Starting phenix.real_space_refine on Wed Sep 17 15:17:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1o_63578/09_2025/9m1o_63578.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1o_63578/09_2025/9m1o_63578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m1o_63578/09_2025/9m1o_63578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1o_63578/09_2025/9m1o_63578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m1o_63578/09_2025/9m1o_63578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1o_63578/09_2025/9m1o_63578.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5810 2.51 5 N 1532 2.21 5 O 1676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9085 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2352 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2631 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 5, 'TRANS': 337} Chain: "G" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 450 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1762 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1812 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 2.24, per 1000 atoms: 0.25 Number of scatterers: 9085 At special positions: 0 Unit cell: (86.87, 118.99, 132.86, 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 67 16.00 O 1676 8.00 N 1532 7.00 C 5810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 220 " - pdb=" SG CYS R 308 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 248.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.1% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 143 through 175 removed outlier: 3.687A pdb=" N ILE R 171 " --> pdb=" O VAL R 167 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL R 172 " --> pdb=" O VAL R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 210 Proline residue: R 202 - end of helix Processing helix chain 'R' and resid 216 through 251 Processing helix chain 'R' and resid 258 through 277 removed outlier: 4.391A pdb=" N MET R 277 " --> pdb=" O ALA R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 283 removed outlier: 3.509A pdb=" N ALA R 281 " --> pdb=" O MET R 277 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET R 283 " --> pdb=" O PRO R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 330 removed outlier: 3.986A pdb=" N ARG R 318 " --> pdb=" O ASN R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 350 removed outlier: 3.534A pdb=" N ARG R 350 " --> pdb=" O ILE R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 369 through 401 removed outlier: 3.923A pdb=" N LYS R 373 " --> pdb=" O ARG R 369 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TRP R 389 " --> pdb=" O PHE R 385 " (cutoff:3.500A) Proline residue: R 391 - end of helix Processing helix chain 'R' and resid 405 through 438 removed outlier: 4.348A pdb=" N TYR R 417 " --> pdb=" O ASN R 413 " (cutoff:3.500A) Proline residue: R 418 - end of helix Proline residue: R 432 - end of helix Processing helix chain 'R' and resid 439 through 443 Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.548A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.616A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.321A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.086A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.745A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.534A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 288 through 293 removed outlier: 3.880A pdb=" N VAL R 305 " --> pdb=" O GLU R 289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.486A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.428A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.771A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.677A 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: 6.460A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.885A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.262A 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: 3.655A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.061A 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: 3.665A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.753A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.335A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.114A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 185 through 189 removed outlier: 6.552A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2899 1.34 - 1.46: 1849 1.46 - 1.57: 4430 1.57 - 1.69: 0 1.69 - 1.81: 101 Bond restraints: 9279 Sorted by residual: bond pdb=" N VAL S 149 " pdb=" CA VAL S 149 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.12e+01 bond pdb=" N ILE R 157 " pdb=" CA ILE R 157 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.14e-02 7.69e+03 7.83e+00 bond pdb=" N PHE R 159 " pdb=" CA PHE R 159 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.16e-02 7.43e+03 7.15e+00 bond pdb=" N PHE R 158 " pdb=" CA PHE R 158 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.16e-02 7.43e+03 6.48e+00 bond pdb=" N VAL S 147 " pdb=" CA VAL S 147 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.23e-02 6.61e+03 6.29e+00 ... (remaining 9274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 12307 1.67 - 3.33: 218 3.33 - 5.00: 39 5.00 - 6.66: 7 6.66 - 8.33: 2 Bond angle restraints: 12573 Sorted by residual: angle pdb=" C GLN A 52 " pdb=" N MET A 53 " pdb=" CA MET A 53 " ideal model delta sigma weight residual 122.73 117.04 5.69 1.61e+00 3.86e-01 1.25e+01 angle pdb=" CA THR S 150 " pdb=" CB THR S 150 " pdb=" OG1 THR S 150 " ideal model delta sigma weight residual 109.60 104.49 5.11 1.50e+00 4.44e-01 1.16e+01 angle pdb=" CA VAL S 149 " pdb=" C VAL S 149 " pdb=" O VAL S 149 " ideal model delta sigma weight residual 121.67 118.38 3.29 1.05e+00 9.07e-01 9.85e+00 angle pdb=" N PHE R 155 " pdb=" CA PHE R 155 " pdb=" C PHE R 155 " ideal model delta sigma weight residual 111.28 107.95 3.33 1.09e+00 8.42e-01 9.34e+00 angle pdb=" CA ILE R 157 " pdb=" C ILE R 157 " pdb=" O ILE R 157 " ideal model delta sigma weight residual 121.27 118.10 3.17 1.04e+00 9.25e-01 9.31e+00 ... (remaining 12568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4701 17.67 - 35.33: 597 35.33 - 53.00: 159 53.00 - 70.67: 31 70.67 - 88.33: 10 Dihedral angle restraints: 5498 sinusoidal: 2115 harmonic: 3383 Sorted by residual: dihedral pdb=" CB CYS R 220 " pdb=" SG CYS R 220 " pdb=" SG CYS R 308 " pdb=" CB CYS R 308 " ideal model delta sinusoidal sigma weight residual -86.00 -160.83 74.83 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CA LYS G 46 " pdb=" C LYS G 46 " pdb=" N GLU G 47 " pdb=" CA GLU G 47 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TYR R 139 " pdb=" C TYR R 139 " pdb=" N TYR R 140 " pdb=" CA TYR R 140 " ideal model delta harmonic sigma weight residual 180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 5495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1085 0.045 - 0.090: 262 0.090 - 0.135: 79 0.135 - 0.180: 1 0.180 - 0.225: 3 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE R 157 " pdb=" N ILE R 157 " pdb=" C ILE R 157 " pdb=" CB ILE R 157 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL S 147 " pdb=" N VAL S 147 " pdb=" C VAL S 147 " pdb=" CB VAL S 147 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 1427 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN L 4 " 0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO L 5 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO L 5 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO L 5 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 431 " 0.040 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO R 432 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 432 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 432 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO S 236 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " -0.024 5.00e-02 4.00e+02 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 209 2.69 - 3.24: 8787 3.24 - 3.80: 14838 3.80 - 4.35: 19697 4.35 - 4.90: 33021 Nonbonded interactions: 76552 Sorted by model distance: nonbonded pdb=" ND2 ASN R 439 " pdb=" OD1 ASN R 441 " model vdw 2.139 3.120 nonbonded pdb=" OG1 THR R 323 " pdb=" OH TYR R 401 " model vdw 2.194 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR S 175 " pdb=" OE2 GLU A 8 " model vdw 2.218 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.226 3.040 ... (remaining 76547 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 0.045 9281 Z= 0.188 Angle : 0.555 8.328 12575 Z= 0.318 Chirality : 0.042 0.225 1430 Planarity : 0.004 0.083 1583 Dihedral : 17.141 88.335 3311 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.51 % Allowed : 24.64 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.26), residues: 1146 helix: 1.84 (0.26), residues: 395 sheet: -0.02 (0.30), residues: 299 loop : -0.39 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 218 TYR 0.014 0.001 TYR S 235 PHE 0.009 0.001 PHE A 354 TRP 0.010 0.001 TRP R 270 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9279) covalent geometry : angle 0.55536 (12573) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.69934 ( 2) hydrogen bonds : bond 0.16693 ( 462) hydrogen bonds : angle 6.84841 ( 1311) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: R 260 LYS cc_start: 0.7716 (ptmm) cc_final: 0.7466 (ptmm) REVERT: R 283 MET cc_start: 0.4704 (ptt) cc_final: 0.4454 (ptt) REVERT: R 319 LYS cc_start: 0.7867 (mttp) cc_final: 0.7636 (ttpt) REVERT: R 397 MET cc_start: 0.6922 (mmp) cc_final: 0.5117 (ttp) REVERT: R 408 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7386 (pt0) REVERT: B 10 GLU cc_start: 0.8586 (tp30) cc_final: 0.8386 (tp30) outliers start: 5 outliers final: 2 residues processed: 171 average time/residue: 0.7135 time to fit residues: 128.4909 Evaluate side-chains 164 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 292 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 247 GLN B 175 GLN A 269 ASN A 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.075917 restraints weight = 12882.155| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.47 r_work: 0.2784 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9281 Z= 0.171 Angle : 0.561 10.260 12575 Z= 0.296 Chirality : 0.043 0.241 1430 Planarity : 0.004 0.059 1583 Dihedral : 4.303 35.052 1257 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.16 % Allowed : 24.03 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1146 helix: 2.03 (0.26), residues: 402 sheet: -0.00 (0.30), residues: 285 loop : -0.42 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 218 TYR 0.016 0.001 TYR S 235 PHE 0.015 0.001 PHE A 196 TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9279) covalent geometry : angle 0.56111 (12573) SS BOND : bond 0.00384 ( 1) SS BOND : angle 0.87148 ( 2) hydrogen bonds : bond 0.04211 ( 462) hydrogen bonds : angle 4.93286 ( 1311) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 163 MET cc_start: 0.7059 (ptm) cc_final: 0.6662 (ppp) REVERT: R 260 LYS cc_start: 0.7493 (ptmm) cc_final: 0.7193 (ptmm) REVERT: R 277 MET cc_start: 0.6765 (ptp) cc_final: 0.6554 (ptt) REVERT: R 397 MET cc_start: 0.7552 (mmp) cc_final: 0.5464 (ttp) REVERT: B 10 GLU cc_start: 0.8231 (tp30) cc_final: 0.7772 (tp30) REVERT: B 137 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7554 (tpt90) REVERT: S 235 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6303 (t80) REVERT: A 32 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7155 (mtm180) outliers start: 31 outliers final: 14 residues processed: 188 average time/residue: 0.6438 time to fit residues: 127.8915 Evaluate side-chains 176 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 225 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 69 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.075794 restraints weight = 12825.211| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.46 r_work: 0.2785 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9281 Z= 0.173 Angle : 0.554 8.747 12575 Z= 0.292 Chirality : 0.043 0.263 1430 Planarity : 0.004 0.048 1583 Dihedral : 4.292 36.632 1257 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.46 % Allowed : 24.44 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1146 helix: 2.17 (0.26), residues: 404 sheet: -0.07 (0.30), residues: 268 loop : -0.57 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 350 TYR 0.019 0.001 TYR S 235 PHE 0.014 0.001 PHE A 196 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9279) covalent geometry : angle 0.55405 (12573) SS BOND : bond 0.00305 ( 1) SS BOND : angle 0.78032 ( 2) hydrogen bonds : bond 0.04013 ( 462) hydrogen bonds : angle 4.76561 ( 1311) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 163 MET cc_start: 0.7082 (ptm) cc_final: 0.6740 (ppp) REVERT: R 260 LYS cc_start: 0.7498 (ptmm) cc_final: 0.7140 (ttpp) REVERT: R 309 ARG cc_start: 0.6010 (pmt-80) cc_final: 0.5559 (pmt-80) REVERT: R 408 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7887 (pt0) REVERT: R 417 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6577 (t80) REVERT: B 10 GLU cc_start: 0.8385 (tp30) cc_final: 0.7949 (tp30) REVERT: B 137 ARG cc_start: 0.8206 (tpp-160) cc_final: 0.7637 (tpt90) REVERT: B 215 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: G 36 ASP cc_start: 0.8652 (m-30) cc_final: 0.8422 (m-30) REVERT: S 235 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6272 (t80) REVERT: A 32 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7219 (mtm180) REVERT: A 232 LEU cc_start: 0.8591 (mt) cc_final: 0.8190 (mt) outliers start: 34 outliers final: 18 residues processed: 190 average time/residue: 0.6444 time to fit residues: 129.5139 Evaluate side-chains 185 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain R residue 405 SER Chi-restraints excluded: chain R residue 417 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 81 optimal weight: 0.0000 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 247 GLN ** R 287 GLN ** 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 = 0.3741 r_free = 0.3741 target = 0.130369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.077798 restraints weight = 12908.748| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.47 r_work: 0.2852 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9281 Z= 0.119 Angle : 0.530 8.171 12575 Z= 0.275 Chirality : 0.041 0.216 1430 Planarity : 0.004 0.053 1583 Dihedral : 4.144 36.580 1255 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.46 % Allowed : 25.15 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.25), residues: 1146 helix: 2.33 (0.26), residues: 401 sheet: -0.12 (0.30), residues: 274 loop : -0.56 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 218 TYR 0.014 0.001 TYR S 235 PHE 0.014 0.001 PHE A 196 TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9279) covalent geometry : angle 0.53020 (12573) SS BOND : bond 0.00000 ( 1) SS BOND : angle 0.20330 ( 2) hydrogen bonds : bond 0.03609 ( 462) hydrogen bonds : angle 4.54774 ( 1311) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 163 MET cc_start: 0.7088 (ptm) cc_final: 0.6762 (ppp) REVERT: R 260 LYS cc_start: 0.7534 (ptmm) cc_final: 0.7225 (ptmm) REVERT: R 397 MET cc_start: 0.7679 (mmp) cc_final: 0.5508 (ttp) REVERT: R 408 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7882 (pt0) REVERT: B 10 GLU cc_start: 0.8467 (tp30) cc_final: 0.8061 (tp30) REVERT: B 137 ARG cc_start: 0.8300 (tpp-160) cc_final: 0.7676 (tpt90) REVERT: B 215 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: G 36 ASP cc_start: 0.8649 (m-30) cc_final: 0.8375 (m-30) REVERT: S 235 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.6038 (t80) REVERT: A 32 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7106 (mtm180) REVERT: A 232 LEU cc_start: 0.8635 (mt) cc_final: 0.8199 (mt) REVERT: A 269 ASN cc_start: 0.9135 (m-40) cc_final: 0.8635 (m-40) outliers start: 34 outliers final: 15 residues processed: 191 average time/residue: 0.7138 time to fit residues: 143.9205 Evaluate side-chains 183 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 32 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 247 GLN ** R 287 GLN ** 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 = 0.3711 r_free = 0.3711 target = 0.127883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.075241 restraints weight = 12917.895| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.46 r_work: 0.2772 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9281 Z= 0.200 Angle : 0.583 12.817 12575 Z= 0.302 Chirality : 0.043 0.277 1430 Planarity : 0.004 0.052 1583 Dihedral : 4.331 37.180 1255 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.77 % Allowed : 25.25 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.25), residues: 1146 helix: 2.21 (0.26), residues: 402 sheet: -0.10 (0.30), residues: 267 loop : -0.66 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 350 TYR 0.020 0.001 TYR S 235 PHE 0.014 0.001 PHE A 354 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 9279) covalent geometry : angle 0.58328 (12573) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.09664 ( 2) hydrogen bonds : bond 0.03936 ( 462) hydrogen bonds : angle 4.67515 ( 1311) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: R 163 MET cc_start: 0.7026 (ptm) cc_final: 0.6704 (ppp) REVERT: R 260 LYS cc_start: 0.7534 (ptmm) cc_final: 0.7174 (ttpp) REVERT: R 283 MET cc_start: 0.4545 (ptt) cc_final: 0.3690 (ppp) REVERT: R 309 ARG cc_start: 0.5843 (OUTLIER) cc_final: 0.5570 (pmt-80) REVERT: R 408 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7863 (pt0) REVERT: R 417 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.6535 (t80) REVERT: B 137 ARG cc_start: 0.8213 (tpp-160) cc_final: 0.7642 (tpt90) REVERT: G 36 ASP cc_start: 0.8575 (m-30) cc_final: 0.8330 (m-30) REVERT: S 235 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.6420 (t80) REVERT: A 232 LEU cc_start: 0.8588 (mt) cc_final: 0.8171 (mt) REVERT: A 269 ASN cc_start: 0.9081 (m-40) cc_final: 0.8561 (m-40) outliers start: 37 outliers final: 23 residues processed: 190 average time/residue: 0.6899 time to fit residues: 138.5185 Evaluate side-chains 186 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain R residue 309 ARG Chi-restraints excluded: chain R residue 405 SER Chi-restraints excluded: chain R residue 417 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 351 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 32 optimal weight: 0.0030 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 55 optimal weight: 0.0970 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 GLN ** R 287 GLN ** 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 = 0.3741 r_free = 0.3741 target = 0.130323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.077862 restraints weight = 12908.431| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.49 r_work: 0.2856 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9281 Z= 0.117 Angle : 0.550 11.549 12575 Z= 0.282 Chirality : 0.042 0.211 1430 Planarity : 0.004 0.050 1583 Dihedral : 4.135 36.621 1255 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.16 % Allowed : 26.68 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1146 helix: 2.27 (0.26), residues: 400 sheet: -0.07 (0.30), residues: 268 loop : -0.63 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 218 TYR 0.015 0.001 TYR R 401 PHE 0.024 0.001 PHE R 159 TRP 0.017 0.002 TRP B 82 HIS 0.002 0.000 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9279) covalent geometry : angle 0.54954 (12573) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.65978 ( 2) hydrogen bonds : bond 0.03543 ( 462) hydrogen bonds : angle 4.50078 ( 1311) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: R 163 MET cc_start: 0.7003 (ptm) cc_final: 0.6670 (ppp) REVERT: R 277 MET cc_start: 0.6828 (ptt) cc_final: 0.6577 (ptt) REVERT: R 283 MET cc_start: 0.4184 (ptt) cc_final: 0.3574 (ppp) REVERT: R 309 ARG cc_start: 0.6034 (pmt-80) cc_final: 0.5806 (pmt-80) REVERT: R 408 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7911 (pt0) REVERT: B 10 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8021 (tp30) REVERT: B 137 ARG cc_start: 0.8324 (tpp-160) cc_final: 0.7712 (tpt90) REVERT: B 215 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8476 (mp0) REVERT: G 36 ASP cc_start: 0.8593 (m-30) cc_final: 0.8359 (m-30) REVERT: S 235 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6025 (t80) REVERT: A 232 LEU cc_start: 0.8631 (mt) cc_final: 0.8204 (mt) REVERT: A 269 ASN cc_start: 0.9179 (m-40) cc_final: 0.8691 (m-40) outliers start: 31 outliers final: 17 residues processed: 190 average time/residue: 0.6942 time to fit residues: 139.4423 Evaluate side-chains 183 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain R residue 405 SER Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 351 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.0470 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 142 HIS R 247 GLN ** R 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 431 ASN S 13 GLN A 311 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.077949 restraints weight = 12954.630| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.49 r_work: 0.2828 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 0.045 9281 Z= 0.121 Angle : 0.561 10.877 12575 Z= 0.286 Chirality : 0.042 0.290 1430 Planarity : 0.004 0.055 1583 Dihedral : 4.097 35.779 1255 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.26 % Allowed : 27.09 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1146 helix: 2.25 (0.26), residues: 403 sheet: -0.07 (0.30), residues: 268 loop : -0.63 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 218 TYR 0.013 0.001 TYR S 235 PHE 0.013 0.001 PHE A 196 TRP 0.021 0.001 TRP R 270 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9279) covalent geometry : angle 0.56095 (12573) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.76698 ( 2) hydrogen bonds : bond 0.03532 ( 462) hydrogen bonds : angle 4.47110 ( 1311) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.400 Fit side-chains REVERT: R 155 PHE cc_start: 0.8559 (t80) cc_final: 0.8325 (t80) REVERT: R 163 MET cc_start: 0.7029 (ptm) cc_final: 0.6689 (ppp) REVERT: R 244 ASP cc_start: 0.8081 (t70) cc_final: 0.7864 (t0) REVERT: R 283 MET cc_start: 0.4189 (ptt) cc_final: 0.3750 (ppp) REVERT: R 309 ARG cc_start: 0.5951 (pmt-80) cc_final: 0.5713 (pmt-80) REVERT: R 408 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7895 (pt0) REVERT: B 10 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8058 (tp30) REVERT: B 137 ARG cc_start: 0.8243 (tpp-160) cc_final: 0.7605 (tpt90) REVERT: B 215 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: G 36 ASP cc_start: 0.8547 (m-30) cc_final: 0.8308 (m-30) REVERT: S 235 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.5995 (t80) REVERT: A 232 LEU cc_start: 0.8562 (mt) cc_final: 0.8129 (mt) REVERT: A 269 ASN cc_start: 0.9156 (m-40) cc_final: 0.8687 (m-40) outliers start: 32 outliers final: 19 residues processed: 187 average time/residue: 0.7117 time to fit residues: 140.7477 Evaluate side-chains 188 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 349 PHE Chi-restraints excluded: chain R residue 404 LEU Chi-restraints excluded: chain R residue 405 SER Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 351 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 109 optimal weight: 0.0270 chunk 97 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 142 HIS R 247 GLN ** R 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.078419 restraints weight = 12879.227| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.47 r_work: 0.2832 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9281 Z= 0.121 Angle : 0.566 10.390 12575 Z= 0.288 Chirality : 0.043 0.319 1430 Planarity : 0.004 0.068 1583 Dihedral : 4.075 35.073 1255 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.46 % Allowed : 26.78 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1146 helix: 2.26 (0.26), residues: 403 sheet: -0.06 (0.30), residues: 268 loop : -0.62 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 218 TYR 0.014 0.001 TYR R 401 PHE 0.030 0.001 PHE R 159 TRP 0.024 0.002 TRP R 270 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9279) covalent geometry : angle 0.56575 (12573) SS BOND : bond 0.00213 ( 1) SS BOND : angle 1.05059 ( 2) hydrogen bonds : bond 0.03511 ( 462) hydrogen bonds : angle 4.44706 ( 1311) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.326 Fit side-chains REVERT: R 155 PHE cc_start: 0.8545 (t80) cc_final: 0.8313 (t80) REVERT: R 163 MET cc_start: 0.6981 (ptm) cc_final: 0.6661 (ppp) REVERT: R 244 ASP cc_start: 0.8118 (t70) cc_final: 0.7898 (t0) REVERT: R 260 LYS cc_start: 0.7845 (ptmm) cc_final: 0.7631 (ttpp) REVERT: R 283 MET cc_start: 0.4145 (ptt) cc_final: 0.3670 (ppp) REVERT: R 309 ARG cc_start: 0.5201 (OUTLIER) cc_final: 0.4896 (pmt-80) REVERT: R 310 GLU cc_start: 0.5782 (tm-30) cc_final: 0.4501 (pp20) REVERT: R 401 TYR cc_start: 0.5212 (m-80) cc_final: 0.4792 (m-80) REVERT: R 408 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7900 (pt0) REVERT: B 10 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8087 (tp30) REVERT: B 137 ARG cc_start: 0.8237 (tpp-160) cc_final: 0.7614 (tpt90) REVERT: B 215 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: G 36 ASP cc_start: 0.8552 (m-30) cc_final: 0.8316 (m-30) REVERT: S 235 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.5912 (t80) REVERT: A 232 LEU cc_start: 0.8561 (mt) cc_final: 0.8129 (mt) REVERT: A 269 ASN cc_start: 0.9162 (m-40) cc_final: 0.8676 (m-40) outliers start: 34 outliers final: 19 residues processed: 193 average time/residue: 0.6552 time to fit residues: 133.7720 Evaluate side-chains 187 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 309 ARG Chi-restraints excluded: chain R residue 349 PHE Chi-restraints excluded: chain R residue 404 LEU Chi-restraints excluded: chain R residue 405 SER Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 351 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 0.0050 chunk 38 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 0.0000 chunk 3 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 142 HIS R 247 GLN ** R 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 431 ASN S 13 GLN A 311 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.131412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.079103 restraints weight = 12769.798| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.45 r_work: 0.2841 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9281 Z= 0.118 Angle : 0.580 13.198 12575 Z= 0.293 Chirality : 0.043 0.336 1430 Planarity : 0.004 0.063 1583 Dihedral : 4.048 35.186 1255 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.44 % Allowed : 27.90 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.25), residues: 1146 helix: 2.27 (0.26), residues: 397 sheet: -0.04 (0.30), residues: 266 loop : -0.61 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 218 TYR 0.015 0.001 TYR R 401 PHE 0.014 0.001 PHE R 199 TRP 0.027 0.002 TRP R 270 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9279) covalent geometry : angle 0.57990 (12573) SS BOND : bond 0.00060 ( 1) SS BOND : angle 1.64820 ( 2) hydrogen bonds : bond 0.03493 ( 462) hydrogen bonds : angle 4.42521 ( 1311) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.380 Fit side-chains REVERT: R 155 PHE cc_start: 0.8534 (t80) cc_final: 0.8294 (t80) REVERT: R 163 MET cc_start: 0.6978 (ptm) cc_final: 0.6659 (ppp) REVERT: R 244 ASP cc_start: 0.8101 (t70) cc_final: 0.7872 (t0) REVERT: R 260 LYS cc_start: 0.7887 (ptmm) cc_final: 0.7667 (ttpp) REVERT: R 283 MET cc_start: 0.4187 (ptt) cc_final: 0.3756 (ppp) REVERT: R 310 GLU cc_start: 0.5883 (tm-30) cc_final: 0.4873 (pp20) REVERT: R 408 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7892 (pt0) REVERT: B 10 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8144 (tp30) REVERT: B 137 ARG cc_start: 0.8239 (tpp-160) cc_final: 0.7621 (tpt90) REVERT: B 262 MET cc_start: 0.8840 (ttp) cc_final: 0.8593 (ptp) REVERT: G 36 ASP cc_start: 0.8534 (m-30) cc_final: 0.8299 (m-30) REVERT: S 235 TYR cc_start: 0.6643 (OUTLIER) cc_final: 0.5842 (t80) REVERT: A 232 LEU cc_start: 0.8551 (mt) cc_final: 0.8125 (mt) REVERT: A 269 ASN cc_start: 0.9181 (m-40) cc_final: 0.8720 (m-40) outliers start: 24 outliers final: 17 residues processed: 184 average time/residue: 0.6814 time to fit residues: 132.5881 Evaluate side-chains 183 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 404 LEU Chi-restraints excluded: chain R residue 405 SER Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 351 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 29 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 142 HIS ** R 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 431 ASN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.078132 restraints weight = 12853.164| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.47 r_work: 0.2858 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9281 Z= 0.135 Angle : 0.594 12.871 12575 Z= 0.302 Chirality : 0.043 0.336 1430 Planarity : 0.004 0.067 1583 Dihedral : 4.148 37.153 1255 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.44 % Allowed : 28.41 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1146 helix: 2.26 (0.26), residues: 398 sheet: -0.02 (0.30), residues: 268 loop : -0.61 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 218 TYR 0.014 0.001 TYR A 302 PHE 0.033 0.001 PHE R 159 TRP 0.023 0.002 TRP R 270 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9279) covalent geometry : angle 0.59385 (12573) SS BOND : bond 0.00083 ( 1) SS BOND : angle 1.85699 ( 2) hydrogen bonds : bond 0.03584 ( 462) hydrogen bonds : angle 4.45872 ( 1311) Misc. bond : bond 0.00011 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.372 Fit side-chains REVERT: R 155 PHE cc_start: 0.8512 (t80) cc_final: 0.8281 (t80) REVERT: R 163 MET cc_start: 0.6925 (ptm) cc_final: 0.6623 (ppp) REVERT: R 244 ASP cc_start: 0.8182 (t70) cc_final: 0.7958 (t0) REVERT: R 260 LYS cc_start: 0.7929 (ptmm) cc_final: 0.7702 (ttpp) REVERT: R 283 MET cc_start: 0.4175 (ptt) cc_final: 0.3796 (ppp) REVERT: R 310 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5149 (pp20) REVERT: R 408 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7883 (pt0) REVERT: B 10 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8042 (tp30) REVERT: B 137 ARG cc_start: 0.8329 (tpp-160) cc_final: 0.7721 (tpt90) REVERT: G 36 ASP cc_start: 0.8588 (m-30) cc_final: 0.8343 (m-30) REVERT: S 235 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.6012 (t80) REVERT: A 52 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: A 232 LEU cc_start: 0.8620 (mt) cc_final: 0.8191 (mt) REVERT: A 269 ASN cc_start: 0.9223 (m-40) cc_final: 0.8767 (m-40) outliers start: 24 outliers final: 18 residues processed: 182 average time/residue: 0.6762 time to fit residues: 130.2043 Evaluate side-chains 183 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 404 LEU Chi-restraints excluded: chain R residue 405 SER Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 351 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.075828 restraints weight = 12757.706| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.46 r_work: 0.2783 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9281 Z= 0.189 Angle : 0.631 12.665 12575 Z= 0.324 Chirality : 0.045 0.340 1430 Planarity : 0.005 0.071 1583 Dihedral : 4.383 39.023 1255 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.34 % Allowed : 28.92 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.25), residues: 1146 helix: 2.17 (0.26), residues: 399 sheet: -0.07 (0.30), residues: 264 loop : -0.68 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 218 TYR 0.018 0.001 TYR S 235 PHE 0.019 0.001 PHE R 199 TRP 0.026 0.002 TRP R 270 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9279) covalent geometry : angle 0.63014 (12573) SS BOND : bond 0.01172 ( 1) SS BOND : angle 3.15743 ( 2) hydrogen bonds : bond 0.03889 ( 462) hydrogen bonds : angle 4.61386 ( 1311) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5436.83 seconds wall clock time: 93 minutes 6.53 seconds (5586.53 seconds total)