Starting phenix.real_space_refine on Wed Sep 17 15:09:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e3y_8978/09_2025/6e3y_8978.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e3y_8978/09_2025/6e3y_8978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6e3y_8978/09_2025/6e3y_8978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e3y_8978/09_2025/6e3y_8978.map" model { file = "/net/cci-nas-00/data/ceres_data/6e3y_8978/09_2025/6e3y_8978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e3y_8978/09_2025/6e3y_8978.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 6023 2.51 5 N 1638 2.21 5 O 1705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9434 Number of models: 1 Model: "" Number of chains: 8 Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 239 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain breaks: 1 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1578 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain breaks: 5 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2545 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 372 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 2813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2813 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 336} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 925 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.47, per 1000 atoms: 0.26 Number of scatterers: 9434 At special positions: 0 Unit cell: (84.8, 166.42, 98.58, 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 68 16.00 O 1705 8.00 N 1638 7.00 C 6023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 430.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 43.0% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.750A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.868A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 40 removed outlier: 3.661A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.549A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 241 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.880A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.680A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.951A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 24 removed outlier: 3.676A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.546A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.896A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 34 through 54 Processing helix chain 'R' and resid 125 through 130 removed outlier: 3.586A pdb=" N VAL R 129 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN R 130 " --> pdb=" O GLN R 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 125 through 130' Processing helix chain 'R' and resid 130 through 167 removed outlier: 3.558A pdb=" N ASN R 140 " --> pdb=" O LYS R 136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS R 167 " --> pdb=" O PHE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 198 removed outlier: 3.825A pdb=" N THR R 196 " --> pdb=" O ILE R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 242 removed outlier: 4.117A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 260 Processing helix chain 'R' and resid 263 through 277 removed outlier: 3.546A pdb=" N ALA R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 removed outlier: 4.050A pdb=" N ILE R 284 " --> pdb=" O ASN R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 321 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 330 through 346 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 347 through 350 Processing helix chain 'R' and resid 364 through 375 Processing helix chain 'R' and resid 375 through 383 removed outlier: 3.598A pdb=" N LEU R 379 " --> pdb=" O PHE R 375 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 399 removed outlier: 3.638A pdb=" N ILE R 394 " --> pdb=" O GLU R 390 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG R 397 " --> pdb=" O ALA R 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 52 removed outlier: 3.895A pdb=" N LEU E 41 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 Processing helix chain 'E' and resid 58 through 81 removed outlier: 5.024A pdb=" N ARG E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 118 through 143 removed outlier: 3.515A pdb=" N PHE E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 3.710A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.581A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.523A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA N 92 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 213 removed outlier: 4.358A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.751A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.618A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.387A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.720A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.540A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.581A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.583A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 68 through 69 Processing sheet with id=AB3, first strand: chain 'R' and resid 82 through 87 456 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3014 1.34 - 1.46: 2373 1.46 - 1.58: 4168 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 9647 Sorted by residual: bond pdb=" C ARG N 98 " pdb=" N CYS N 99 " ideal model delta sigma weight residual 1.329 1.293 0.036 1.60e-02 3.91e+03 5.12e+00 bond pdb=" CB THR E 130 " pdb=" CG2 THR E 130 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.94e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.437 0.061 3.10e-02 1.04e+03 3.91e+00 bond pdb=" C PHE R 262 " pdb=" N PRO R 263 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.08e+00 bond pdb=" CB VAL B 71 " pdb=" CG2 VAL B 71 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 3.03e+00 ... (remaining 9642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 12573 2.25 - 4.50: 448 4.50 - 6.75: 51 6.75 - 9.00: 16 9.00 - 11.25: 5 Bond angle restraints: 13093 Sorted by residual: angle pdb=" C LYS N 76 " pdb=" N ASN N 77 " pdb=" CA ASN N 77 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.74e+01 angle pdb=" C LEU R 276 " pdb=" N TYR R 277 " pdb=" CA TYR R 277 " ideal model delta sigma weight residual 122.44 117.30 5.14 1.19e+00 7.06e-01 1.87e+01 angle pdb=" N TYR R 277 " pdb=" CA TYR R 277 " pdb=" C TYR R 277 " ideal model delta sigma weight residual 111.02 117.01 -5.99 1.52e+00 4.33e-01 1.56e+01 angle pdb=" N PHE R 262 " pdb=" CA PHE R 262 " pdb=" C PHE R 262 " ideal model delta sigma weight residual 109.81 118.29 -8.48 2.21e+00 2.05e-01 1.47e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 ... (remaining 13088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 5377 15.10 - 30.21: 228 30.21 - 45.31: 60 45.31 - 60.41: 8 60.41 - 75.52: 6 Dihedral angle restraints: 5679 sinusoidal: 2206 harmonic: 3473 Sorted by residual: dihedral pdb=" CB CYS R 212 " pdb=" SG CYS R 212 " pdb=" SG CYS R 282 " pdb=" CB CYS R 282 " ideal model delta sinusoidal sigma weight residual 93.00 136.24 -43.24 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS P 2 " pdb=" SG CYS P 2 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 128.07 -35.07 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1151 0.067 - 0.134: 282 0.134 - 0.201: 34 0.201 - 0.269: 4 0.269 - 0.336: 1 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CB ILE R 352 " pdb=" CA ILE R 352 " pdb=" CG1 ILE R 352 " pdb=" CG2 ILE R 352 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA VAL R 78 " pdb=" N VAL R 78 " pdb=" C VAL R 78 " pdb=" CB VAL R 78 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1469 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 293 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ILE R 293 " -0.056 2.00e-02 2.50e+03 pdb=" O ILE R 293 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE R 294 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 266 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.97e+00 pdb=" C PRO R 266 " -0.055 2.00e-02 2.50e+03 pdb=" O PRO R 266 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA R 267 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 352 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO R 353 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 353 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO R 353 " 0.041 5.00e-02 4.00e+02 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2635 2.81 - 3.33: 8328 3.33 - 3.85: 15936 3.85 - 4.38: 17713 4.38 - 4.90: 31201 Nonbonded interactions: 75813 Sorted by model distance: nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR N 91 " pdb=" O VAL N 124 " model vdw 2.290 3.040 nonbonded pdb=" O HIS P 10 " pdb=" OG SER R 286 " model vdw 2.296 3.040 nonbonded pdb=" O PRO A 313 " pdb=" NH1 ARG A 317 " model vdw 2.322 3.120 nonbonded pdb=" O GLY P 33 " pdb=" NE1 TRP R 121 " model vdw 2.332 3.120 ... (remaining 75808 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.050 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.007 0.106 9657 Z= 0.345 Angle : 1.007 11.253 13111 Z= 0.574 Chirality : 0.058 0.336 1472 Planarity : 0.008 0.074 1656 Dihedral : 9.693 75.517 3402 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.20), residues: 1160 helix: -2.15 (0.19), residues: 457 sheet: -1.04 (0.31), residues: 229 loop : -2.17 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 317 TYR 0.020 0.003 TYR N 94 PHE 0.037 0.003 PHE R 163 TRP 0.026 0.003 TRP R 229 HIS 0.013 0.003 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00704 ( 9647) covalent geometry : angle 1.00402 (13093) SS BOND : bond 0.00480 ( 9) SS BOND : angle 2.36637 ( 18) hydrogen bonds : bond 0.15753 ( 456) hydrogen bonds : angle 6.84388 ( 1311) Misc. bond : bond 0.10563 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 31 ASN cc_start: 0.9207 (t0) cc_final: 0.8948 (t0) REVERT: N 34 MET cc_start: 0.8439 (mtp) cc_final: 0.8186 (mtp) REVERT: N 65 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8701 (mtmt) REVERT: N 73 ASP cc_start: 0.8302 (t0) cc_final: 0.8027 (p0) REVERT: N 82 GLN cc_start: 0.8305 (tp40) cc_final: 0.7989 (tm-30) REVERT: N 122 THR cc_start: 0.9089 (p) cc_final: 0.8879 (p) REVERT: N 125 THR cc_start: 0.9207 (m) cc_final: 0.8972 (p) REVERT: A 229 ASP cc_start: 0.8799 (m-30) cc_final: 0.8199 (t0) REVERT: A 240 ASP cc_start: 0.8843 (m-30) cc_final: 0.8569 (m-30) REVERT: A 271 LYS cc_start: 0.9240 (mmmt) cc_final: 0.9035 (mmtm) REVERT: B 20 ASP cc_start: 0.9514 (m-30) cc_final: 0.9197 (m-30) REVERT: B 44 GLN cc_start: 0.8859 (pm20) cc_final: 0.7961 (pm20) REVERT: B 155 ASN cc_start: 0.8973 (t160) cc_final: 0.8413 (t0) REVERT: B 210 LEU cc_start: 0.9198 (tp) cc_final: 0.8977 (tp) REVERT: B 254 ASP cc_start: 0.8085 (t0) cc_final: 0.7808 (t0) REVERT: B 301 LYS cc_start: 0.8716 (mmmm) cc_final: 0.8290 (mttp) REVERT: R 42 MET cc_start: 0.9294 (mmp) cc_final: 0.8923 (mmp) REVERT: R 96 ASP cc_start: 0.8606 (t0) cc_final: 0.8398 (t0) REVERT: R 99 GLU cc_start: 0.7661 (tp30) cc_final: 0.7269 (tm-30) REVERT: R 178 LYS cc_start: 0.8831 (mttt) cc_final: 0.8623 (mtpp) REVERT: R 280 ASP cc_start: 0.9133 (t0) cc_final: 0.8605 (p0) REVERT: R 332 MET cc_start: 0.7634 (mmm) cc_final: 0.7400 (tmm) REVERT: R 373 MET cc_start: 0.8709 (ttm) cc_final: 0.8399 (tmm) REVERT: E 58 ASP cc_start: 0.9376 (t0) cc_final: 0.9161 (t0) REVERT: E 67 ARG cc_start: 0.8668 (ptt180) cc_final: 0.8301 (ptm160) REVERT: E 76 MET cc_start: 0.9150 (tpp) cc_final: 0.8935 (mmp) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1540 time to fit residues: 48.6144 Evaluate side-chains 130 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 HIS A 23 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 88 ASN B 155 ASN B 259 GLN R 54 GLN R 172 GLN R 208 ASN R 270 HIS R 281 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 388 ASN R 398 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.071986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.056223 restraints weight = 33434.407| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.99 r_work: 0.3027 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9657 Z= 0.161 Angle : 0.630 10.324 13111 Z= 0.331 Chirality : 0.043 0.170 1472 Planarity : 0.004 0.050 1656 Dihedral : 4.782 59.242 1294 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.88 % Allowed : 9.91 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.23), residues: 1160 helix: 0.51 (0.23), residues: 460 sheet: -0.63 (0.32), residues: 230 loop : -1.44 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 64 TYR 0.017 0.002 TYR A 358 PHE 0.021 0.002 PHE E 92 TRP 0.023 0.002 TRP R 229 HIS 0.005 0.001 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9647) covalent geometry : angle 0.62818 (13093) SS BOND : bond 0.00238 ( 9) SS BOND : angle 1.39049 ( 18) hydrogen bonds : bond 0.04019 ( 456) hydrogen bonds : angle 4.91490 ( 1311) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 31 ASN cc_start: 0.9305 (t0) cc_final: 0.9062 (t0) REVERT: N 11 LEU cc_start: 0.9235 (tp) cc_final: 0.8911 (mm) REVERT: N 65 LYS cc_start: 0.9098 (mmmm) cc_final: 0.8573 (mtmt) REVERT: N 73 ASP cc_start: 0.8675 (t0) cc_final: 0.8280 (t0) REVERT: N 82 GLN cc_start: 0.8330 (tp40) cc_final: 0.8127 (tm-30) REVERT: N 125 THR cc_start: 0.9327 (m) cc_final: 0.8875 (p) REVERT: A 27 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9110 (mm-30) REVERT: A 286 SER cc_start: 0.9160 (m) cc_final: 0.8801 (p) REVERT: B 19 ARG cc_start: 0.9064 (ttp-110) cc_final: 0.8797 (ttp-110) REVERT: B 20 ASP cc_start: 0.9583 (m-30) cc_final: 0.9335 (m-30) REVERT: B 32 GLN cc_start: 0.9143 (mt0) cc_final: 0.8942 (mt0) REVERT: B 44 GLN cc_start: 0.8959 (pm20) cc_final: 0.8415 (pm20) REVERT: B 155 ASN cc_start: 0.9191 (t0) cc_final: 0.8745 (t0) REVERT: B 215 GLU cc_start: 0.8779 (mp0) cc_final: 0.8423 (mp0) REVERT: B 254 ASP cc_start: 0.8415 (t0) cc_final: 0.8111 (t0) REVERT: B 301 LYS cc_start: 0.8669 (mmmm) cc_final: 0.8314 (mttp) REVERT: R 42 MET cc_start: 0.9459 (mmp) cc_final: 0.9157 (mmp) REVERT: R 99 GLU cc_start: 0.7789 (tp30) cc_final: 0.7561 (tp30) REVERT: R 332 MET cc_start: 0.7719 (mmm) cc_final: 0.7424 (tmm) REVERT: R 373 MET cc_start: 0.9046 (ttm) cc_final: 0.8658 (tmm) REVERT: E 58 ASP cc_start: 0.9491 (t0) cc_final: 0.9260 (t0) REVERT: E 67 ARG cc_start: 0.8602 (ptt180) cc_final: 0.8146 (ptm160) REVERT: E 76 MET cc_start: 0.9344 (tpp) cc_final: 0.8981 (mmp) REVERT: E 91 ARG cc_start: 0.9266 (mtp85) cc_final: 0.8973 (ptp90) outliers start: 19 outliers final: 10 residues processed: 161 average time/residue: 0.1252 time to fit residues: 26.6341 Evaluate side-chains 140 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 53 MET Chi-restraints excluded: chain R residue 100 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 170 SER Chi-restraints excluded: chain R residue 282 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.070027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054110 restraints weight = 33976.327| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.99 r_work: 0.2966 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9657 Z= 0.189 Angle : 0.612 11.854 13111 Z= 0.321 Chirality : 0.043 0.165 1472 Planarity : 0.004 0.052 1656 Dihedral : 4.724 52.218 1294 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.38 % Allowed : 10.41 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.25), residues: 1160 helix: 1.65 (0.25), residues: 458 sheet: -0.51 (0.32), residues: 230 loop : -1.10 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 18 TYR 0.027 0.001 TYR N 80 PHE 0.016 0.002 PHE B 199 TRP 0.017 0.001 TRP R 229 HIS 0.005 0.001 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9647) covalent geometry : angle 0.60539 (13093) SS BOND : bond 0.00684 ( 9) SS BOND : angle 2.47448 ( 18) hydrogen bonds : bond 0.03659 ( 456) hydrogen bonds : angle 4.62034 ( 1311) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 31 ASN cc_start: 0.9325 (t0) cc_final: 0.9081 (t0) REVERT: N 11 LEU cc_start: 0.9268 (tp) cc_final: 0.8895 (mm) REVERT: N 34 MET cc_start: 0.9072 (mtp) cc_final: 0.8386 (mmm) REVERT: N 69 THR cc_start: 0.8943 (m) cc_final: 0.8578 (t) REVERT: N 73 ASP cc_start: 0.8770 (t0) cc_final: 0.8342 (t0) REVERT: N 82 GLN cc_start: 0.8336 (tp40) cc_final: 0.8113 (tm-30) REVERT: N 125 THR cc_start: 0.9397 (m) cc_final: 0.8933 (p) REVERT: A 27 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9144 (mm-30) REVERT: A 286 SER cc_start: 0.9185 (m) cc_final: 0.8646 (p) REVERT: B 32 GLN cc_start: 0.9117 (mt0) cc_final: 0.8816 (mt0) REVERT: B 44 GLN cc_start: 0.9008 (pm20) cc_final: 0.8439 (pm20) REVERT: B 217 MET cc_start: 0.8848 (pmm) cc_final: 0.8646 (pmm) REVERT: B 254 ASP cc_start: 0.8466 (t0) cc_final: 0.8217 (t0) REVERT: B 301 LYS cc_start: 0.8727 (mmmm) cc_final: 0.8271 (mttp) REVERT: G 38 MET cc_start: 0.9378 (ttp) cc_final: 0.8746 (ptp) REVERT: R 38 ARG cc_start: 0.9331 (mmt180) cc_final: 0.9020 (tpp80) REVERT: R 42 MET cc_start: 0.9438 (mmp) cc_final: 0.9141 (mmp) REVERT: R 96 ASP cc_start: 0.8010 (t0) cc_final: 0.7437 (t0) REVERT: R 99 GLU cc_start: 0.7781 (tp30) cc_final: 0.7578 (mm-30) REVERT: R 332 MET cc_start: 0.7873 (mmm) cc_final: 0.7515 (tmm) REVERT: E 58 ASP cc_start: 0.9532 (t0) cc_final: 0.9300 (t0) REVERT: E 67 ARG cc_start: 0.8412 (ptt180) cc_final: 0.7911 (ptm160) outliers start: 24 outliers final: 18 residues processed: 148 average time/residue: 0.1424 time to fit residues: 27.6204 Evaluate side-chains 145 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 100 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.066452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.050545 restraints weight = 34527.076| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.86 r_work: 0.2866 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 9657 Z= 0.348 Angle : 0.725 9.487 13111 Z= 0.382 Chirality : 0.046 0.156 1472 Planarity : 0.004 0.046 1656 Dihedral : 4.953 44.729 1294 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.87 % Allowed : 12.19 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.25), residues: 1160 helix: 1.73 (0.24), residues: 461 sheet: -0.46 (0.33), residues: 228 loop : -1.09 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 18 TYR 0.025 0.002 TYR B 105 PHE 0.017 0.002 PHE B 199 TRP 0.018 0.002 TRP R 229 HIS 0.006 0.002 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00760 ( 9647) covalent geometry : angle 0.71831 (13093) SS BOND : bond 0.00338 ( 9) SS BOND : angle 2.75412 ( 18) hydrogen bonds : bond 0.04136 ( 456) hydrogen bonds : angle 4.76891 ( 1311) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 3 ASP cc_start: 0.7628 (p0) cc_final: 0.7395 (t0) REVERT: P 6 THR cc_start: 0.9140 (p) cc_final: 0.8871 (p) REVERT: P 18 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8473 (ttp80) REVERT: P 31 ASN cc_start: 0.9346 (t0) cc_final: 0.9107 (t0) REVERT: N 11 LEU cc_start: 0.9364 (tp) cc_final: 0.8957 (mm) REVERT: N 69 THR cc_start: 0.8953 (m) cc_final: 0.8560 (t) REVERT: N 73 ASP cc_start: 0.8926 (t0) cc_final: 0.8622 (t0) REVERT: N 80 TYR cc_start: 0.8963 (m-80) cc_final: 0.8691 (m-10) REVERT: N 125 THR cc_start: 0.9387 (m) cc_final: 0.8986 (p) REVERT: A 286 SER cc_start: 0.9225 (m) cc_final: 0.8703 (p) REVERT: A 386 MET cc_start: 0.9002 (ttm) cc_final: 0.8400 (tmm) REVERT: B 7 LEU cc_start: 0.8089 (mm) cc_final: 0.7849 (mt) REVERT: B 32 GLN cc_start: 0.9110 (mt0) cc_final: 0.8812 (mt0) REVERT: B 44 GLN cc_start: 0.9030 (pm20) cc_final: 0.8330 (pm20) REVERT: B 254 ASP cc_start: 0.8445 (t0) cc_final: 0.8161 (t0) REVERT: B 301 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8300 (mmtp) REVERT: G 38 MET cc_start: 0.9382 (ttp) cc_final: 0.8841 (ptm) REVERT: R 38 ARG cc_start: 0.9364 (mmt180) cc_final: 0.9076 (tpp80) REVERT: R 42 MET cc_start: 0.9394 (mmp) cc_final: 0.9180 (mmp) REVERT: R 96 ASP cc_start: 0.8193 (t0) cc_final: 0.7358 (t0) REVERT: R 99 GLU cc_start: 0.7808 (tp30) cc_final: 0.7586 (mm-30) REVERT: R 332 MET cc_start: 0.7941 (mmm) cc_final: 0.7614 (tmm) REVERT: R 373 MET cc_start: 0.9139 (ttm) cc_final: 0.8687 (tmm) REVERT: E 58 ASP cc_start: 0.9505 (t0) cc_final: 0.9290 (t0) REVERT: E 67 ARG cc_start: 0.8495 (ptt180) cc_final: 0.7930 (ptm160) REVERT: E 76 MET cc_start: 0.9378 (ttm) cc_final: 0.8971 (ttt) REVERT: E 83 PHE cc_start: 0.8635 (p90) cc_final: 0.8347 (p90) outliers start: 29 outliers final: 23 residues processed: 147 average time/residue: 0.1302 time to fit residues: 25.2686 Evaluate side-chains 143 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 100 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 380 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 340 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.068426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.052668 restraints weight = 33951.180| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.93 r_work: 0.2929 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9657 Z= 0.140 Angle : 0.592 9.129 13111 Z= 0.311 Chirality : 0.042 0.186 1472 Planarity : 0.003 0.046 1656 Dihedral : 4.703 40.352 1294 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.48 % Allowed : 13.38 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.25), residues: 1160 helix: 1.91 (0.25), residues: 468 sheet: -0.30 (0.33), residues: 232 loop : -1.07 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 102 TYR 0.014 0.001 TYR B 105 PHE 0.014 0.001 PHE E 83 TRP 0.017 0.001 TRP B 99 HIS 0.004 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9647) covalent geometry : angle 0.58597 (13093) SS BOND : bond 0.00238 ( 9) SS BOND : angle 2.30189 ( 18) hydrogen bonds : bond 0.03579 ( 456) hydrogen bonds : angle 4.45360 ( 1311) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8393 (ttp80) REVERT: P 31 ASN cc_start: 0.9335 (t0) cc_final: 0.9090 (t0) REVERT: N 11 LEU cc_start: 0.9328 (tp) cc_final: 0.8921 (mm) REVERT: N 69 THR cc_start: 0.8903 (m) cc_final: 0.8622 (t) REVERT: N 73 ASP cc_start: 0.8990 (t0) cc_final: 0.8624 (t0) REVERT: N 80 TYR cc_start: 0.9093 (m-80) cc_final: 0.8679 (m-10) REVERT: N 125 THR cc_start: 0.9418 (m) cc_final: 0.8949 (p) REVERT: A 286 SER cc_start: 0.9160 (m) cc_final: 0.8594 (p) REVERT: A 386 MET cc_start: 0.8949 (ttm) cc_final: 0.8498 (tmm) REVERT: B 32 GLN cc_start: 0.9136 (mt0) cc_final: 0.8828 (mt0) REVERT: B 44 GLN cc_start: 0.9061 (pm20) cc_final: 0.8375 (pm20) REVERT: B 254 ASP cc_start: 0.8456 (t0) cc_final: 0.8168 (t0) REVERT: B 266 HIS cc_start: 0.9105 (t-90) cc_final: 0.8861 (t-90) REVERT: B 301 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8320 (mmtp) REVERT: G 38 MET cc_start: 0.9357 (ttp) cc_final: 0.8857 (ptm) REVERT: R 38 ARG cc_start: 0.9309 (mmt180) cc_final: 0.8988 (tpp80) REVERT: R 42 MET cc_start: 0.9379 (mmp) cc_final: 0.9115 (mmp) REVERT: R 96 ASP cc_start: 0.8100 (t0) cc_final: 0.7292 (t0) REVERT: R 99 GLU cc_start: 0.7732 (tp30) cc_final: 0.7524 (mm-30) REVERT: R 332 MET cc_start: 0.7845 (mmm) cc_final: 0.7516 (tmm) REVERT: E 58 ASP cc_start: 0.9465 (t0) cc_final: 0.9239 (t0) REVERT: E 67 ARG cc_start: 0.8404 (ptt180) cc_final: 0.7871 (ptm160) REVERT: E 76 MET cc_start: 0.9317 (ttm) cc_final: 0.9070 (ttm) outliers start: 25 outliers final: 20 residues processed: 149 average time/residue: 0.1273 time to fit residues: 24.7383 Evaluate side-chains 137 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 100 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 107 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 112 optimal weight: 0.0270 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 0.0010 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.2048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.069271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053520 restraints weight = 33881.842| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.95 r_work: 0.2951 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9657 Z= 0.116 Angle : 0.572 7.539 13111 Z= 0.300 Chirality : 0.041 0.148 1472 Planarity : 0.003 0.046 1656 Dihedral : 4.534 35.125 1294 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.38 % Allowed : 13.68 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.25), residues: 1160 helix: 2.08 (0.25), residues: 468 sheet: -0.36 (0.33), residues: 234 loop : -0.99 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.010 0.001 TYR B 105 PHE 0.017 0.001 PHE E 83 TRP 0.013 0.001 TRP R 229 HIS 0.004 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9647) covalent geometry : angle 0.56734 (13093) SS BOND : bond 0.00348 ( 9) SS BOND : angle 2.12711 ( 18) hydrogen bonds : bond 0.03373 ( 456) hydrogen bonds : angle 4.35613 ( 1311) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 ARG cc_start: 0.8673 (ttp80) cc_final: 0.8386 (ttp80) REVERT: P 31 ASN cc_start: 0.9339 (t0) cc_final: 0.9080 (t0) REVERT: N 11 LEU cc_start: 0.9355 (tp) cc_final: 0.8938 (mm) REVERT: N 34 MET cc_start: 0.9297 (mmm) cc_final: 0.9007 (mmm) REVERT: N 73 ASP cc_start: 0.8992 (t0) cc_final: 0.8664 (t70) REVERT: N 80 TYR cc_start: 0.9107 (m-80) cc_final: 0.8625 (m-80) REVERT: N 125 THR cc_start: 0.9407 (m) cc_final: 0.8924 (p) REVERT: A 286 SER cc_start: 0.9146 (m) cc_final: 0.8571 (p) REVERT: A 386 MET cc_start: 0.9004 (ttm) cc_final: 0.8493 (tmm) REVERT: B 44 GLN cc_start: 0.9069 (pm20) cc_final: 0.8380 (pm20) REVERT: B 226 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8624 (mt-10) REVERT: B 254 ASP cc_start: 0.8458 (t0) cc_final: 0.8181 (t0) REVERT: B 266 HIS cc_start: 0.9196 (t-90) cc_final: 0.8749 (t70) REVERT: B 301 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8331 (mttp) REVERT: G 38 MET cc_start: 0.9323 (ttp) cc_final: 0.8863 (ptm) REVERT: R 38 ARG cc_start: 0.9296 (mmt180) cc_final: 0.8999 (tpp80) REVERT: R 42 MET cc_start: 0.9369 (mmp) cc_final: 0.9094 (mmp) REVERT: R 96 ASP cc_start: 0.8152 (t0) cc_final: 0.7477 (t0) REVERT: R 99 GLU cc_start: 0.7713 (tp30) cc_final: 0.7498 (mm-30) REVERT: R 332 MET cc_start: 0.7874 (mmm) cc_final: 0.7523 (tmm) REVERT: E 48 MET cc_start: 0.8957 (tpp) cc_final: 0.8755 (tpp) REVERT: E 58 ASP cc_start: 0.9482 (t0) cc_final: 0.9251 (t0) REVERT: E 67 ARG cc_start: 0.8370 (ptt180) cc_final: 0.7843 (ptm160) REVERT: E 76 MET cc_start: 0.9279 (ttm) cc_final: 0.9005 (ttm) outliers start: 24 outliers final: 16 residues processed: 147 average time/residue: 0.1310 time to fit residues: 25.1628 Evaluate side-chains 135 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 100 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 64 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 34 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.0770 chunk 75 optimal weight: 7.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.068378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.052566 restraints weight = 33700.728| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.89 r_work: 0.2924 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9657 Z= 0.184 Angle : 0.644 14.678 13111 Z= 0.338 Chirality : 0.043 0.274 1472 Planarity : 0.004 0.046 1656 Dihedral : 4.486 34.403 1294 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.38 % Allowed : 14.67 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.25), residues: 1160 helix: 2.05 (0.25), residues: 469 sheet: -0.30 (0.33), residues: 235 loop : -0.98 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.014 0.001 TYR B 264 PHE 0.017 0.001 PHE E 83 TRP 0.011 0.001 TRP R 229 HIS 0.021 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9647) covalent geometry : angle 0.63369 (13093) SS BOND : bond 0.00521 ( 9) SS BOND : angle 3.11811 ( 18) hydrogen bonds : bond 0.03666 ( 456) hydrogen bonds : angle 4.39224 ( 1311) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8388 (ttp80) REVERT: P 31 ASN cc_start: 0.9348 (t0) cc_final: 0.9089 (t0) REVERT: N 11 LEU cc_start: 0.9379 (tp) cc_final: 0.8941 (mm) REVERT: N 34 MET cc_start: 0.9314 (mmm) cc_final: 0.8994 (mmm) REVERT: N 73 ASP cc_start: 0.8997 (t0) cc_final: 0.8594 (t0) REVERT: N 80 TYR cc_start: 0.9124 (m-80) cc_final: 0.8510 (m-10) REVERT: N 82 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7971 (tm-30) REVERT: N 125 THR cc_start: 0.9416 (m) cc_final: 0.8961 (p) REVERT: A 286 SER cc_start: 0.9154 (m) cc_final: 0.8607 (p) REVERT: A 386 MET cc_start: 0.9015 (ttm) cc_final: 0.8502 (tmm) REVERT: B 44 GLN cc_start: 0.9045 (pm20) cc_final: 0.8406 (pm20) REVERT: B 226 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8425 (mm-30) REVERT: B 254 ASP cc_start: 0.8475 (t0) cc_final: 0.8238 (t0) REVERT: B 266 HIS cc_start: 0.9250 (t-90) cc_final: 0.8702 (t70) REVERT: B 301 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8355 (mttp) REVERT: G 38 MET cc_start: 0.9346 (ttp) cc_final: 0.8884 (ptm) REVERT: R 38 ARG cc_start: 0.9304 (mmt180) cc_final: 0.9002 (tpp80) REVERT: R 42 MET cc_start: 0.9366 (mmp) cc_final: 0.9114 (mmp) REVERT: R 96 ASP cc_start: 0.8314 (t0) cc_final: 0.7671 (t0) REVERT: R 99 GLU cc_start: 0.7710 (tp30) cc_final: 0.7496 (mm-30) REVERT: R 332 MET cc_start: 0.7896 (mmm) cc_final: 0.7548 (tmm) REVERT: R 373 MET cc_start: 0.9056 (ttm) cc_final: 0.8631 (tmm) REVERT: E 58 ASP cc_start: 0.9464 (t0) cc_final: 0.9246 (t0) REVERT: E 67 ARG cc_start: 0.8286 (ptt180) cc_final: 0.7732 (ptm160) REVERT: E 76 MET cc_start: 0.9314 (ttm) cc_final: 0.9045 (ttm) REVERT: E 91 ARG cc_start: 0.9362 (mtp85) cc_final: 0.9073 (ptp-110) outliers start: 24 outliers final: 19 residues processed: 141 average time/residue: 0.1272 time to fit residues: 23.6174 Evaluate side-chains 138 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 100 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 53 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.068927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.053207 restraints weight = 33614.927| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.88 r_work: 0.2942 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9657 Z= 0.144 Angle : 0.609 8.424 13111 Z= 0.321 Chirality : 0.042 0.148 1472 Planarity : 0.003 0.046 1656 Dihedral : 4.420 33.926 1294 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.18 % Allowed : 14.97 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.25), residues: 1160 helix: 2.17 (0.25), residues: 469 sheet: -0.30 (0.34), residues: 234 loop : -0.90 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 102 TYR 0.012 0.001 TYR B 264 PHE 0.017 0.001 PHE E 83 TRP 0.012 0.001 TRP E 56 HIS 0.004 0.001 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9647) covalent geometry : angle 0.60232 (13093) SS BOND : bond 0.00362 ( 9) SS BOND : angle 2.52617 ( 18) hydrogen bonds : bond 0.03445 ( 456) hydrogen bonds : angle 4.33150 ( 1311) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 ARG cc_start: 0.8673 (ttp80) cc_final: 0.8397 (ttp80) REVERT: P 31 ASN cc_start: 0.9332 (t0) cc_final: 0.9062 (t0) REVERT: N 11 LEU cc_start: 0.9365 (tp) cc_final: 0.8931 (mm) REVERT: N 18 LEU cc_start: 0.8235 (tp) cc_final: 0.7971 (tt) REVERT: N 34 MET cc_start: 0.9317 (mmm) cc_final: 0.8993 (mmm) REVERT: N 65 LYS cc_start: 0.9047 (mttm) cc_final: 0.8749 (mtpp) REVERT: N 73 ASP cc_start: 0.8986 (t0) cc_final: 0.8604 (t0) REVERT: N 80 TYR cc_start: 0.9079 (m-80) cc_final: 0.8497 (m-10) REVERT: N 82 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7985 (tm-30) REVERT: N 125 THR cc_start: 0.9390 (m) cc_final: 0.8818 (p) REVERT: A 27 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9047 (mm-30) REVERT: A 286 SER cc_start: 0.9150 (m) cc_final: 0.8569 (p) REVERT: A 386 MET cc_start: 0.9026 (ttm) cc_final: 0.8509 (tmm) REVERT: B 32 GLN cc_start: 0.9070 (mt0) cc_final: 0.8817 (pt0) REVERT: B 226 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8527 (mm-30) REVERT: B 254 ASP cc_start: 0.8499 (t0) cc_final: 0.8218 (t0) REVERT: B 266 HIS cc_start: 0.9238 (t-90) cc_final: 0.8530 (t-90) REVERT: B 301 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8414 (mttp) REVERT: G 38 MET cc_start: 0.9321 (ttp) cc_final: 0.8876 (ptm) REVERT: R 38 ARG cc_start: 0.9311 (mmt180) cc_final: 0.9027 (tpp80) REVERT: R 42 MET cc_start: 0.9352 (mmp) cc_final: 0.9098 (mmp) REVERT: R 96 ASP cc_start: 0.8334 (t0) cc_final: 0.7698 (t0) REVERT: R 99 GLU cc_start: 0.7699 (tp30) cc_final: 0.7478 (mm-30) REVERT: R 332 MET cc_start: 0.7854 (mmm) cc_final: 0.7548 (tmm) REVERT: R 373 MET cc_start: 0.9047 (ttm) cc_final: 0.8627 (tmm) REVERT: E 44 PHE cc_start: 0.8847 (t80) cc_final: 0.8484 (t80) REVERT: E 58 ASP cc_start: 0.9441 (t0) cc_final: 0.9013 (p0) REVERT: E 67 ARG cc_start: 0.8337 (ptt180) cc_final: 0.7768 (ptm160) REVERT: E 76 MET cc_start: 0.9293 (ttm) cc_final: 0.9030 (ttm) REVERT: E 91 ARG cc_start: 0.9368 (mtp85) cc_final: 0.9073 (ptp-110) REVERT: E 102 ARG cc_start: 0.8829 (mmt180) cc_final: 0.8334 (mmt180) outliers start: 22 outliers final: 20 residues processed: 138 average time/residue: 0.1307 time to fit residues: 23.6783 Evaluate side-chains 142 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 100 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 202 GLN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.068454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.052675 restraints weight = 33578.625| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.86 r_work: 0.2929 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9657 Z= 0.168 Angle : 0.630 7.828 13111 Z= 0.334 Chirality : 0.042 0.156 1472 Planarity : 0.003 0.046 1656 Dihedral : 4.404 33.490 1294 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.98 % Allowed : 15.56 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.25), residues: 1160 helix: 2.11 (0.25), residues: 469 sheet: -0.34 (0.34), residues: 235 loop : -0.90 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 102 TYR 0.012 0.001 TYR B 105 PHE 0.017 0.001 PHE E 83 TRP 0.015 0.001 TRP E 56 HIS 0.005 0.001 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9647) covalent geometry : angle 0.62313 (13093) SS BOND : bond 0.00375 ( 9) SS BOND : angle 2.49271 ( 18) hydrogen bonds : bond 0.03522 ( 456) hydrogen bonds : angle 4.40923 ( 1311) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8400 (ttp80) REVERT: N 11 LEU cc_start: 0.9392 (tp) cc_final: 0.8961 (mm) REVERT: N 18 LEU cc_start: 0.8214 (tp) cc_final: 0.7944 (tt) REVERT: N 65 LYS cc_start: 0.9113 (mttm) cc_final: 0.8759 (mtpp) REVERT: N 73 ASP cc_start: 0.8986 (t0) cc_final: 0.8548 (t0) REVERT: N 80 TYR cc_start: 0.9036 (m-80) cc_final: 0.8555 (m-10) REVERT: N 82 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7946 (tm-30) REVERT: N 125 THR cc_start: 0.9383 (m) cc_final: 0.8820 (p) REVERT: A 27 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9068 (mm-30) REVERT: A 286 SER cc_start: 0.9155 (m) cc_final: 0.8600 (p) REVERT: A 386 MET cc_start: 0.9040 (ttm) cc_final: 0.8524 (tmm) REVERT: B 226 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8525 (mm-30) REVERT: B 254 ASP cc_start: 0.8497 (t0) cc_final: 0.8251 (t0) REVERT: B 266 HIS cc_start: 0.9228 (t-90) cc_final: 0.8518 (t70) REVERT: B 301 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8406 (mttp) REVERT: G 21 MET cc_start: 0.8880 (tmm) cc_final: 0.8594 (tmm) REVERT: G 38 MET cc_start: 0.9300 (ttp) cc_final: 0.8873 (ptm) REVERT: R 38 ARG cc_start: 0.9321 (mmt180) cc_final: 0.9051 (tpp80) REVERT: R 42 MET cc_start: 0.9347 (mmp) cc_final: 0.9098 (mmp) REVERT: R 96 ASP cc_start: 0.8370 (t0) cc_final: 0.7747 (t0) REVERT: R 332 MET cc_start: 0.7815 (mmm) cc_final: 0.7502 (tmm) REVERT: R 373 MET cc_start: 0.9049 (ttm) cc_final: 0.8621 (tmm) REVERT: E 44 PHE cc_start: 0.8850 (t80) cc_final: 0.8507 (t80) REVERT: E 58 ASP cc_start: 0.9429 (t0) cc_final: 0.8977 (p0) REVERT: E 67 ARG cc_start: 0.8382 (ptt180) cc_final: 0.7886 (ptm160) REVERT: E 76 MET cc_start: 0.9297 (ttm) cc_final: 0.9036 (ttm) REVERT: E 91 ARG cc_start: 0.9368 (mtp85) cc_final: 0.9070 (ptp-110) outliers start: 20 outliers final: 18 residues processed: 138 average time/residue: 0.1161 time to fit residues: 21.0586 Evaluate side-chains 136 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 65 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.066688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.051640 restraints weight = 34204.462| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.72 r_work: 0.2907 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9657 Z= 0.190 Angle : 0.656 9.071 13111 Z= 0.347 Chirality : 0.043 0.152 1472 Planarity : 0.003 0.046 1656 Dihedral : 4.460 33.588 1294 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.18 % Allowed : 15.36 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.25), residues: 1160 helix: 2.07 (0.25), residues: 470 sheet: -0.37 (0.34), residues: 235 loop : -0.91 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 102 TYR 0.013 0.001 TYR B 105 PHE 0.016 0.001 PHE E 83 TRP 0.019 0.001 TRP E 56 HIS 0.005 0.001 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9647) covalent geometry : angle 0.64985 (13093) SS BOND : bond 0.00387 ( 9) SS BOND : angle 2.48726 ( 18) hydrogen bonds : bond 0.03635 ( 456) hydrogen bonds : angle 4.44242 ( 1311) Misc. bond : bond 0.00042 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8411 (ttp80) REVERT: N 11 LEU cc_start: 0.9404 (tp) cc_final: 0.8971 (mm) REVERT: N 65 LYS cc_start: 0.9111 (mttm) cc_final: 0.8770 (mtpp) REVERT: N 73 ASP cc_start: 0.8909 (t0) cc_final: 0.8492 (t0) REVERT: N 80 TYR cc_start: 0.9037 (m-80) cc_final: 0.8567 (m-10) REVERT: N 82 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7920 (tm-30) REVERT: N 125 THR cc_start: 0.9389 (m) cc_final: 0.8835 (p) REVERT: A 27 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9104 (mm-30) REVERT: A 218 ASN cc_start: 0.8909 (m-40) cc_final: 0.7962 (p0) REVERT: A 286 SER cc_start: 0.9135 (m) cc_final: 0.8565 (p) REVERT: A 386 MET cc_start: 0.9030 (ttm) cc_final: 0.8544 (tmm) REVERT: B 13 GLN cc_start: 0.9260 (pp30) cc_final: 0.9017 (pp30) REVERT: B 226 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8519 (mm-30) REVERT: B 254 ASP cc_start: 0.8477 (t0) cc_final: 0.8202 (t0) REVERT: B 266 HIS cc_start: 0.9137 (t-90) cc_final: 0.8427 (t70) REVERT: B 301 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8383 (mttp) REVERT: G 38 MET cc_start: 0.9278 (ttp) cc_final: 0.8894 (ptm) REVERT: R 38 ARG cc_start: 0.9279 (mmt180) cc_final: 0.9034 (tpp80) REVERT: R 42 MET cc_start: 0.9332 (mmp) cc_final: 0.9062 (mmp) REVERT: R 96 ASP cc_start: 0.8439 (t0) cc_final: 0.7927 (t0) REVERT: R 99 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6868 (mp0) REVERT: R 332 MET cc_start: 0.7870 (mmm) cc_final: 0.7563 (tmm) REVERT: R 373 MET cc_start: 0.9018 (ttm) cc_final: 0.8602 (tmm) REVERT: E 44 PHE cc_start: 0.8834 (t80) cc_final: 0.8496 (t80) REVERT: E 58 ASP cc_start: 0.9397 (t0) cc_final: 0.8970 (p0) REVERT: E 67 ARG cc_start: 0.8463 (ptt180) cc_final: 0.7977 (ptm160) REVERT: E 76 MET cc_start: 0.9270 (ttm) cc_final: 0.9019 (ttm) REVERT: E 91 ARG cc_start: 0.9370 (mtp85) cc_final: 0.9080 (ptp-110) outliers start: 22 outliers final: 20 residues processed: 137 average time/residue: 0.1349 time to fit residues: 24.2364 Evaluate side-chains 137 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.066724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.051685 restraints weight = 34019.349| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.71 r_work: 0.2910 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9657 Z= 0.183 Angle : 0.650 9.604 13111 Z= 0.344 Chirality : 0.043 0.156 1472 Planarity : 0.003 0.046 1656 Dihedral : 4.450 33.450 1294 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.28 % Allowed : 15.36 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.25), residues: 1160 helix: 2.00 (0.25), residues: 470 sheet: -0.35 (0.34), residues: 224 loop : -0.94 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 64 TYR 0.013 0.001 TYR B 105 PHE 0.016 0.001 PHE E 83 TRP 0.019 0.001 TRP E 56 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9647) covalent geometry : angle 0.64444 (13093) SS BOND : bond 0.00359 ( 9) SS BOND : angle 2.43392 ( 18) hydrogen bonds : bond 0.03630 ( 456) hydrogen bonds : angle 4.46758 ( 1311) Misc. bond : bond 0.00044 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2354.73 seconds wall clock time: 41 minutes 12.70 seconds (2472.70 seconds total)