Starting phenix.real_space_refine on Tue Mar 3 20:14:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wj5_32543/03_2026/7wj5_32543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wj5_32543/03_2026/7wj5_32543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wj5_32543/03_2026/7wj5_32543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wj5_32543/03_2026/7wj5_32543.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wj5_32543/03_2026/7wj5_32543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wj5_32543/03_2026/7wj5_32543.map" } resolution = 3.72 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= 0.000 sd= 1.033 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 65 5.16 5 C 5551 2.51 5 N 1476 2.21 5 O 1568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8660 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1653 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2226 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8660 At special positions: 0 Unit cell: (106.112, 124.35, 117.718, 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 65 16.00 O 1568 8.00 N 1476 7.00 C 5551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS S 3 " - pdb=" SG CYS S 14 " 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: 0.67 Conformation dependent library (CDL) restraints added in 345.5 milliseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 16 sheets defined 35.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.895A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.209A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.735A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.560A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 removed outlier: 3.776A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.902A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 72 through 75 removed outlier: 3.822A pdb=" N LYS R 75 " --> pdb=" O ALA R 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 72 through 75' Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 95 through 106 removed outlier: 4.283A pdb=" N LEU R 99 " --> pdb=" O GLY R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 146 Processing helix chain 'R' and resid 148 through 153 removed outlier: 4.055A pdb=" N LYS R 152 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 173 Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 202 through 217 removed outlier: 3.658A pdb=" N THR R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 237 Processing helix chain 'R' and resid 251 through 282 Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 287 through 315 removed outlier: 3.891A pdb=" N TYR R 302 " --> pdb=" O VAL R 298 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 9.613A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 9.613A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.652A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.649A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.090A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.569A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.572A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.791A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.685A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.270A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 147 Processing sheet with id=AB6, first strand: chain 'R' and resid 181 through 185 Processing sheet with id=AB7, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.544A pdb=" N PHE S 7 " --> pdb=" O THR S 10 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.92 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: 2743 1.34 - 1.46: 2191 1.46 - 1.58: 3818 1.58 - 1.70: 0 1.70 - 1.81: 94 Bond restraints: 8846 Sorted by residual: bond pdb=" CA SER B 189 " pdb=" CB SER B 189 " ideal model delta sigma weight residual 1.535 1.516 0.019 1.90e-02 2.77e+03 1.02e+00 bond pdb=" CB PRO E 224 " pdb=" CG PRO E 224 " ideal model delta sigma weight residual 1.506 1.471 0.035 3.90e-02 6.57e+02 8.06e-01 bond pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 1.498 1.472 0.026 3.10e-02 1.04e+03 7.01e-01 bond pdb=" CG1 ILE R 209 " pdb=" CD1 ILE R 209 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.79e-01 bond pdb=" C ILE A 264 " pdb=" N ILE A 265 " ideal model delta sigma weight residual 1.327 1.304 0.023 2.97e-02 1.13e+03 5.99e-01 ... (remaining 8841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11837 1.79 - 3.58: 133 3.58 - 5.37: 15 5.37 - 7.17: 6 7.17 - 8.96: 3 Bond angle restraints: 11994 Sorted by residual: angle pdb=" N LEU R 96 " pdb=" CA LEU R 96 " pdb=" C LEU R 96 " ideal model delta sigma weight residual 109.81 115.83 -6.02 2.21e+00 2.05e-01 7.42e+00 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 125.26 -8.96 3.50e+00 8.16e-02 6.55e+00 angle pdb=" C ARG R 241 " pdb=" N VAL R 242 " pdb=" CA VAL R 242 " ideal model delta sigma weight residual 121.97 126.42 -4.45 1.80e+00 3.09e-01 6.10e+00 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 124.90 -8.60 3.50e+00 8.16e-02 6.03e+00 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 113.65 110.08 3.57 1.47e+00 4.63e-01 5.91e+00 ... (remaining 11989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 4868 16.60 - 33.19: 297 33.19 - 49.79: 47 49.79 - 66.38: 7 66.38 - 82.98: 1 Dihedral angle restraints: 5220 sinusoidal: 1953 harmonic: 3267 Sorted by residual: dihedral pdb=" CA TYR A 320 " pdb=" C TYR A 320 " pdb=" N THR A 321 " pdb=" CA THR A 321 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 844 0.032 - 0.064: 374 0.064 - 0.096: 112 0.096 - 0.127: 46 0.127 - 0.159: 6 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1379 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO B 236 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 287 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO R 288 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 288 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 288 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 108 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO R 109 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO R 109 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 109 " 0.016 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 344 2.72 - 3.26: 8665 3.26 - 3.81: 14372 3.81 - 4.35: 17028 4.35 - 4.90: 30051 Nonbonded interactions: 70460 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.173 3.040 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" O SER R 244 " model vdw 2.199 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.206 3.040 nonbonded pdb=" O LYS A 349 " pdb=" ND2 ASN R 318 " model vdw 2.244 3.120 ... (remaining 70455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 8850 Z= 0.161 Angle : 0.547 8.958 12002 Z= 0.288 Chirality : 0.041 0.159 1382 Planarity : 0.003 0.031 1495 Dihedral : 10.788 82.979 3102 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.05 % Allowed : 7.63 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1111 helix: 2.25 (0.28), residues: 349 sheet: 0.33 (0.30), residues: 283 loop : -0.19 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 27 TYR 0.010 0.001 TYR R 211 PHE 0.012 0.001 PHE E 27 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8846) covalent geometry : angle 0.54618 (11994) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.00454 ( 8) hydrogen bonds : bond 0.11251 ( 426) hydrogen bonds : angle 5.58782 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.6043 (mmt) cc_final: 0.5559 (mpp) REVERT: B 57 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7614 (mtpt) REVERT: B 59 TYR cc_start: 0.8299 (m-80) cc_final: 0.8076 (m-80) REVERT: B 75 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: B 76 ASP cc_start: 0.8563 (p0) cc_final: 0.8320 (p0) REVERT: B 234 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: B 267 ASP cc_start: 0.7322 (m-30) cc_final: 0.6783 (m-30) REVERT: R 51 PHE cc_start: 0.7190 (m-10) cc_final: 0.6873 (m-10) REVERT: R 180 TYR cc_start: 0.7496 (m-10) cc_final: 0.7110 (m-10) outliers start: 28 outliers final: 12 residues processed: 221 average time/residue: 0.0928 time to fit residues: 27.7929 Evaluate side-chains 189 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 220 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.168336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.128692 restraints weight = 11306.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129958 restraints weight = 8827.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131701 restraints weight = 7338.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131935 restraints weight = 5414.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132226 restraints weight = 5156.503| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8850 Z= 0.132 Angle : 0.558 8.195 12002 Z= 0.291 Chirality : 0.042 0.150 1382 Planarity : 0.004 0.031 1495 Dihedral : 5.660 59.998 1238 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 3.16 % Allowed : 10.46 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1111 helix: 2.25 (0.28), residues: 349 sheet: 0.45 (0.30), residues: 280 loop : -0.21 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 206 TYR 0.016 0.001 TYR A 320 PHE 0.010 0.001 PHE A 250 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8846) covalent geometry : angle 0.55730 (11994) SS BOND : bond 0.00289 ( 4) SS BOND : angle 0.90058 ( 8) hydrogen bonds : bond 0.03734 ( 426) hydrogen bonds : angle 4.65078 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.6014 (mmt) cc_final: 0.5804 (tpp) REVERT: B 57 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7619 (mtpt) REVERT: B 59 TYR cc_start: 0.8357 (m-80) cc_final: 0.8141 (m-80) REVERT: B 234 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: B 267 ASP cc_start: 0.7118 (m-30) cc_final: 0.6556 (m-30) REVERT: R 51 PHE cc_start: 0.7066 (m-10) cc_final: 0.6809 (m-10) REVERT: R 180 TYR cc_start: 0.7290 (m-10) cc_final: 0.6948 (m-10) REVERT: R 251 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.5445 (mp0) outliers start: 29 outliers final: 19 residues processed: 205 average time/residue: 0.0899 time to fit residues: 25.3969 Evaluate side-chains 190 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 GLU Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.165813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126990 restraints weight = 11299.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.128950 restraints weight = 8858.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129863 restraints weight = 7787.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130294 restraints weight = 5751.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130488 restraints weight = 5373.587| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8850 Z= 0.173 Angle : 0.582 9.054 12002 Z= 0.305 Chirality : 0.043 0.152 1382 Planarity : 0.004 0.032 1495 Dihedral : 5.287 58.603 1231 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 4.90 % Allowed : 11.22 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.89 (0.25), residues: 1111 helix: 2.17 (0.28), residues: 347 sheet: 0.23 (0.30), residues: 277 loop : -0.30 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 42 TYR 0.012 0.002 TYR A 320 PHE 0.013 0.001 PHE E 27 TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8846) covalent geometry : angle 0.58159 (11994) SS BOND : bond 0.00346 ( 4) SS BOND : angle 0.95093 ( 8) hydrogen bonds : bond 0.03867 ( 426) hydrogen bonds : angle 4.64821 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.6081 (mmt) cc_final: 0.5345 (mmm) REVERT: B 57 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7756 (mtpt) REVERT: B 76 ASP cc_start: 0.8449 (p0) cc_final: 0.8229 (p0) REVERT: B 234 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: R 51 PHE cc_start: 0.7071 (m-10) cc_final: 0.6802 (m-10) REVERT: R 153 TRP cc_start: 0.5867 (OUTLIER) cc_final: 0.5394 (m-10) REVERT: R 251 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5286 (mp0) outliers start: 45 outliers final: 27 residues processed: 205 average time/residue: 0.0938 time to fit residues: 26.2725 Evaluate side-chains 193 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 GLU Chi-restraints excluded: chain R residue 255 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 220 GLN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.166015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125604 restraints weight = 11412.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127056 restraints weight = 9256.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128222 restraints weight = 7814.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128462 restraints weight = 5945.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128737 restraints weight = 5612.537| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8850 Z= 0.166 Angle : 0.572 8.760 12002 Z= 0.300 Chirality : 0.042 0.152 1382 Planarity : 0.004 0.033 1495 Dihedral : 5.243 59.684 1231 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 4.58 % Allowed : 14.16 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.81 (0.25), residues: 1111 helix: 2.11 (0.28), residues: 342 sheet: 0.15 (0.30), residues: 277 loop : -0.30 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 206 TYR 0.012 0.002 TYR R 205 PHE 0.012 0.001 PHE E 27 TRP 0.017 0.001 TRP R 197 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8846) covalent geometry : angle 0.57226 (11994) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.84994 ( 8) hydrogen bonds : bond 0.03846 ( 426) hydrogen bonds : angle 4.62464 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.6693 (ptp90) REVERT: A 243 MET cc_start: 0.6123 (mmt) cc_final: 0.5386 (mmm) REVERT: B 57 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7728 (mtpt) REVERT: B 234 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: E 206 ARG cc_start: 0.7566 (mtm110) cc_final: 0.7195 (ptp90) REVERT: R 51 PHE cc_start: 0.7126 (m-10) cc_final: 0.6837 (m-10) REVERT: R 153 TRP cc_start: 0.5908 (OUTLIER) cc_final: 0.5414 (m-10) REVERT: R 251 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5337 (mp0) outliers start: 42 outliers final: 32 residues processed: 200 average time/residue: 0.0933 time to fit residues: 25.5649 Evaluate side-chains 201 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN C 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124420 restraints weight = 11449.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.125362 restraints weight = 9615.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127175 restraints weight = 7881.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127119 restraints weight = 6288.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127559 restraints weight = 5756.759| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8850 Z= 0.214 Angle : 0.621 9.727 12002 Z= 0.323 Chirality : 0.044 0.157 1382 Planarity : 0.004 0.034 1495 Dihedral : 5.417 59.757 1231 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 5.12 % Allowed : 14.71 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.64 (0.25), residues: 1111 helix: 1.94 (0.28), residues: 341 sheet: 0.05 (0.30), residues: 277 loop : -0.36 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 42 TYR 0.012 0.002 TYR A 320 PHE 0.014 0.002 PHE E 27 TRP 0.017 0.002 TRP R 197 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 8846) covalent geometry : angle 0.62091 (11994) SS BOND : bond 0.00376 ( 4) SS BOND : angle 1.00776 ( 8) hydrogen bonds : bond 0.04093 ( 426) hydrogen bonds : angle 4.75468 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.6064 (tt0) REVERT: A 208 ARG cc_start: 0.7292 (mtm-85) cc_final: 0.6616 (ptp90) REVERT: A 243 MET cc_start: 0.6129 (mmt) cc_final: 0.5453 (mmm) REVERT: B 57 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7927 (mtpt) REVERT: B 234 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: E 206 ARG cc_start: 0.7624 (mtm110) cc_final: 0.7250 (ptp90) REVERT: R 51 PHE cc_start: 0.7108 (m-10) cc_final: 0.6819 (m-10) REVERT: R 74 MET cc_start: 0.5276 (ppp) cc_final: 0.4944 (ppp) REVERT: R 153 TRP cc_start: 0.5890 (OUTLIER) cc_final: 0.5346 (m-10) outliers start: 47 outliers final: 34 residues processed: 204 average time/residue: 0.0889 time to fit residues: 25.1477 Evaluate side-chains 202 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 255 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.167533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127328 restraints weight = 11380.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128569 restraints weight = 9145.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130168 restraints weight = 7585.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130152 restraints weight = 5996.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130423 restraints weight = 5613.607| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8850 Z= 0.129 Angle : 0.554 8.244 12002 Z= 0.291 Chirality : 0.042 0.152 1382 Planarity : 0.004 0.032 1495 Dihedral : 5.131 59.239 1229 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 4.79 % Allowed : 16.01 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.73 (0.26), residues: 1111 helix: 2.05 (0.28), residues: 348 sheet: 0.03 (0.30), residues: 279 loop : -0.33 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 42 TYR 0.012 0.001 TYR R 205 PHE 0.011 0.001 PHE A 334 TRP 0.022 0.001 TRP R 197 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8846) covalent geometry : angle 0.55119 (11994) SS BOND : bond 0.00861 ( 4) SS BOND : angle 2.09386 ( 8) hydrogen bonds : bond 0.03640 ( 426) hydrogen bonds : angle 4.54754 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.331 Fit side-chains REVERT: A 208 ARG cc_start: 0.7306 (mtm-85) cc_final: 0.6237 (mmp80) REVERT: A 243 MET cc_start: 0.6203 (mmt) cc_final: 0.5493 (mmm) REVERT: B 57 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7785 (mtpt) REVERT: B 76 ASP cc_start: 0.8278 (p0) cc_final: 0.8034 (p0) REVERT: B 101 MET cc_start: 0.8666 (mmt) cc_final: 0.7812 (mmt) REVERT: B 188 MET cc_start: 0.7505 (mtt) cc_final: 0.7125 (mtt) REVERT: B 234 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: E 206 ARG cc_start: 0.7538 (mtm110) cc_final: 0.7245 (ptp90) REVERT: R 51 PHE cc_start: 0.7109 (m-10) cc_final: 0.6771 (m-10) REVERT: R 74 MET cc_start: 0.5338 (ppp) cc_final: 0.4867 (ppp) REVERT: R 153 TRP cc_start: 0.5865 (OUTLIER) cc_final: 0.5392 (m-10) REVERT: R 194 THR cc_start: 0.7863 (t) cc_final: 0.7632 (t) REVERT: R 248 LYS cc_start: 0.7289 (mtmm) cc_final: 0.6698 (mptt) outliers start: 44 outliers final: 30 residues processed: 208 average time/residue: 0.0918 time to fit residues: 26.3044 Evaluate side-chains 204 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 310 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN R 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.164509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125281 restraints weight = 11579.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127161 restraints weight = 9110.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128129 restraints weight = 7965.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128415 restraints weight = 5871.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.128761 restraints weight = 5475.182| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8850 Z= 0.203 Angle : 0.626 9.713 12002 Z= 0.326 Chirality : 0.044 0.161 1382 Planarity : 0.004 0.033 1495 Dihedral : 5.392 58.330 1229 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 5.34 % Allowed : 16.45 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1111 helix: 1.83 (0.28), residues: 342 sheet: -0.11 (0.30), residues: 279 loop : -0.31 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 42 TYR 0.010 0.002 TYR R 211 PHE 0.014 0.001 PHE E 27 TRP 0.028 0.002 TRP R 197 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8846) covalent geometry : angle 0.62420 (11994) SS BOND : bond 0.00359 ( 4) SS BOND : angle 1.82121 ( 8) hydrogen bonds : bond 0.04001 ( 426) hydrogen bonds : angle 4.73355 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.326 Fit side-chains REVERT: A 208 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.6203 (mmp80) REVERT: A 243 MET cc_start: 0.6169 (mmt) cc_final: 0.5492 (mmm) REVERT: B 76 ASP cc_start: 0.8291 (p0) cc_final: 0.8077 (p0) REVERT: B 188 MET cc_start: 0.7330 (mtt) cc_final: 0.6917 (mtt) REVERT: B 234 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8301 (m-80) REVERT: C 38 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7309 (mtm) REVERT: R 51 PHE cc_start: 0.7064 (m-10) cc_final: 0.6731 (m-10) REVERT: R 74 MET cc_start: 0.5334 (ppp) cc_final: 0.4838 (ppp) REVERT: R 153 TRP cc_start: 0.5863 (OUTLIER) cc_final: 0.5352 (m-10) REVERT: R 194 THR cc_start: 0.7763 (t) cc_final: 0.7556 (t) REVERT: R 305 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.7827 (t) outliers start: 49 outliers final: 32 residues processed: 204 average time/residue: 0.0910 time to fit residues: 25.3065 Evaluate side-chains 202 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 310 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.0370 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 102 optimal weight: 0.0670 chunk 88 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.167063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126776 restraints weight = 11427.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128673 restraints weight = 9457.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129488 restraints weight = 7549.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.129937 restraints weight = 6163.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130285 restraints weight = 5492.702| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8850 Z= 0.139 Angle : 0.588 12.180 12002 Z= 0.304 Chirality : 0.042 0.168 1382 Planarity : 0.004 0.035 1495 Dihedral : 5.165 58.282 1229 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 3.70 % Allowed : 18.74 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1111 helix: 1.91 (0.28), residues: 348 sheet: -0.14 (0.30), residues: 282 loop : -0.31 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 206 TYR 0.011 0.001 TYR E 178 PHE 0.011 0.001 PHE E 27 TRP 0.033 0.001 TRP R 197 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8846) covalent geometry : angle 0.58649 (11994) SS BOND : bond 0.00300 ( 4) SS BOND : angle 1.47434 ( 8) hydrogen bonds : bond 0.03655 ( 426) hydrogen bonds : angle 4.54659 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.245 Fit side-chains REVERT: A 208 ARG cc_start: 0.7302 (mtm-85) cc_final: 0.6176 (mmp80) REVERT: A 243 MET cc_start: 0.6215 (mmt) cc_final: 0.5507 (mmm) REVERT: B 188 MET cc_start: 0.7257 (mtt) cc_final: 0.6913 (mtt) REVERT: B 234 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: C 38 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7300 (mtm) REVERT: E 206 ARG cc_start: 0.7591 (mtm110) cc_final: 0.7193 (ptp90) REVERT: R 131 PHE cc_start: 0.6665 (m-80) cc_final: 0.6408 (m-80) REVERT: R 153 TRP cc_start: 0.5891 (OUTLIER) cc_final: 0.5398 (m-10) REVERT: R 194 THR cc_start: 0.7743 (t) cc_final: 0.7527 (t) REVERT: R 229 LEU cc_start: 0.8499 (tt) cc_final: 0.8237 (tp) REVERT: R 305 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7696 (t) outliers start: 34 outliers final: 29 residues processed: 196 average time/residue: 0.0906 time to fit residues: 24.3923 Evaluate side-chains 203 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 310 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.166322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126028 restraints weight = 11418.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127615 restraints weight = 9385.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128856 restraints weight = 7169.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128961 restraints weight = 6115.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129396 restraints weight = 5712.652| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8850 Z= 0.154 Angle : 0.600 11.858 12002 Z= 0.312 Chirality : 0.042 0.186 1382 Planarity : 0.004 0.035 1495 Dihedral : 5.167 58.224 1229 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 4.14 % Allowed : 18.63 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.61 (0.25), residues: 1111 helix: 1.88 (0.28), residues: 349 sheet: -0.08 (0.30), residues: 277 loop : -0.32 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 206 TYR 0.011 0.001 TYR E 178 PHE 0.011 0.001 PHE E 27 TRP 0.031 0.001 TRP R 197 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8846) covalent geometry : angle 0.59923 (11994) SS BOND : bond 0.00327 ( 4) SS BOND : angle 1.45814 ( 8) hydrogen bonds : bond 0.03696 ( 426) hydrogen bonds : angle 4.56034 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.239 Fit side-chains REVERT: A 208 ARG cc_start: 0.7287 (mtm-85) cc_final: 0.6203 (mmp80) REVERT: A 243 MET cc_start: 0.6209 (mmt) cc_final: 0.5491 (mmm) REVERT: B 188 MET cc_start: 0.7258 (mtt) cc_final: 0.6898 (mtt) REVERT: B 234 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8303 (m-80) REVERT: C 38 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7325 (mtm) REVERT: E 206 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7164 (ptp90) REVERT: R 131 PHE cc_start: 0.6660 (m-80) cc_final: 0.6434 (m-80) REVERT: R 153 TRP cc_start: 0.5904 (OUTLIER) cc_final: 0.5411 (m-10) REVERT: R 194 THR cc_start: 0.7700 (t) cc_final: 0.7479 (t) REVERT: R 305 SER cc_start: 0.8005 (OUTLIER) cc_final: 0.7719 (t) outliers start: 38 outliers final: 31 residues processed: 193 average time/residue: 0.0881 time to fit residues: 23.5263 Evaluate side-chains 203 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 164 MET Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 310 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 3 optimal weight: 0.0370 chunk 33 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.170349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130464 restraints weight = 11470.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132021 restraints weight = 9500.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133617 restraints weight = 7179.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133772 restraints weight = 5864.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133984 restraints weight = 5632.421| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8850 Z= 0.113 Angle : 0.561 11.862 12002 Z= 0.293 Chirality : 0.041 0.172 1382 Planarity : 0.004 0.031 1495 Dihedral : 4.811 57.303 1229 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 2.94 % Allowed : 19.93 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.73 (0.25), residues: 1111 helix: 2.01 (0.28), residues: 348 sheet: 0.17 (0.31), residues: 255 loop : -0.38 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 206 TYR 0.012 0.001 TYR E 178 PHE 0.011 0.001 PHE R 127 TRP 0.034 0.001 TRP R 197 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8846) covalent geometry : angle 0.55989 (11994) SS BOND : bond 0.00272 ( 4) SS BOND : angle 1.18973 ( 8) hydrogen bonds : bond 0.03363 ( 426) hydrogen bonds : angle 4.33241 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.303 Fit side-chains REVERT: A 208 ARG cc_start: 0.7296 (mtm-85) cc_final: 0.6514 (ptp90) REVERT: A 243 MET cc_start: 0.6262 (mmt) cc_final: 0.5553 (mmm) REVERT: B 188 MET cc_start: 0.6964 (mtt) cc_final: 0.6745 (mtt) REVERT: B 234 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: C 38 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7289 (mtm) REVERT: E 206 ARG cc_start: 0.7513 (mtm110) cc_final: 0.7228 (ptp90) REVERT: R 131 PHE cc_start: 0.6528 (m-80) cc_final: 0.6311 (m-80) REVERT: R 153 TRP cc_start: 0.5862 (OUTLIER) cc_final: 0.5379 (m-10) REVERT: R 229 LEU cc_start: 0.8496 (tt) cc_final: 0.8214 (tp) outliers start: 27 outliers final: 22 residues processed: 189 average time/residue: 0.0927 time to fit residues: 24.1483 Evaluate side-chains 187 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 97 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.171384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131575 restraints weight = 11417.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134027 restraints weight = 9160.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134911 restraints weight = 7309.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.135530 restraints weight = 5416.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135647 restraints weight = 5106.155| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8850 Z= 0.119 Angle : 0.574 11.959 12002 Z= 0.298 Chirality : 0.041 0.178 1382 Planarity : 0.004 0.031 1495 Dihedral : 4.720 56.984 1227 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.16 % Allowed : 20.26 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.74 (0.25), residues: 1111 helix: 2.02 (0.28), residues: 349 sheet: 0.15 (0.31), residues: 257 loop : -0.36 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 42 TYR 0.012 0.001 TYR E 178 PHE 0.011 0.001 PHE A 334 TRP 0.035 0.001 TRP R 197 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8846) covalent geometry : angle 0.57319 (11994) SS BOND : bond 0.00288 ( 4) SS BOND : angle 1.29448 ( 8) hydrogen bonds : bond 0.03420 ( 426) hydrogen bonds : angle 4.33547 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1429.62 seconds wall clock time: 25 minutes 28.76 seconds (1528.76 seconds total)