Starting phenix.real_space_refine on Thu Feb 13 19:58:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e3y_8978/02_2025/6e3y_8978.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e3y_8978/02_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_8978/02_2025/6e3y_8978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e3y_8978/02_2025/6e3y_8978.map" model { file = "/net/cci-nas-00/data/ceres_data/6e3y_8978/02_2025/6e3y_8978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e3y_8978/02_2025/6e3y_8978.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} 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: {'GLN:plan1': 1, 'GLU:plan': 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: 5.68, per 1000 atoms: 0.60 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: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.95 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: 2.68 Time building geometry restraints manager: 2.64 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.190 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- 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 0.066 9647 Z= 0.469 Angle : 1.004 11.253 13093 Z= 0.572 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.003 TRP R 229 HIS 0.013 0.003 HIS R 374 PHE 0.037 0.003 PHE R 163 TYR 0.020 0.003 TYR N 94 ARG 0.009 0.001 ARG A 317 *********************** 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 : 0.943 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 31 ASN cc_start: 0.9207 (t0) cc_final: 0.8949 (t0) REVERT: N 34 MET cc_start: 0.8439 (mtp) cc_final: 0.8185 (mtp) REVERT: N 65 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8701 (mtmt) 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: 0.8878 (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: 0.9250 (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: 0.8414 (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: 0.8624 (mtpp) REVERT: R 280 ASP cc_start: 0.9133 (t0) cc_final: 0.8604 (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: 0.8400 (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: 0.3207 time to fit residues: 100.9650 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 : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.0870 chunk 67 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.071769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.055940 restraints weight = 33394.743| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.99 r_work: 0.3013 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9647 Z= 0.242 Angle : 0.640 11.067 13093 Z= 0.337 Chirality : 0.043 0.168 1472 Planarity : 0.004 0.050 1656 Dihedral : 4.809 59.918 1294 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.98 % Allowed : 9.51 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1160 helix: 0.49 (0.23), residues: 460 sheet: -0.72 (0.32), residues: 226 loop : -1.44 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 229 HIS 0.006 0.001 HIS R 374 PHE 0.019 0.002 PHE E 92 TYR 0.018 0.002 TYR A 358 ARG 0.011 0.001 ARG E 64 *********************** 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: 20 poor density : 149 time to evaluate : 1.053 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: 0.9315 (t0) cc_final: 0.9076 (t0) REVERT: N 11 LEU cc_start: 0.9239 (tp) cc_final: 0.8915 (mm) REVERT: N 65 LYS cc_start: 0.9105 (mmmm) cc_final: 0.8573 (mtmt) REVERT: N 69 THR cc_start: 0.8936 (m) cc_final: 0.8494 (t) REVERT: N 73 ASP cc_start: 0.7421 (p0) cc_final: 0.7166 (p0) REVERT: N 82 GLN cc_start: 0.8293 (tp40) cc_final: 0.8044 (tm-30) REVERT: N 125 THR cc_start: 0.9329 (m) cc_final: 0.8881 (p) REVERT: A 27 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9097 (mm-30) REVERT: A 392 GLU cc_start: 0.8246 (pm20) cc_final: 0.7976 (pm20) REVERT: B 32 GLN cc_start: 0.9146 (mt0) cc_final: 0.8943 (mt0) REVERT: B 44 GLN cc_start: 0.8959 (pm20) cc_final: 0.8408 (pm20) REVERT: B 155 ASN cc_start: 0.9204 (t0) cc_final: 0.8743 (t0) REVERT: B 215 GLU cc_start: 0.8797 (mp0) cc_final: 0.8458 (mp0) REVERT: B 254 ASP cc_start: 0.8417 (t0) cc_final: 0.8110 (t0) REVERT: B 301 LYS cc_start: 0.8668 (mmmm) cc_final: 0.8311 (mttp) REVERT: R 42 MET cc_start: 0.9467 (mmp) cc_final: 0.9170 (mmp) REVERT: R 99 GLU cc_start: 0.7801 (tp30) cc_final: 0.7546 (tp30) REVERT: R 332 MET cc_start: 0.7721 (mmm) cc_final: 0.7421 (tmm) REVERT: R 373 MET cc_start: 0.9046 (ttm) cc_final: 0.8664 (tmm) REVERT: E 44 PHE cc_start: 0.8927 (t80) cc_final: 0.8700 (t80) REVERT: E 58 ASP cc_start: 0.9506 (t0) cc_final: 0.9268 (t0) REVERT: E 67 ARG cc_start: 0.8468 (ptt180) cc_final: 0.7978 (ptm160) REVERT: E 76 MET cc_start: 0.9352 (tpp) cc_final: 0.8993 (mmp) REVERT: E 83 PHE cc_start: 0.8545 (p90) cc_final: 0.8286 (p90) REVERT: E 91 ARG cc_start: 0.9264 (mtp85) cc_final: 0.8959 (ptp90) outliers start: 20 outliers final: 11 residues processed: 161 average time/residue: 0.2716 time to fit residues: 57.6221 Evaluate side-chains 137 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 106 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.071331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.055493 restraints weight = 34001.079| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 4.02 r_work: 0.3005 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9647 Z= 0.210 Angle : 0.588 11.626 13093 Z= 0.308 Chirality : 0.042 0.168 1472 Planarity : 0.004 0.047 1656 Dihedral : 4.705 53.317 1294 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.49 % Allowed : 12.29 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1160 helix: 1.59 (0.24), residues: 458 sheet: -0.46 (0.32), residues: 234 loop : -1.19 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 229 HIS 0.004 0.001 HIS R 374 PHE 0.015 0.001 PHE B 199 TYR 0.026 0.001 TYR N 80 ARG 0.011 0.001 ARG P 18 *********************** 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 154 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.178 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 31 ASN cc_start: 0.9320 (t0) cc_final: 0.9108 (t0) REVERT: N 11 LEU cc_start: 0.9232 (tp) cc_final: 0.8876 (mm) REVERT: N 34 MET cc_start: 0.9062 (mtp) cc_final: 0.8489 (mmm) REVERT: N 69 THR cc_start: 0.8942 (m) cc_final: 0.8527 (t) REVERT: N 73 ASP cc_start: 0.7480 (p0) cc_final: 0.7164 (p0) REVERT: N 125 THR cc_start: 0.9359 (m) cc_final: 0.8910 (p) REVERT: A 27 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9149 (mm-30) REVERT: B 32 GLN cc_start: 0.9115 (mt0) cc_final: 0.8889 (mt0) REVERT: B 44 GLN cc_start: 0.9001 (pm20) cc_final: 0.8437 (pm20) REVERT: B 215 GLU cc_start: 0.8821 (mp0) cc_final: 0.8592 (mp0) REVERT: B 254 ASP cc_start: 0.8445 (t0) cc_final: 0.8197 (t0) REVERT: B 301 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8258 (mttp) REVERT: G 38 MET cc_start: 0.9375 (ttp) cc_final: 0.8834 (ptm) REVERT: R 42 MET cc_start: 0.9439 (mmp) cc_final: 0.9113 (mmp) REVERT: R 99 GLU cc_start: 0.7751 (tp30) cc_final: 0.7465 (tp30) REVERT: R 332 MET cc_start: 0.7824 (mmm) cc_final: 0.7488 (tmm) REVERT: E 58 ASP cc_start: 0.9524 (t0) cc_final: 0.9290 (t0) REVERT: E 67 ARG cc_start: 0.8414 (ptt180) cc_final: 0.7906 (ptm160) REVERT: E 83 PHE cc_start: 0.8555 (p90) cc_final: 0.8286 (p90) outliers start: 15 outliers final: 10 residues processed: 146 average time/residue: 0.2918 time to fit residues: 56.0485 Evaluate side-chains 137 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 0.5980 chunk 108 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.070550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054650 restraints weight = 33885.456| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.98 r_work: 0.2983 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9647 Z= 0.217 Angle : 0.578 9.247 13093 Z= 0.306 Chirality : 0.042 0.173 1472 Planarity : 0.004 0.058 1656 Dihedral : 4.549 46.791 1294 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.48 % Allowed : 12.09 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1160 helix: 1.95 (0.25), residues: 458 sheet: -0.28 (0.33), residues: 234 loop : -1.06 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 229 HIS 0.004 0.001 HIS R 374 PHE 0.014 0.001 PHE B 199 TYR 0.024 0.001 TYR N 80 ARG 0.011 0.001 ARG P 18 *********************** 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 163 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.189 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 3 ASP cc_start: 0.7356 (p0) cc_final: 0.7133 (t0) REVERT: P 31 ASN cc_start: 0.9322 (t0) cc_final: 0.9084 (t0) REVERT: N 11 LEU cc_start: 0.9271 (tp) cc_final: 0.8882 (mm) REVERT: N 34 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8397 (mmm) REVERT: N 69 THR cc_start: 0.8881 (m) cc_final: 0.8555 (t) REVERT: N 125 THR cc_start: 0.9371 (m) cc_final: 0.8936 (p) REVERT: A 27 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9133 (mm-30) REVERT: A 229 ASP cc_start: 0.9152 (m-30) cc_final: 0.8466 (t70) REVERT: A 240 ASP cc_start: 0.9144 (m-30) cc_final: 0.8913 (m-30) REVERT: B 32 GLN cc_start: 0.9122 (mt0) cc_final: 0.8823 (mt0) REVERT: B 44 GLN cc_start: 0.8997 (pm20) cc_final: 0.8432 (pm20) REVERT: B 215 GLU cc_start: 0.8861 (mp0) cc_final: 0.8641 (mp0) REVERT: B 254 ASP cc_start: 0.8418 (t0) cc_final: 0.8137 (t0) REVERT: B 301 LYS cc_start: 0.8741 (mmmm) cc_final: 0.8267 (mttp) REVERT: G 38 MET cc_start: 0.9348 (ttp) cc_final: 0.8854 (ptm) REVERT: R 38 ARG cc_start: 0.9315 (mmt180) cc_final: 0.8999 (tpp80) REVERT: R 42 MET cc_start: 0.9413 (mmp) cc_final: 0.9073 (mmp) REVERT: R 85 MET cc_start: 0.8753 (tmm) cc_final: 0.7385 (tmm) REVERT: R 96 ASP cc_start: 0.7541 (t0) cc_final: 0.6933 (t0) REVERT: R 99 GLU cc_start: 0.7739 (tp30) cc_final: 0.7197 (mm-30) REVERT: R 332 MET cc_start: 0.7835 (mmm) cc_final: 0.7496 (tmm) REVERT: E 58 ASP cc_start: 0.9499 (t0) cc_final: 0.9263 (t0) REVERT: E 67 ARG cc_start: 0.8443 (ptt180) cc_final: 0.7893 (ptm160) REVERT: E 76 MET cc_start: 0.9357 (ttm) cc_final: 0.8958 (ttt) REVERT: E 83 PHE cc_start: 0.8548 (p90) cc_final: 0.8310 (p90) REVERT: E 99 ARG cc_start: 0.9050 (ptm160) cc_final: 0.8590 (tmm-80) REVERT: E 102 ARG cc_start: 0.8954 (ptt-90) cc_final: 0.8658 (ptt-90) outliers start: 25 outliers final: 15 residues processed: 154 average time/residue: 0.2703 time to fit residues: 55.4307 Evaluate side-chains 141 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 34 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 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 144 LEU Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 64 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN A 390 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 = 0.3495 r_free = 0.3495 target = 0.068964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053015 restraints weight = 34114.275| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.93 r_work: 0.2937 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9647 Z= 0.277 Angle : 0.597 8.374 13093 Z= 0.315 Chirality : 0.042 0.149 1472 Planarity : 0.004 0.045 1656 Dihedral : 4.510 40.133 1294 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.38 % Allowed : 12.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1160 helix: 2.08 (0.25), residues: 462 sheet: -0.25 (0.34), residues: 238 loop : -0.94 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 229 HIS 0.005 0.001 HIS R 374 PHE 0.014 0.002 PHE E 44 TYR 0.015 0.001 TYR B 105 ARG 0.009 0.001 ARG P 18 *********************** 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: 24 poor density : 132 time to evaluate : 1.105 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: P 3 ASP cc_start: 0.7486 (p0) cc_final: 0.7238 (t0) REVERT: P 31 ASN cc_start: 0.9331 (t0) cc_final: 0.9078 (t0) REVERT: N 11 LEU cc_start: 0.9312 (tp) cc_final: 0.8920 (mm) REVERT: N 34 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8852 (mmm) REVERT: N 69 THR cc_start: 0.8847 (m) cc_final: 0.8481 (t) REVERT: N 73 ASP cc_start: 0.7656 (p0) cc_final: 0.7347 (p0) REVERT: N 80 TYR cc_start: 0.9009 (m-80) cc_final: 0.8465 (m-10) REVERT: N 125 THR cc_start: 0.9427 (m) cc_final: 0.9011 (p) REVERT: A 229 ASP cc_start: 0.9134 (m-30) cc_final: 0.8307 (t0) REVERT: A 240 ASP cc_start: 0.9133 (m-30) cc_final: 0.8838 (m-30) REVERT: A 386 MET cc_start: 0.9056 (ttm) cc_final: 0.8558 (tmm) REVERT: B 32 GLN cc_start: 0.9138 (mt0) cc_final: 0.8902 (mt0) REVERT: B 44 GLN cc_start: 0.9042 (pm20) cc_final: 0.8448 (pm20) REVERT: B 215 GLU cc_start: 0.8725 (mp0) cc_final: 0.8512 (mp0) REVERT: B 254 ASP cc_start: 0.8496 (t0) cc_final: 0.8244 (t0) REVERT: B 301 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8311 (mmtp) REVERT: G 38 MET cc_start: 0.9334 (ttp) cc_final: 0.8891 (ptm) REVERT: R 38 ARG cc_start: 0.9317 (mmt180) cc_final: 0.9009 (tpp80) REVERT: R 42 MET cc_start: 0.9394 (mmp) cc_final: 0.9095 (mmp) REVERT: R 96 ASP cc_start: 0.7650 (t0) cc_final: 0.6965 (t0) REVERT: R 99 GLU cc_start: 0.7952 (tp30) cc_final: 0.7716 (mm-30) REVERT: R 332 MET cc_start: 0.7858 (mmm) cc_final: 0.7522 (tmm) REVERT: R 390 GLU cc_start: 0.8670 (pm20) cc_final: 0.8405 (pm20) REVERT: E 58 ASP cc_start: 0.9492 (t0) cc_final: 0.9279 (t0) REVERT: E 67 ARG cc_start: 0.8400 (ptt180) cc_final: 0.7849 (ptm160) REVERT: E 76 MET cc_start: 0.9293 (ttm) cc_final: 0.9039 (ttm) REVERT: E 83 PHE cc_start: 0.8665 (p90) cc_final: 0.8351 (p90) REVERT: E 102 ARG cc_start: 0.8957 (ptt-90) cc_final: 0.8692 (ptt-90) outliers start: 24 outliers final: 19 residues processed: 146 average time/residue: 0.2709 time to fit residues: 52.4748 Evaluate side-chains 141 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 37 VAL 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 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 144 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 57 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 266 HIS ** 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 = 0.3453 r_free = 0.3453 target = 0.067225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.051342 restraints weight = 34312.882| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.90 r_work: 0.2895 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9647 Z= 0.380 Angle : 0.650 9.948 13093 Z= 0.344 Chirality : 0.044 0.154 1472 Planarity : 0.004 0.045 1656 Dihedral : 4.653 36.885 1294 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.87 % Allowed : 13.08 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1160 helix: 2.04 (0.25), residues: 470 sheet: -0.26 (0.35), residues: 230 loop : -1.02 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.005 0.001 HIS R 374 PHE 0.014 0.002 PHE E 44 TYR 0.019 0.001 TYR B 105 ARG 0.013 0.001 ARG P 18 *********************** 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 158 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 11 LEU cc_start: 0.9358 (tp) cc_final: 0.8936 (mm) REVERT: N 19 ARG cc_start: 0.8748 (tpp80) cc_final: 0.8494 (tpp80) REVERT: N 69 THR cc_start: 0.8832 (m) cc_final: 0.8546 (t) REVERT: N 73 ASP cc_start: 0.7653 (p0) cc_final: 0.7424 (p0) REVERT: N 125 THR cc_start: 0.9391 (m) cc_final: 0.8849 (p) REVERT: A 209 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6925 (tm-30) REVERT: A 229 ASP cc_start: 0.9146 (m-30) cc_final: 0.8306 (t0) REVERT: A 240 ASP cc_start: 0.9132 (m-30) cc_final: 0.8858 (m-30) REVERT: A 286 SER cc_start: 0.9054 (m) cc_final: 0.8595 (p) REVERT: A 386 MET cc_start: 0.9076 (ttm) cc_final: 0.8580 (tmm) REVERT: B 44 GLN cc_start: 0.9008 (pm20) cc_final: 0.8309 (pm20) REVERT: B 215 GLU cc_start: 0.8690 (mp0) cc_final: 0.8424 (mp0) REVERT: B 254 ASP cc_start: 0.8505 (t0) cc_final: 0.8235 (t0) REVERT: B 266 HIS cc_start: 0.9229 (t-90) cc_final: 0.8857 (t70) REVERT: B 301 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8336 (mmtp) REVERT: G 38 MET cc_start: 0.9366 (ttp) cc_final: 0.8914 (ptm) REVERT: R 38 ARG cc_start: 0.9321 (mmt180) cc_final: 0.9006 (tpp80) REVERT: R 42 MET cc_start: 0.9393 (mmp) cc_final: 0.9139 (mmp) REVERT: R 99 GLU cc_start: 0.7966 (tp30) cc_final: 0.7719 (mm-30) REVERT: R 332 MET cc_start: 0.7956 (mmm) cc_final: 0.7649 (tmm) REVERT: E 58 ASP cc_start: 0.9482 (t0) cc_final: 0.9270 (t0) REVERT: E 67 ARG cc_start: 0.8432 (ptt180) cc_final: 0.7874 (ptm160) REVERT: E 76 MET cc_start: 0.9272 (ttm) cc_final: 0.9026 (ttm) REVERT: E 83 PHE cc_start: 0.8776 (p90) cc_final: 0.8479 (p90) REVERT: E 91 ARG cc_start: 0.9348 (mtp85) cc_final: 0.9088 (ptp-110) REVERT: E 99 ARG cc_start: 0.9066 (ptm160) cc_final: 0.8510 (tmm-80) REVERT: E 102 ARG cc_start: 0.8968 (ptt-90) cc_final: 0.8549 (ptt-90) outliers start: 29 outliers final: 20 residues processed: 149 average time/residue: 0.2772 time to fit residues: 54.4601 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 : 1.046 ------------------------------------------------------------------------------- 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 210 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 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 19 LEU Chi-restraints excluded: chain G residue 52 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 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 = 0.3481 r_free = 0.3481 target = 0.068398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.052592 restraints weight = 34386.621| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.94 r_work: 0.2928 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9647 Z= 0.217 Angle : 0.629 14.889 13093 Z= 0.332 Chirality : 0.043 0.277 1472 Planarity : 0.004 0.045 1656 Dihedral : 4.551 33.949 1294 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.78 % Allowed : 14.77 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1160 helix: 2.15 (0.25), residues: 470 sheet: -0.27 (0.35), residues: 237 loop : -0.99 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 229 HIS 0.008 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.014 0.001 TYR B 105 ARG 0.008 0.000 ARG P 18 *********************** 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 146 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 11 LEU cc_start: 0.9382 (tp) cc_final: 0.8953 (mm) REVERT: N 19 ARG cc_start: 0.8744 (tpp80) cc_final: 0.8443 (tpp80) REVERT: N 125 THR cc_start: 0.9371 (m) cc_final: 0.8845 (p) REVERT: A 217 VAL cc_start: 0.9279 (t) cc_final: 0.8971 (m) REVERT: A 229 ASP cc_start: 0.9146 (m-30) cc_final: 0.8274 (t0) REVERT: A 240 ASP cc_start: 0.9167 (m-30) cc_final: 0.8881 (m-30) REVERT: A 286 SER cc_start: 0.9036 (m) cc_final: 0.8527 (p) REVERT: A 386 MET cc_start: 0.9062 (ttm) cc_final: 0.8567 (tmm) REVERT: A 392 GLU cc_start: 0.8195 (mp0) cc_final: 0.7942 (pm20) REVERT: B 32 GLN cc_start: 0.9120 (mt0) cc_final: 0.8901 (mt0) REVERT: B 44 GLN cc_start: 0.9041 (pm20) cc_final: 0.8308 (pm20) REVERT: B 215 GLU cc_start: 0.8690 (mp0) cc_final: 0.8427 (mp0) REVERT: B 226 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8699 (mt-10) REVERT: B 254 ASP cc_start: 0.8501 (t0) cc_final: 0.8247 (t0) REVERT: B 266 HIS cc_start: 0.9234 (t-90) cc_final: 0.8738 (t70) REVERT: B 301 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8335 (mttp) REVERT: G 38 MET cc_start: 0.9340 (ttp) cc_final: 0.8861 (ptm) REVERT: R 38 ARG cc_start: 0.9318 (mmt180) cc_final: 0.9030 (tpp80) REVERT: R 42 MET cc_start: 0.9370 (mmp) cc_final: 0.9116 (mmp) REVERT: R 99 GLU cc_start: 0.7974 (tp30) cc_final: 0.7764 (mm-30) REVERT: R 332 MET cc_start: 0.7855 (mmm) cc_final: 0.7520 (tmm) REVERT: E 58 ASP cc_start: 0.9454 (t0) cc_final: 0.9237 (t0) REVERT: E 67 ARG cc_start: 0.8377 (ptt180) cc_final: 0.7843 (ptm160) REVERT: E 76 MET cc_start: 0.9313 (ttm) cc_final: 0.9040 (ttm) REVERT: E 83 PHE cc_start: 0.8700 (p90) cc_final: 0.8452 (p90) REVERT: E 91 ARG cc_start: 0.9343 (mtp85) cc_final: 0.9077 (ptp-110) REVERT: E 99 ARG cc_start: 0.9036 (ptm160) cc_final: 0.8440 (tmm-80) outliers start: 18 outliers final: 15 residues processed: 140 average time/residue: 0.2786 time to fit residues: 51.2225 Evaluate side-chains 135 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 210 THR 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 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 342 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 46 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 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 = 0.3454 r_free = 0.3454 target = 0.067300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051336 restraints weight = 34928.617| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.93 r_work: 0.2893 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9647 Z= 0.332 Angle : 0.658 10.511 13093 Z= 0.349 Chirality : 0.043 0.177 1472 Planarity : 0.004 0.046 1656 Dihedral : 4.591 33.896 1294 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.28 % Allowed : 14.67 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1160 helix: 2.10 (0.25), residues: 470 sheet: -0.29 (0.34), residues: 235 loop : -0.95 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 229 HIS 0.009 0.001 HIS A 220 PHE 0.013 0.002 PHE R 262 TYR 0.016 0.001 TYR B 105 ARG 0.010 0.001 ARG P 18 *********************** 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 149 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 3 ASP cc_start: 0.7905 (p0) cc_final: 0.7682 (t70) REVERT: N 19 ARG cc_start: 0.8788 (tpp80) cc_final: 0.8469 (tpp80) REVERT: N 34 MET cc_start: 0.9352 (mmm) cc_final: 0.9117 (mmm) REVERT: N 73 ASP cc_start: 0.7867 (p0) cc_final: 0.7177 (p0) REVERT: N 125 THR cc_start: 0.9379 (m) cc_final: 0.9131 (p) REVERT: A 27 GLU cc_start: 0.9340 (mm-30) cc_final: 0.9055 (mm-30) REVERT: A 217 VAL cc_start: 0.9274 (t) cc_final: 0.8974 (m) REVERT: A 229 ASP cc_start: 0.9166 (m-30) cc_final: 0.8278 (t0) REVERT: A 240 ASP cc_start: 0.9135 (m-30) cc_final: 0.8925 (m-30) REVERT: A 286 SER cc_start: 0.9057 (m) cc_final: 0.8584 (p) REVERT: A 386 MET cc_start: 0.9093 (ttm) cc_final: 0.8595 (tmm) REVERT: B 44 GLN cc_start: 0.9014 (pm20) cc_final: 0.8300 (pm20) REVERT: B 215 GLU cc_start: 0.8714 (mp0) cc_final: 0.8461 (mp0) REVERT: B 226 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8502 (mm-30) REVERT: B 254 ASP cc_start: 0.8498 (t0) cc_final: 0.8234 (t0) REVERT: B 266 HIS cc_start: 0.9229 (t-90) cc_final: 0.8503 (t-170) REVERT: B 301 LYS cc_start: 0.8832 (mmmm) cc_final: 0.8341 (mttp) REVERT: G 38 MET cc_start: 0.9346 (ttp) cc_final: 0.8885 (ptm) REVERT: R 38 ARG cc_start: 0.9328 (mmt180) cc_final: 0.9038 (tpp80) REVERT: R 42 MET cc_start: 0.9371 (mmp) cc_final: 0.9129 (mmp) REVERT: R 85 MET cc_start: 0.8918 (tpp) cc_final: 0.8547 (tpp) REVERT: R 332 MET cc_start: 0.7914 (mmm) cc_final: 0.7590 (tmm) REVERT: E 44 PHE cc_start: 0.8808 (t80) cc_final: 0.8448 (t80) REVERT: E 58 ASP cc_start: 0.9469 (t0) cc_final: 0.9006 (p0) REVERT: E 67 ARG cc_start: 0.8382 (ptt180) cc_final: 0.7857 (ptm160) REVERT: E 76 MET cc_start: 0.9293 (ttm) cc_final: 0.9039 (ttm) REVERT: E 83 PHE cc_start: 0.8749 (p90) cc_final: 0.8488 (p90) REVERT: E 91 ARG cc_start: 0.9376 (mtp85) cc_final: 0.9126 (ptp-110) REVERT: E 99 ARG cc_start: 0.9093 (ptm160) cc_final: 0.8539 (tmm-80) REVERT: E 102 ARG cc_start: 0.9018 (ptt-90) cc_final: 0.8602 (ptt-90) outliers start: 23 outliers final: 20 residues processed: 141 average time/residue: 0.2760 time to fit residues: 51.0206 Evaluate side-chains 144 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 210 THR 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 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 54 THR Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 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 = 0.3485 r_free = 0.3485 target = 0.068614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052767 restraints weight = 33985.960| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.90 r_work: 0.2934 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9647 Z= 0.211 Angle : 0.616 8.855 13093 Z= 0.328 Chirality : 0.042 0.166 1472 Planarity : 0.003 0.046 1656 Dihedral : 4.417 33.328 1294 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.68 % Allowed : 15.66 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1160 helix: 2.21 (0.25), residues: 470 sheet: -0.26 (0.34), residues: 227 loop : -0.91 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 56 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.001 PHE R 142 TYR 0.011 0.001 TYR B 105 ARG 0.006 0.000 ARG A 317 *********************** 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 147 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 3 ASP cc_start: 0.7857 (p0) cc_final: 0.7592 (t70) REVERT: N 34 MET cc_start: 0.9321 (mmm) cc_final: 0.9000 (mmm) REVERT: N 65 LYS cc_start: 0.9052 (mttm) cc_final: 0.8689 (mtpp) REVERT: N 73 ASP cc_start: 0.8045 (p0) cc_final: 0.6630 (p0) REVERT: N 125 THR cc_start: 0.9365 (m) cc_final: 0.9122 (p) REVERT: A 27 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9079 (mm-30) REVERT: A 217 VAL cc_start: 0.9246 (t) cc_final: 0.8942 (m) REVERT: A 229 ASP cc_start: 0.9145 (m-30) cc_final: 0.8245 (t0) REVERT: A 240 ASP cc_start: 0.9158 (m-30) cc_final: 0.8865 (m-30) REVERT: A 286 SER cc_start: 0.9017 (m) cc_final: 0.8502 (p) REVERT: A 386 MET cc_start: 0.9095 (ttm) cc_final: 0.8605 (tmm) REVERT: B 44 GLN cc_start: 0.9029 (pm20) cc_final: 0.8287 (pm20) REVERT: B 215 GLU cc_start: 0.8749 (mp0) cc_final: 0.8504 (mp0) REVERT: B 226 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8489 (mm-30) REVERT: B 254 ASP cc_start: 0.8492 (t0) cc_final: 0.8244 (t0) REVERT: B 266 HIS cc_start: 0.9253 (t-90) cc_final: 0.8491 (t-170) REVERT: B 301 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8419 (mttp) REVERT: G 38 MET cc_start: 0.9304 (ttp) cc_final: 0.8865 (ptm) REVERT: R 38 ARG cc_start: 0.9304 (mmt180) cc_final: 0.9031 (tpp80) REVERT: R 42 MET cc_start: 0.9357 (mmp) cc_final: 0.9112 (mmp) REVERT: R 96 ASP cc_start: 0.8202 (t0) cc_final: 0.7959 (t0) REVERT: R 332 MET cc_start: 0.7770 (mmm) cc_final: 0.7564 (tmm) REVERT: R 373 MET cc_start: 0.9011 (ttm) cc_final: 0.8602 (tmm) REVERT: R 390 GLU cc_start: 0.8667 (pm20) cc_final: 0.8222 (pm20) REVERT: E 44 PHE cc_start: 0.8833 (t80) cc_final: 0.8481 (t80) REVERT: E 58 ASP cc_start: 0.9405 (t0) cc_final: 0.8979 (p0) REVERT: E 67 ARG cc_start: 0.8423 (ptt180) cc_final: 0.7943 (ptm160) REVERT: E 76 MET cc_start: 0.9310 (ttm) cc_final: 0.9059 (ttm) REVERT: E 91 ARG cc_start: 0.9368 (mtp85) cc_final: 0.9122 (ptp-110) REVERT: E 99 ARG cc_start: 0.9047 (ptm160) cc_final: 0.8516 (tmm-80) outliers start: 17 outliers final: 14 residues processed: 140 average time/residue: 0.2883 time to fit residues: 53.3224 Evaluate side-chains 137 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 2 VAL 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 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 342 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 0.2980 chunk 90 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 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 = 0.3443 r_free = 0.3443 target = 0.066947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051835 restraints weight = 34658.729| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.73 r_work: 0.2915 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9647 Z= 0.246 Angle : 0.637 7.841 13093 Z= 0.338 Chirality : 0.043 0.168 1472 Planarity : 0.003 0.046 1656 Dihedral : 4.443 32.669 1294 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.98 % Allowed : 15.46 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1160 helix: 2.12 (0.25), residues: 470 sheet: -0.16 (0.35), residues: 225 loop : -0.93 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 56 HIS 0.007 0.001 HIS A 220 PHE 0.024 0.001 PHE E 83 TYR 0.012 0.001 TYR B 105 ARG 0.005 0.000 ARG E 64 ********************** 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 143 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 34 MET cc_start: 0.9333 (mmm) cc_final: 0.9028 (mmm) REVERT: N 65 LYS cc_start: 0.9037 (mttm) cc_final: 0.8684 (mtpp) REVERT: N 125 THR cc_start: 0.9361 (m) cc_final: 0.9122 (p) REVERT: A 27 GLU cc_start: 0.9365 (mm-30) cc_final: 0.9099 (mm-30) REVERT: A 217 VAL cc_start: 0.9296 (t) cc_final: 0.9017 (m) REVERT: A 218 ASN cc_start: 0.8859 (m-40) cc_final: 0.7823 (p0) REVERT: A 229 ASP cc_start: 0.9140 (m-30) cc_final: 0.8249 (t0) REVERT: A 240 ASP cc_start: 0.9109 (m-30) cc_final: 0.8815 (m-30) REVERT: A 286 SER cc_start: 0.9002 (m) cc_final: 0.8492 (p) REVERT: A 386 MET cc_start: 0.9058 (ttm) cc_final: 0.8608 (tmm) REVERT: B 7 LEU cc_start: 0.8006 (mm) cc_final: 0.7742 (mt) REVERT: B 44 GLN cc_start: 0.9077 (pm20) cc_final: 0.8360 (pm20) REVERT: B 215 GLU cc_start: 0.8695 (mp0) cc_final: 0.8488 (mp0) REVERT: B 226 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8538 (mm-30) REVERT: B 254 ASP cc_start: 0.8467 (t0) cc_final: 0.8234 (t0) REVERT: B 266 HIS cc_start: 0.9150 (t-90) cc_final: 0.8403 (t-170) REVERT: B 301 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8429 (mttp) REVERT: G 38 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8895 (ptm) REVERT: R 38 ARG cc_start: 0.9282 (mmt180) cc_final: 0.9031 (tpp80) REVERT: R 42 MET cc_start: 0.9350 (mmp) cc_final: 0.9112 (mmp) REVERT: R 332 MET cc_start: 0.7896 (mmm) cc_final: 0.7604 (tmm) REVERT: R 373 MET cc_start: 0.9010 (ttm) cc_final: 0.8617 (tmm) REVERT: E 44 PHE cc_start: 0.8851 (t80) cc_final: 0.8515 (t80) REVERT: E 58 ASP cc_start: 0.9353 (t0) cc_final: 0.8964 (p0) REVERT: E 67 ARG cc_start: 0.8436 (ptt180) cc_final: 0.7969 (ptm160) REVERT: E 76 MET cc_start: 0.9283 (ttm) cc_final: 0.9027 (ttm) REVERT: E 91 ARG cc_start: 0.9346 (mtp85) cc_final: 0.9107 (ptp-110) REVERT: E 99 ARG cc_start: 0.8867 (ptm160) cc_final: 0.8457 (tmm-80) outliers start: 20 outliers final: 15 residues processed: 134 average time/residue: 0.2690 time to fit residues: 47.9067 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 : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 2 VAL 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 38 MET 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 342 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 39 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 112 optimal weight: 0.0770 chunk 113 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 overall best weight: 2.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 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 = 0.3442 r_free = 0.3442 target = 0.066910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.051922 restraints weight = 34547.222| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.70 r_work: 0.2915 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9647 Z= 0.238 Angle : 0.645 9.858 13093 Z= 0.340 Chirality : 0.043 0.159 1472 Planarity : 0.003 0.046 1656 Dihedral : 4.411 32.602 1294 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.78 % Allowed : 15.56 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1160 helix: 2.07 (0.25), residues: 470 sheet: -0.20 (0.35), residues: 226 loop : -0.92 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 56 HIS 0.007 0.001 HIS A 220 PHE 0.025 0.001 PHE E 83 TYR 0.012 0.001 TYR B 105 ARG 0.005 0.000 ARG E 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4318.33 seconds wall clock time: 77 minutes 32.67 seconds (4652.67 seconds total)