sheet: -0.48 (0.36), residues: 203 loop : -1.51 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS B 54 PHE 0.016 0.002 PHE A 212 TYR 0.017 0.001 TYR R 76 ARG 0.008 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 392) hydrogen bonds : angle 4.37573 ( 1122) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.63565 ( 2) covalent geometry : bond 0.00280 ( 8139) covalent geometry : angle 0.52509 (11072) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.6628 (pp30) cc_final: 0.6407 (pp30) REVERT: A 20 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6464 (mmp-170) REVERT: A 227 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7286 (mm-40) REVERT: A 299 GLU cc_start: 0.5908 (OUTLIER) cc_final: 0.5613 (pp20) REVERT: B 125 ASN cc_start: 0.7436 (t0) cc_final: 0.7216 (t0) REVERT: B 212 ASP cc_start: 0.6653 (t70) cc_final: 0.6352 (t0) REVERT: B 234 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: B 255 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6797 (mt) REVERT: B 262 MET cc_start: 0.7578 (tpt) cc_final: 0.7238 (tpt) REVERT: B 314 ARG cc_start: 0.7288 (ttt90) cc_final: 0.7066 (ttt90) REVERT: C 15 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7430 (tm) REVERT: N 50 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7232 (p0) REVERT: N 80 TYR cc_start: 0.7609 (m-80) cc_final: 0.7347 (m-80) REVERT: R 9 CYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5474 (m) REVERT: R 155 HIS cc_start: 0.6523 (m90) cc_final: 0.5960 (m90) REVERT: R 169 PHE cc_start: 0.6225 (t80) cc_final: 0.5542 (t80) REVERT: R 223 LYS cc_start: 0.8130 (ttmm) cc_final: 0.7695 (ttmm) REVERT: R 277 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7234 (mt) outliers start: 40 outliers final: 25 residues processed: 167 average time/residue: 0.2306 time to fit residues: 50.2270 Evaluate side-chains 169 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 9 CYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 13 optimal weight: 0.0470 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN B 340 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.168471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.151626 restraints weight = 11061.322| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.84 r_work: 0.3894 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8140 Z= 0.126 Angle : 0.525 6.762 11074 Z= 0.279 Chirality : 0.041 0.152 1254 Planarity : 0.004 0.063 1425 Dihedral : 4.330 46.889 1125 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.87 % Allowed : 20.44 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.26), residues: 1023 helix: 2.08 (0.26), residues: 390 sheet: -0.44 (0.36), residues: 203 loop : -1.51 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.003 0.001 HIS B 54 PHE 0.016 0.001 PHE A 212 TYR 0.017 0.001 TYR N 115 ARG 0.009 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 392) hydrogen bonds : angle 4.32047 ( 1122) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.64610 ( 2) covalent geometry : bond 0.00278 ( 8139) covalent geometry : angle 0.52526 (11072) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6464 (mmp-170) REVERT: A 227 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7242 (mm-40) REVERT: A 270 LEU cc_start: 0.8263 (mt) cc_final: 0.7929 (mp) REVERT: A 299 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5505 (pp20) REVERT: B 212 ASP cc_start: 0.6560 (t70) cc_final: 0.6246 (t0) REVERT: B 234 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: B 262 MET cc_start: 0.7583 (tpt) cc_final: 0.7305 (tpt) REVERT: B 314 ARG cc_start: 0.7425 (ttt90) cc_final: 0.7216 (ttt90) REVERT: C 15 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7445 (tm) REVERT: N 80 TYR cc_start: 0.7612 (m-80) cc_final: 0.7354 (m-80) REVERT: R 9 CYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5491 (m) REVERT: R 155 HIS cc_start: 0.6542 (m90) cc_final: 0.6281 (m-70) REVERT: R 169 PHE cc_start: 0.6270 (t80) cc_final: 0.5555 (t80) REVERT: R 277 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7205 (mt) outliers start: 40 outliers final: 24 residues processed: 160 average time/residue: 0.2311 time to fit residues: 48.9528 Evaluate side-chains 159 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 9 CYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.0170 chunk 21 optimal weight: 0.7980 chunk 95 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 3 optimal weight: 0.9980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.169019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.152065 restraints weight = 11014.254| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.84 r_work: 0.3898 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8140 Z= 0.121 Angle : 0.526 6.827 11074 Z= 0.281 Chirality : 0.041 0.187 1254 Planarity : 0.004 0.062 1425 Dihedral : 4.324 47.409 1125 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.01 % Allowed : 20.92 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.26), residues: 1023 helix: 2.10 (0.26), residues: 391 sheet: -0.40 (0.36), residues: 203 loop : -1.51 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS B 54 PHE 0.015 0.001 PHE A 212 TYR 0.023 0.001 TYR N 115 ARG 0.009 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 392) hydrogen bonds : angle 4.30278 ( 1122) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.61770 ( 2) covalent geometry : bond 0.00266 ( 8139) covalent geometry : angle 0.52625 (11072) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6476 (mmp-170) REVERT: A 270 LEU cc_start: 0.8257 (mt) cc_final: 0.7914 (mp) REVERT: A 299 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5515 (pp20) REVERT: B 61 MET cc_start: 0.8019 (ppp) cc_final: 0.7356 (ppp) REVERT: B 212 ASP cc_start: 0.6612 (t70) cc_final: 0.6289 (t0) REVERT: B 234 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: B 245 SER cc_start: 0.6880 (m) cc_final: 0.6259 (t) REVERT: B 262 MET cc_start: 0.7568 (tpt) cc_final: 0.7294 (tpt) REVERT: B 314 ARG cc_start: 0.7443 (ttt90) cc_final: 0.7226 (ttt90) REVERT: C 15 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7434 (tm) REVERT: N 80 TYR cc_start: 0.7626 (m-80) cc_final: 0.7369 (m-80) REVERT: R 9 CYS cc_start: 0.5882 (OUTLIER) cc_final: 0.5422 (m) REVERT: R 169 PHE cc_start: 0.6274 (t80) cc_final: 0.5572 (t80) outliers start: 33 outliers final: 24 residues processed: 150 average time/residue: 0.2943 time to fit residues: 59.9719 Evaluate side-chains 154 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 9 CYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 264 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 241 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.163621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.146505 restraints weight = 11186.711| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.84 r_work: 0.3823 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 8140 Z= 0.290 Angle : 0.663 7.806 11074 Z= 0.352 Chirality : 0.046 0.183 1254 Planarity : 0.005 0.067 1425 Dihedral : 4.807 43.504 1125 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.87 % Allowed : 20.56 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.25), residues: 1023 helix: 1.38 (0.26), residues: 393 sheet: -0.60 (0.36), residues: 195 loop : -1.61 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 234 HIS 0.007 0.002 HIS B 54 PHE 0.023 0.003 PHE R 107 TYR 0.029 0.003 TYR N 115 ARG 0.008 0.001 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 392) hydrogen bonds : angle 4.69645 ( 1122) SS BOND : bond 0.00136 ( 1) SS BOND : angle 1.11268 ( 2) covalent geometry : bond 0.00668 ( 8139) covalent geometry : angle 0.66324 (11072) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7360 (mt-10) REVERT: A 299 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5659 (pp20) REVERT: B 61 MET cc_start: 0.7993 (ppp) cc_final: 0.7358 (ppp) REVERT: B 170 ASP cc_start: 0.7091 (t70) cc_final: 0.6739 (t0) REVERT: B 212 ASP cc_start: 0.6903 (t70) cc_final: 0.6570 (t0) REVERT: B 234 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: B 262 MET cc_start: 0.7741 (tpt) cc_final: 0.7518 (tpt) REVERT: B 314 ARG cc_start: 0.7456 (ttt90) cc_final: 0.7104 (ttt90) REVERT: C 15 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7528 (tm) REVERT: N 91 THR cc_start: 0.6895 (OUTLIER) cc_final: 0.6551 (p) REVERT: R 52 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7003 (mp) REVERT: R 155 HIS cc_start: 0.6663 (m90) cc_final: 0.6300 (m-70) REVERT: R 277 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7234 (mt) outliers start: 40 outliers final: 28 residues processed: 156 average time/residue: 0.2262 time to fit residues: 46.8680 Evaluate side-chains 162 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 9 CYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 0.0270 chunk 22 optimal weight: 4.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.166097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.149119 restraints weight = 10959.552| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.82 r_work: 0.3860 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8140 Z= 0.170 Angle : 0.586 6.735 11074 Z= 0.313 Chirality : 0.043 0.266 1254 Planarity : 0.004 0.065 1425 Dihedral : 4.680 44.767 1125 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.65 % Allowed : 23.11 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.26), residues: 1023 helix: 1.78 (0.27), residues: 385 sheet: -0.62 (0.36), residues: 200 loop : -1.54 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.005 0.001 HIS B 54 PHE 0.019 0.002 PHE A 222 TYR 0.030 0.002 TYR N 115 ARG 0.010 0.001 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 392) hydrogen bonds : angle 4.53345 ( 1122) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.70073 ( 2) covalent geometry : bond 0.00390 ( 8139) covalent geometry : angle 0.58605 (11072) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 299 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.5177 (pp20) REVERT: B 61 MET cc_start: 0.7750 (ppp) cc_final: 0.7293 (ptm) REVERT: B 170 ASP cc_start: 0.7201 (t70) cc_final: 0.6839 (t0) REVERT: B 212 ASP cc_start: 0.6791 (t70) cc_final: 0.6480 (t0) REVERT: B 234 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: B 262 MET cc_start: 0.7629 (tpt) cc_final: 0.7381 (tpt) REVERT: B 314 ARG cc_start: 0.7499 (ttt90) cc_final: 0.7253 (ttt90) REVERT: C 15 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7523 (tm) REVERT: N 98 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7699 (ttp80) REVERT: R 155 HIS cc_start: 0.6629 (m90) cc_final: 0.6292 (m-70) REVERT: R 169 PHE cc_start: 0.6469 (t80) cc_final: 0.5488 (t80) outliers start: 30 outliers final: 23 residues processed: 148 average time/residue: 0.2626 time to fit residues: 51.7216 Evaluate side-chains 162 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 9 CYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.0040 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 0.0770 chunk 41 optimal weight: 0.3980 chunk 18 optimal weight: 0.0670 chunk 85 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 overall best weight: 0.2288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.169100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.152314 restraints weight = 11038.000| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.84 r_work: 0.3905 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 8140 Z= 0.113 Angle : 0.535 6.661 11074 Z= 0.285 Chirality : 0.041 0.246 1254 Planarity : 0.004 0.064 1425 Dihedral : 4.396 46.175 1125 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.28 % Allowed : 23.36 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.26), residues: 1023 helix: 2.22 (0.27), residues: 384 sheet: -0.47 (0.36), residues: 198 loop : -1.53 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 281 HIS 0.004 0.001 HIS B 54 PHE 0.014 0.001 PHE R 172 TYR 0.027 0.001 TYR N 115 ARG 0.010 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 392) hydrogen bonds : angle 4.25326 ( 1122) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.56264 ( 2) covalent geometry : bond 0.00243 ( 8139) covalent geometry : angle 0.53536 (11072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5066.50 seconds wall clock time: 89 minutes 27.22 seconds (5367.22 seconds total)