Starting phenix.real_space_refine on Wed Feb 4 00:46:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jft_61439/02_2026/9jft_61439.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jft_61439/02_2026/9jft_61439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jft_61439/02_2026/9jft_61439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jft_61439/02_2026/9jft_61439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jft_61439/02_2026/9jft_61439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jft_61439/02_2026/9jft_61439.map" } resolution = 3.27 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= 0.002 sd= 0.034 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 52 5.16 5 C 5069 2.51 5 N 1385 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7996 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1860 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2555 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 403 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2211 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 1.83, per 1000 atoms: 0.23 Number of scatterers: 7996 At special positions: 0 Unit cell: (74.88, 97.76, 135.2, 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 52 16.00 O 1490 8.00 N 1385 7.00 C 5069 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 170 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 310.4 milliseconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 42.3% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.879A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.657A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.674A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.032A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.809A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.508A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 56 removed outlier: 3.541A pdb=" N GLY N 55 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA N 56 " --> pdb=" O GLN N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 52 through 56' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.880A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.921A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 45 removed outlier: 4.129A pdb=" N PHE R 17 " --> pdb=" O ASP R 13 " (cutoff:3.500A) Proline residue: R 18 - end of helix Proline residue: R 30 - end of helix Processing helix chain 'R' and resid 47 through 76 Proline residue: R 68 - end of helix Processing helix chain 'R' and resid 83 through 117 Processing helix chain 'R' and resid 127 through 152 removed outlier: 4.306A pdb=" N VAL R 148 " --> pdb=" O ILE R 144 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N MET R 149 " --> pdb=" O PHE R 145 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU R 150 " --> pdb=" O ASN R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 191 Processing helix chain 'R' and resid 192 through 213 Processing helix chain 'R' and resid 217 through 254 Proline residue: R 241 - end of helix Processing helix chain 'R' and resid 264 through 281 Processing helix chain 'R' and resid 281 through 292 Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 294 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.222A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.450A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.688A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.838A 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: 5.975A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.868A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.334A 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: 6.819A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.254A 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: 3.822A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 4.189A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.508A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.206A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1200 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: 1.33 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2630 1.34 - 1.46: 1969 1.46 - 1.58: 3492 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 8161 Sorted by residual: bond pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " ideal model delta sigma weight residual 1.529 1.549 -0.020 1.74e-02 3.30e+03 1.32e+00 bond pdb=" CA ASP R 286 " pdb=" C ASP R 286 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.22e+00 bond pdb=" CB ARG G 13 " pdb=" CG ARG G 13 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CA ASP R 286 " pdb=" CB ASP R 286 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.58e-02 4.01e+03 1.08e+00 bond pdb=" CA TYR A 381 " pdb=" C TYR A 381 " ideal model delta sigma weight residual 1.526 1.515 0.012 1.21e-02 6.83e+03 9.13e-01 ... (remaining 8156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 10838 1.75 - 3.51: 219 3.51 - 5.26: 30 5.26 - 7.01: 7 7.01 - 8.76: 2 Bond angle restraints: 11096 Sorted by residual: angle pdb=" N VAL R 284 " pdb=" CA VAL R 284 " pdb=" C VAL R 284 " ideal model delta sigma weight residual 113.42 107.75 5.67 1.17e+00 7.31e-01 2.35e+01 angle pdb=" N ASP R 286 " pdb=" CA ASP R 286 " pdb=" C ASP R 286 " ideal model delta sigma weight residual 109.81 116.48 -6.67 2.21e+00 2.05e-01 9.11e+00 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 127.29 -5.75 1.91e+00 2.74e-01 9.07e+00 angle pdb=" CB ARG G 13 " pdb=" CG ARG G 13 " pdb=" CD ARG G 13 " ideal model delta sigma weight residual 111.30 118.16 -6.86 2.30e+00 1.89e-01 8.90e+00 angle pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " ideal model delta sigma weight residual 112.60 115.48 -2.88 1.00e+00 1.00e+00 8.30e+00 ... (remaining 11091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4193 17.72 - 35.44: 481 35.44 - 53.17: 126 53.17 - 70.89: 21 70.89 - 88.61: 12 Dihedral angle restraints: 4833 sinusoidal: 1800 harmonic: 3033 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -135.71 49.71 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA TYR A 381 " pdb=" C TYR A 381 " pdb=" N GLU A 382 " pdb=" CA GLU A 382 " ideal model delta harmonic sigma weight residual -180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA LEU R 176 " pdb=" C LEU R 176 " pdb=" N GLU R 177 " pdb=" CA GLU R 177 " ideal model delta harmonic sigma weight residual 180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 4830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 996 0.049 - 0.098: 230 0.098 - 0.147: 44 0.147 - 0.197: 2 0.197 - 0.246: 1 Chirality restraints: 1273 Sorted by residual: chirality pdb=" CA ASP R 286 " pdb=" N ASP R 286 " pdb=" C ASP R 286 " pdb=" CB ASP R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB THR N 28 " pdb=" CA THR N 28 " pdb=" OG1 THR N 28 " pdb=" CG2 THR N 28 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA THR B 196 " pdb=" N THR B 196 " pdb=" C THR B 196 " pdb=" CB THR B 196 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1270 not shown) Planarity restraints: 1419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 195 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.10e+00 pdb=" CG ASP B 195 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASP B 195 " 0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP B 195 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 195 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ASP B 195 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP B 195 " -0.011 2.00e-02 2.50e+03 pdb=" N THR B 196 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 189 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C CYS R 189 " 0.029 2.00e-02 2.50e+03 pdb=" O CYS R 189 " -0.011 2.00e-02 2.50e+03 pdb=" N THR R 190 " -0.010 2.00e-02 2.50e+03 ... (remaining 1416 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1738 2.77 - 3.30: 7890 3.30 - 3.84: 13652 3.84 - 4.37: 15783 4.37 - 4.90: 27201 Nonbonded interactions: 66264 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD2 ASP B 76 " model vdw 2.242 3.040 nonbonded pdb=" OE2 GLU R 154 " pdb=" NE2 GLN R 180 " model vdw 2.242 3.120 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.243 3.040 nonbonded pdb=" O GLU R 142 " pdb=" ND2 ASN R 146 " model vdw 2.288 3.120 nonbonded pdb=" NH1 ARG N 19 " pdb=" OE1 GLN N 82 " model vdw 2.294 3.120 ... (remaining 66259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 0.035 8164 Z= 0.165 Angle : 0.607 8.763 11102 Z= 0.335 Chirality : 0.042 0.246 1273 Planarity : 0.004 0.040 1419 Dihedral : 16.729 88.611 2860 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 4.07 % Allowed : 27.39 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 1021 helix: 1.46 (0.26), residues: 405 sheet: -0.02 (0.34), residues: 215 loop : -0.96 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 46 TYR 0.021 0.001 TYR R 99 PHE 0.011 0.001 PHE B 278 TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8161) covalent geometry : angle 0.60716 (11096) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.76439 ( 6) hydrogen bonds : bond 0.17350 ( 413) hydrogen bonds : angle 6.74168 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9070 (m) cc_final: 0.8830 (t) REVERT: B 6 GLN cc_start: 0.7669 (pp30) cc_final: 0.6985 (pp30) REVERT: B 12 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7417 (tm-30) REVERT: B 197 ARG cc_start: 0.8496 (mtp-110) cc_final: 0.8213 (mtp-110) REVERT: B 259 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: G 48 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7089 (m-30) REVERT: R 13 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.4234 (t70) REVERT: R 94 MET cc_start: 0.7473 (ttm) cc_final: 0.6191 (tmm) REVERT: R 211 ARG cc_start: 0.8025 (tpp-160) cc_final: 0.7683 (tpt170) REVERT: R 218 ASN cc_start: 0.6914 (OUTLIER) cc_final: 0.6451 (t0) REVERT: R 273 ARG cc_start: 0.6783 (mtm180) cc_final: 0.6519 (mtm180) outliers start: 34 outliers final: 27 residues processed: 253 average time/residue: 0.1254 time to fit residues: 40.1825 Evaluate side-chains 264 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 218 ASN Chi-restraints excluded: chain R residue 288 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN B 6 GLN B 16 ASN B 32 GLN B 75 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 10 HIS R 32 ASN R 146 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.089259 restraints weight = 15133.569| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.28 r_work: 0.3193 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8164 Z= 0.156 Angle : 0.568 10.712 11102 Z= 0.305 Chirality : 0.043 0.250 1273 Planarity : 0.004 0.042 1419 Dihedral : 6.598 49.245 1181 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.55 % Favored : 97.36 % Rotamer: Outliers : 4.90 % Allowed : 24.40 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1021 helix: 1.79 (0.26), residues: 404 sheet: 0.02 (0.35), residues: 214 loop : -0.88 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 187 TYR 0.015 0.001 TYR R 99 PHE 0.010 0.001 PHE R 235 TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8161) covalent geometry : angle 0.56747 (11096) SS BOND : bond 0.00273 ( 3) SS BOND : angle 1.14757 ( 6) hydrogen bonds : bond 0.04836 ( 413) hydrogen bonds : angle 5.23728 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 GLU cc_start: 0.7660 (tp30) cc_final: 0.7226 (tp30) REVERT: B 6 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7320 (pp30) REVERT: B 10 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6928 (mt-10) REVERT: B 12 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7526 (tm-30) REVERT: B 234 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: G 32 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8545 (tptt) REVERT: N 108 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8798 (m-80) REVERT: R 94 MET cc_start: 0.7529 (ttm) cc_final: 0.6299 (tmm) REVERT: R 97 ASN cc_start: 0.5045 (OUTLIER) cc_final: 0.4825 (t0) REVERT: R 128 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7852 (mtt180) REVERT: R 232 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7640 (t) outliers start: 41 outliers final: 18 residues processed: 254 average time/residue: 0.1269 time to fit residues: 40.7234 Evaluate side-chains 240 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 76 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 31 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 75 GLN ** N 35 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 = 0.3549 r_free = 0.3549 target = 0.105884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.090087 restraints weight = 14955.314| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.29 r_work: 0.3205 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8164 Z= 0.129 Angle : 0.539 7.441 11102 Z= 0.290 Chirality : 0.042 0.245 1273 Planarity : 0.004 0.046 1419 Dihedral : 5.097 52.079 1140 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.35 % Favored : 97.55 % Rotamer: Outliers : 4.55 % Allowed : 23.68 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.27), residues: 1021 helix: 1.89 (0.26), residues: 410 sheet: -0.05 (0.35), residues: 206 loop : -0.84 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.015 0.001 TYR R 99 PHE 0.009 0.001 PHE R 239 TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8161) covalent geometry : angle 0.53838 (11096) SS BOND : bond 0.00479 ( 3) SS BOND : angle 1.05573 ( 6) hydrogen bonds : bond 0.04415 ( 413) hydrogen bonds : angle 4.99214 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8521 (pp30) cc_final: 0.8214 (pp30) REVERT: A 323 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7877 (mtm180) REVERT: A 361 ASN cc_start: 0.8495 (m-40) cc_final: 0.8253 (m-40) REVERT: B 12 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7536 (tm-30) REVERT: B 78 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8465 (mtpp) REVERT: B 200 VAL cc_start: 0.8948 (m) cc_final: 0.8579 (p) REVERT: B 234 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: G 32 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8460 (tptt) REVERT: N 108 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8769 (m-80) REVERT: R 36 LEU cc_start: 0.8003 (mt) cc_final: 0.7727 (mt) REVERT: R 58 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7053 (tt) REVERT: R 94 MET cc_start: 0.7520 (ttm) cc_final: 0.6300 (tmm) REVERT: R 97 ASN cc_start: 0.5032 (OUTLIER) cc_final: 0.4793 (t0) REVERT: R 218 ASN cc_start: 0.6766 (OUTLIER) cc_final: 0.6360 (t0) REVERT: R 232 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7563 (t) REVERT: R 291 CYS cc_start: 0.8161 (m) cc_final: 0.7705 (p) outliers start: 38 outliers final: 18 residues processed: 245 average time/residue: 0.1212 time to fit residues: 37.7359 Evaluate side-chains 237 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 212 HIS Chi-restraints excluded: chain R residue 218 ASN Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 288 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088959 restraints weight = 15297.416| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.31 r_work: 0.3184 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8164 Z= 0.160 Angle : 0.559 8.165 11102 Z= 0.298 Chirality : 0.043 0.246 1273 Planarity : 0.004 0.049 1419 Dihedral : 4.856 54.125 1137 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.23 % Favored : 96.67 % Rotamer: Outliers : 4.55 % Allowed : 24.88 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1021 helix: 1.89 (0.26), residues: 410 sheet: -0.14 (0.34), residues: 221 loop : -0.87 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 46 TYR 0.014 0.001 TYR R 99 PHE 0.011 0.001 PHE R 235 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8161) covalent geometry : angle 0.55812 (11096) SS BOND : bond 0.00530 ( 3) SS BOND : angle 1.23273 ( 6) hydrogen bonds : bond 0.04421 ( 413) hydrogen bonds : angle 4.88119 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8523 (pp30) cc_final: 0.7977 (pp30) REVERT: A 253 TYR cc_start: 0.8491 (m-10) cc_final: 0.8169 (m-10) REVERT: A 290 LYS cc_start: 0.8640 (tttt) cc_final: 0.8169 (tttt) REVERT: A 358 ASP cc_start: 0.8095 (t0) cc_final: 0.7781 (m-30) REVERT: A 361 ASN cc_start: 0.8509 (m-40) cc_final: 0.8244 (m-40) REVERT: B 6 GLN cc_start: 0.7722 (pp30) cc_final: 0.7069 (pp30) REVERT: B 10 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7126 (mt-10) REVERT: B 12 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7351 (tm-30) REVERT: B 16 ASN cc_start: 0.8171 (m-40) cc_final: 0.7817 (m-40) REVERT: B 78 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8459 (mtpp) REVERT: B 234 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: G 32 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8473 (tptt) REVERT: R 36 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7704 (mt) REVERT: R 58 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7064 (tt) REVERT: R 94 MET cc_start: 0.7514 (ttm) cc_final: 0.6285 (tmm) REVERT: R 97 ASN cc_start: 0.4707 (t0) cc_final: 0.4429 (t0) REVERT: R 218 ASN cc_start: 0.6837 (OUTLIER) cc_final: 0.6398 (t0) REVERT: R 232 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7621 (t) outliers start: 38 outliers final: 23 residues processed: 240 average time/residue: 0.1186 time to fit residues: 36.4602 Evaluate side-chains 245 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 212 HIS Chi-restraints excluded: chain R residue 218 ASN Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 288 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 31 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.105525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.089732 restraints weight = 15210.535| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.31 r_work: 0.3196 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8164 Z= 0.135 Angle : 0.538 6.919 11102 Z= 0.288 Chirality : 0.041 0.240 1273 Planarity : 0.004 0.050 1419 Dihedral : 4.706 55.562 1136 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 4.78 % Allowed : 26.32 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1021 helix: 1.94 (0.26), residues: 410 sheet: -0.19 (0.34), residues: 211 loop : -0.91 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 46 TYR 0.014 0.001 TYR R 99 PHE 0.009 0.001 PHE A 212 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8161) covalent geometry : angle 0.53726 (11096) SS BOND : bond 0.00413 ( 3) SS BOND : angle 0.95787 ( 6) hydrogen bonds : bond 0.04084 ( 413) hydrogen bonds : angle 4.75979 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8524 (pp30) cc_final: 0.8099 (pp30) REVERT: A 253 TYR cc_start: 0.8498 (m-10) cc_final: 0.8174 (m-10) REVERT: A 290 LYS cc_start: 0.8646 (tttt) cc_final: 0.8250 (tttt) REVERT: A 358 ASP cc_start: 0.8095 (t0) cc_final: 0.7844 (m-30) REVERT: A 361 ASN cc_start: 0.8475 (m-40) cc_final: 0.8223 (m-40) REVERT: B 12 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7300 (tm-30) REVERT: B 16 ASN cc_start: 0.8106 (m-40) cc_final: 0.7737 (m110) REVERT: B 197 ARG cc_start: 0.8445 (mtp-110) cc_final: 0.8225 (mtp-110) REVERT: B 234 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: G 32 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8439 (tptt) REVERT: N 108 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: R 58 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7176 (tt) REVERT: R 94 MET cc_start: 0.7499 (ttm) cc_final: 0.6270 (tmm) REVERT: R 97 ASN cc_start: 0.4748 (OUTLIER) cc_final: 0.4463 (t0) REVERT: R 218 ASN cc_start: 0.6954 (OUTLIER) cc_final: 0.6579 (t0) REVERT: R 232 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7536 (t) outliers start: 40 outliers final: 26 residues processed: 247 average time/residue: 0.1211 time to fit residues: 38.0523 Evaluate side-chains 252 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 212 HIS Chi-restraints excluded: chain R residue 218 ASN Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 75 GLN R 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.102984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.087403 restraints weight = 15115.494| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.27 r_work: 0.3155 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8164 Z= 0.222 Angle : 0.604 6.956 11102 Z= 0.325 Chirality : 0.044 0.239 1273 Planarity : 0.005 0.080 1419 Dihedral : 5.007 57.199 1136 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 5.38 % Allowed : 26.44 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.26), residues: 1021 helix: 1.85 (0.26), residues: 403 sheet: -0.38 (0.33), residues: 223 loop : -0.89 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 46 TYR 0.015 0.002 TYR A 329 PHE 0.018 0.002 PHE R 235 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 8161) covalent geometry : angle 0.60348 (11096) SS BOND : bond 0.00326 ( 3) SS BOND : angle 1.28841 ( 6) hydrogen bonds : bond 0.04745 ( 413) hydrogen bonds : angle 4.91410 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.8119 (t0) cc_final: 0.7849 (m-30) REVERT: A 361 ASN cc_start: 0.8480 (m-40) cc_final: 0.8213 (m-40) REVERT: B 6 GLN cc_start: 0.7654 (pp30) cc_final: 0.7047 (pp30) REVERT: B 10 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7078 (mt-10) REVERT: B 12 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7514 (tm-30) REVERT: B 234 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: G 32 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8564 (tptt) REVERT: N 38 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7254 (ptm160) REVERT: N 108 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8764 (m-80) REVERT: R 58 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7090 (tt) REVERT: R 94 MET cc_start: 0.7549 (ttm) cc_final: 0.6308 (tmm) REVERT: R 97 ASN cc_start: 0.4746 (OUTLIER) cc_final: 0.4225 (t0) REVERT: R 146 ASN cc_start: 0.7543 (m110) cc_final: 0.7124 (m110) REVERT: R 218 ASN cc_start: 0.7042 (OUTLIER) cc_final: 0.6641 (t0) REVERT: R 232 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7766 (t) REVERT: R 291 CYS cc_start: 0.8134 (m) cc_final: 0.7682 (p) outliers start: 45 outliers final: 29 residues processed: 251 average time/residue: 0.1140 time to fit residues: 36.4999 Evaluate side-chains 251 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 212 HIS Chi-restraints excluded: chain R residue 218 ASN Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.104505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.088910 restraints weight = 15261.430| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.30 r_work: 0.3179 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8164 Z= 0.146 Angle : 0.565 6.938 11102 Z= 0.300 Chirality : 0.042 0.234 1273 Planarity : 0.004 0.070 1419 Dihedral : 4.896 57.742 1136 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.26 % Rotamer: Outliers : 4.90 % Allowed : 27.15 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.26), residues: 1021 helix: 2.00 (0.26), residues: 403 sheet: -0.26 (0.34), residues: 211 loop : -0.86 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 187 TYR 0.013 0.001 TYR R 99 PHE 0.010 0.001 PHE R 235 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8161) covalent geometry : angle 0.56430 (11096) SS BOND : bond 0.00370 ( 3) SS BOND : angle 0.90682 ( 6) hydrogen bonds : bond 0.04179 ( 413) hydrogen bonds : angle 4.75100 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8554 (t70) cc_final: 0.8188 (m-30) REVERT: A 213 GLN cc_start: 0.8519 (pp30) cc_final: 0.8167 (pp30) REVERT: A 253 TYR cc_start: 0.8557 (m-10) cc_final: 0.7732 (m-10) REVERT: A 290 LYS cc_start: 0.8606 (tttt) cc_final: 0.7807 (ttpt) REVERT: A 304 GLU cc_start: 0.8600 (tp30) cc_final: 0.8309 (tp30) REVERT: A 358 ASP cc_start: 0.8151 (t0) cc_final: 0.7895 (m-30) REVERT: A 361 ASN cc_start: 0.8482 (m-40) cc_final: 0.8240 (m-40) REVERT: B 6 GLN cc_start: 0.7698 (pp30) cc_final: 0.7140 (pp30) REVERT: B 10 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7068 (mt-10) REVERT: B 12 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 13 GLN cc_start: 0.8282 (tp40) cc_final: 0.7942 (tp40) REVERT: B 197 ARG cc_start: 0.8420 (mtp-110) cc_final: 0.8130 (mtp180) REVERT: B 220 GLN cc_start: 0.8113 (mt0) cc_final: 0.7902 (mt0) REVERT: B 234 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: G 29 LYS cc_start: 0.8433 (mtpp) cc_final: 0.8100 (mtpp) REVERT: G 32 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8459 (tptt) REVERT: N 108 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8698 (m-80) REVERT: R 36 LEU cc_start: 0.7831 (mt) cc_final: 0.7580 (mt) REVERT: R 58 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7083 (tt) REVERT: R 94 MET cc_start: 0.7542 (ttm) cc_final: 0.6321 (tmm) REVERT: R 97 ASN cc_start: 0.4700 (OUTLIER) cc_final: 0.4491 (t0) REVERT: R 218 ASN cc_start: 0.6895 (OUTLIER) cc_final: 0.6516 (t0) REVERT: R 226 LYS cc_start: 0.6818 (tmtt) cc_final: 0.6396 (tttm) REVERT: R 232 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7623 (t) outliers start: 41 outliers final: 27 residues processed: 241 average time/residue: 0.0989 time to fit residues: 30.6220 Evaluate side-chains 248 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 212 HIS Chi-restraints excluded: chain R residue 218 ASN Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 88 optimal weight: 0.0050 chunk 100 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.105289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089696 restraints weight = 15087.090| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.29 r_work: 0.3195 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8164 Z= 0.132 Angle : 0.558 7.600 11102 Z= 0.297 Chirality : 0.042 0.233 1273 Planarity : 0.004 0.051 1419 Dihedral : 4.791 57.637 1136 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Rotamer: Outliers : 4.67 % Allowed : 27.63 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1021 helix: 2.08 (0.25), residues: 403 sheet: -0.31 (0.34), residues: 213 loop : -0.80 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 46 TYR 0.014 0.001 TYR R 99 PHE 0.022 0.001 PHE R 242 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8161) covalent geometry : angle 0.55813 (11096) SS BOND : bond 0.00261 ( 3) SS BOND : angle 0.86047 ( 6) hydrogen bonds : bond 0.03972 ( 413) hydrogen bonds : angle 4.65381 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8464 (t70) cc_final: 0.8132 (m-30) REVERT: A 213 GLN cc_start: 0.8498 (pp30) cc_final: 0.8286 (pp30) REVERT: A 253 TYR cc_start: 0.8546 (m-10) cc_final: 0.7758 (m-80) REVERT: A 290 LYS cc_start: 0.8628 (tttt) cc_final: 0.7775 (tttt) REVERT: A 304 GLU cc_start: 0.8577 (tp30) cc_final: 0.8319 (tp30) REVERT: A 358 ASP cc_start: 0.8169 (t0) cc_final: 0.7825 (m-30) REVERT: A 361 ASN cc_start: 0.8524 (m-40) cc_final: 0.8281 (m-40) REVERT: B 6 GLN cc_start: 0.7697 (pp30) cc_final: 0.7051 (pp30) REVERT: B 10 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7015 (mt-10) REVERT: B 12 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7381 (tm-30) REVERT: B 13 GLN cc_start: 0.8239 (tp40) cc_final: 0.7894 (tp40) REVERT: B 200 VAL cc_start: 0.8957 (m) cc_final: 0.8573 (p) REVERT: B 234 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: G 32 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8412 (tptt) REVERT: N 38 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7292 (ptm160) REVERT: N 108 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8702 (m-80) REVERT: R 58 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7161 (tt) REVERT: R 94 MET cc_start: 0.7477 (ttm) cc_final: 0.6241 (tmm) REVERT: R 97 ASN cc_start: 0.4723 (OUTLIER) cc_final: 0.4477 (t0) REVERT: R 218 ASN cc_start: 0.6851 (OUTLIER) cc_final: 0.6458 (t0) REVERT: R 226 LYS cc_start: 0.6842 (tmtt) cc_final: 0.6422 (tttm) REVERT: R 232 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7522 (t) REVERT: R 249 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.6017 (ttt180) outliers start: 39 outliers final: 26 residues processed: 243 average time/residue: 0.1107 time to fit residues: 34.1458 Evaluate side-chains 249 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 218 ASN Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 249 ARG Chi-restraints excluded: chain R residue 288 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 66 optimal weight: 0.0370 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 88 optimal weight: 0.0270 chunk 100 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN N 13 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.106274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090723 restraints weight = 15167.581| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.30 r_work: 0.3191 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8164 Z= 0.120 Angle : 0.562 8.482 11102 Z= 0.297 Chirality : 0.041 0.227 1273 Planarity : 0.004 0.067 1419 Dihedral : 4.719 57.360 1136 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Rotamer: Outliers : 4.43 % Allowed : 27.63 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.27), residues: 1021 helix: 2.20 (0.26), residues: 403 sheet: -0.26 (0.33), residues: 229 loop : -0.78 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 46 TYR 0.013 0.001 TYR R 99 PHE 0.010 0.001 PHE A 212 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8161) covalent geometry : angle 0.56211 (11096) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.86277 ( 6) hydrogen bonds : bond 0.03773 ( 413) hydrogen bonds : angle 4.57471 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8574 (tp30) cc_final: 0.8349 (tp30) REVERT: A 358 ASP cc_start: 0.8127 (t0) cc_final: 0.7871 (m-30) REVERT: A 361 ASN cc_start: 0.8499 (m-40) cc_final: 0.8271 (m-40) REVERT: B 6 GLN cc_start: 0.7630 (pp30) cc_final: 0.6953 (pp30) REVERT: B 10 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7071 (mt-10) REVERT: B 12 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7368 (tm-30) REVERT: B 13 GLN cc_start: 0.8233 (tp40) cc_final: 0.7889 (tp40) REVERT: B 78 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8443 (mttm) REVERT: B 137 ARG cc_start: 0.7507 (tpp80) cc_final: 0.7288 (tpp80) REVERT: B 200 VAL cc_start: 0.8958 (m) cc_final: 0.8588 (p) REVERT: B 234 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: G 32 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8390 (tptt) REVERT: N 95 TYR cc_start: 0.8875 (m-80) cc_final: 0.8502 (m-80) REVERT: N 108 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8694 (m-80) REVERT: R 58 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7131 (tt) REVERT: R 94 MET cc_start: 0.7493 (ttm) cc_final: 0.6245 (tmm) REVERT: R 97 ASN cc_start: 0.4736 (OUTLIER) cc_final: 0.4467 (t0) REVERT: R 218 ASN cc_start: 0.6840 (OUTLIER) cc_final: 0.6477 (t0) REVERT: R 226 LYS cc_start: 0.6878 (tmtt) cc_final: 0.6212 (tmtt) REVERT: R 232 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7393 (t) outliers start: 37 outliers final: 29 residues processed: 235 average time/residue: 0.1064 time to fit residues: 31.8766 Evaluate side-chains 245 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 207 TYR Chi-restraints excluded: chain R residue 212 HIS Chi-restraints excluded: chain R residue 218 ASN Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089434 restraints weight = 15000.618| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.28 r_work: 0.3193 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8164 Z= 0.157 Angle : 0.610 15.520 11102 Z= 0.318 Chirality : 0.043 0.229 1273 Planarity : 0.004 0.062 1419 Dihedral : 4.792 57.672 1136 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.23 % Favored : 96.67 % Rotamer: Outliers : 4.31 % Allowed : 27.39 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 1021 helix: 1.99 (0.25), residues: 409 sheet: -0.31 (0.33), residues: 229 loop : -0.77 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 187 TYR 0.014 0.001 TYR R 99 PHE 0.011 0.001 PHE R 235 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 10 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8161) covalent geometry : angle 0.60902 (11096) SS BOND : bond 0.00278 ( 3) SS BOND : angle 1.28195 ( 6) hydrogen bonds : bond 0.04050 ( 413) hydrogen bonds : angle 4.65257 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8483 (t70) cc_final: 0.8183 (m-30) REVERT: A 304 GLU cc_start: 0.8583 (tp30) cc_final: 0.8377 (tp30) REVERT: A 358 ASP cc_start: 0.8171 (t0) cc_final: 0.7862 (m-30) REVERT: A 361 ASN cc_start: 0.8482 (m-40) cc_final: 0.8232 (m-40) REVERT: B 12 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7398 (tm-30) REVERT: B 78 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8459 (mttm) REVERT: B 82 TRP cc_start: 0.7077 (OUTLIER) cc_final: 0.6032 (p90) REVERT: B 137 ARG cc_start: 0.7564 (tpp80) cc_final: 0.7326 (tpp80) REVERT: B 200 VAL cc_start: 0.8964 (m) cc_final: 0.8581 (p) REVERT: B 214 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7570 (mtt90) REVERT: B 234 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: G 32 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8436 (tptt) REVERT: N 95 TYR cc_start: 0.8878 (m-80) cc_final: 0.8490 (m-80) REVERT: N 108 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8695 (m-80) REVERT: R 58 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7208 (tt) REVERT: R 94 MET cc_start: 0.7491 (ttm) cc_final: 0.6236 (tmm) REVERT: R 97 ASN cc_start: 0.4741 (OUTLIER) cc_final: 0.4355 (t0) REVERT: R 218 ASN cc_start: 0.6923 (OUTLIER) cc_final: 0.6573 (t0) REVERT: R 226 LYS cc_start: 0.6956 (tmtt) cc_final: 0.6534 (tttm) REVERT: R 232 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7545 (t) outliers start: 36 outliers final: 29 residues processed: 229 average time/residue: 0.1133 time to fit residues: 33.1643 Evaluate side-chains 245 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 207 TYR Chi-restraints excluded: chain R residue 212 HIS Chi-restraints excluded: chain R residue 218 ASN Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 97 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 32 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.105402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089658 restraints weight = 14966.897| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.31 r_work: 0.3177 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8164 Z= 0.146 Angle : 0.611 19.319 11102 Z= 0.316 Chirality : 0.042 0.229 1273 Planarity : 0.004 0.063 1419 Dihedral : 4.792 57.826 1136 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Rotamer: Outliers : 4.67 % Allowed : 27.51 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 1021 helix: 2.03 (0.25), residues: 409 sheet: -0.36 (0.33), residues: 231 loop : -0.78 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 187 TYR 0.014 0.001 TYR R 99 PHE 0.010 0.001 PHE R 235 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8161) covalent geometry : angle 0.61085 (11096) SS BOND : bond 0.00245 ( 3) SS BOND : angle 1.11479 ( 6) hydrogen bonds : bond 0.03978 ( 413) hydrogen bonds : angle 4.66047 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.14 seconds wall clock time: 37 minutes 43.28 seconds (2263.28 seconds total)