Starting phenix.real_space_refine on Wed Jul 30 04:54:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gda_29944/07_2025/8gda_29944_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gda_29944/07_2025/8gda_29944.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/8gda_29944/07_2025/8gda_29944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gda_29944/07_2025/8gda_29944.map" model { file = "/net/cci-nas-00/data/ceres_data/8gda_29944/07_2025/8gda_29944_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gda_29944/07_2025/8gda_29944_neut.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= 0.001 sd= 0.016 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 5445 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 4881 2.51 5 N 1349 2.21 5 O 1370 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7650 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1750 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2477 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 12, 'ASN%COO:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 391 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "N" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 922 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2080 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'YZV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.65 Number of scatterers: 7650 At special positions: 0 Unit cell: (95.2, 124.1, 100.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 F 2 9.00 O 1370 8.00 N 1349 7.00 C 4881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 916.2 milliseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1946 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 40.1% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 10 through 32 removed outlier: 3.865A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.605A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.756A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.674A pdb=" N ASP A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 removed outlier: 4.134A pdb=" N ASP A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 388 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.628A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.533A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 4.036A 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 87 through 91 removed outlier: 3.904A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 44 removed outlier: 3.877A pdb=" N MET R 27 " --> pdb=" O ILE R 23 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE R 28 " --> pdb=" O PRO R 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN R 35 " --> pdb=" O GLY R 31 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 38 " --> pdb=" O GLY R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 50 Processing helix chain 'R' and resid 52 through 83 removed outlier: 4.044A pdb=" N THR R 56 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU R 57 " --> pdb=" O THR R 53 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 88 through 123 removed outlier: 3.663A pdb=" N ILE R 110 " --> pdb=" O GLY R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 131 Processing helix chain 'R' and resid 132 through 152 removed outlier: 3.708A pdb=" N ALA R 136 " --> pdb=" O ASP R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 157 removed outlier: 3.797A pdb=" N GLY R 157 " --> pdb=" O PRO R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 206 removed outlier: 3.527A pdb=" N TYR R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER R 185 " --> pdb=" O HIS R 181 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE R 194 " --> pdb=" O GLY R 190 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU R 195 " --> pdb=" O PHE R 191 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE R 196 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 221 Processing helix chain 'R' and resid 267 through 298 removed outlier: 3.668A pdb=" N VAL R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU R 282 " --> pdb=" O SER R 278 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 305 through 309 removed outlier: 3.712A pdb=" N ASN R 309 " --> pdb=" O VAL R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 319 Processing helix chain 'R' and resid 320 through 330 Proline residue: R 326 - end of helix Processing helix chain 'R' and resid 333 through 344 removed outlier: 3.603A pdb=" N LYS R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.771A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.662A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.978A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.630A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.696A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.589A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.718A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.648A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.556A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLY N 16 " --> pdb=" O SER N 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.142A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1089 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: 2.18 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1220 1.31 - 1.44: 2167 1.44 - 1.56: 4348 1.56 - 1.68: 2 1.68 - 1.81: 65 Bond restraints: 7802 Sorted by residual: bond pdb=" C13 YZV R 501 " pdb=" C14 YZV R 501 " ideal model delta sigma weight residual 1.525 1.221 0.304 2.00e-02 2.50e+03 2.31e+02 bond pdb=" C11 YZV R 501 " pdb=" N01 YZV R 501 " ideal model delta sigma weight residual 1.458 1.211 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C15 YZV R 501 " pdb=" N01 YZV R 501 " ideal model delta sigma weight residual 1.445 1.237 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C12 YZV R 501 " pdb=" O02 YZV R 501 " ideal model delta sigma weight residual 1.420 1.300 0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C10 YZV R 501 " pdb=" C11 YZV R 501 " ideal model delta sigma weight residual 1.504 1.612 -0.108 2.00e-02 2.50e+03 2.89e+01 ... (remaining 7797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 10482 2.29 - 4.58: 119 4.58 - 6.87: 19 6.87 - 9.16: 4 9.16 - 11.45: 2 Bond angle restraints: 10626 Sorted by residual: angle pdb=" C11 YZV R 501 " pdb=" N01 YZV R 501 " pdb=" C12 YZV R 501 " ideal model delta sigma weight residual 112.24 100.79 11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C09 YZV R 501 " pdb=" C08 YZV R 501 " pdb=" O01 YZV R 501 " ideal model delta sigma weight residual 114.12 103.54 10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C ILE R 286 " pdb=" CA ILE R 286 " pdb=" CB ILE R 286 " ideal model delta sigma weight residual 114.35 110.80 3.55 1.06e+00 8.90e-01 1.12e+01 angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 122.11 116.67 5.44 1.64e+00 3.72e-01 1.10e+01 angle pdb=" N ILE R 23 " pdb=" CA ILE R 23 " pdb=" C ILE R 23 " ideal model delta sigma weight residual 108.88 115.97 -7.09 2.16e+00 2.14e-01 1.08e+01 ... (remaining 10621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 4160 15.96 - 31.93: 331 31.93 - 47.89: 78 47.89 - 63.86: 23 63.86 - 79.82: 10 Dihedral angle restraints: 4602 sinusoidal: 1594 harmonic: 3008 Sorted by residual: dihedral pdb=" CA GLY A 353 " pdb=" C GLY A 353 " pdb=" N ASP A 354 " pdb=" CA ASP A 354 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CB CYS R 92 " pdb=" SG CYS R 92 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 132.74 -39.74 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -117.05 31.05 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 4599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1050 0.062 - 0.123: 189 0.123 - 0.185: 10 0.185 - 0.247: 1 0.247 - 0.308: 2 Chirality restraints: 1252 Sorted by residual: chirality pdb=" C08 YZV R 501 " pdb=" C07 YZV R 501 " pdb=" C09 YZV R 501 " pdb=" O01 YZV R 501 " both_signs ideal model delta sigma weight residual False 2.37 2.68 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA SER R 319 " pdb=" N SER R 319 " pdb=" C SER R 319 " pdb=" CB SER R 319 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ILE R 23 " pdb=" N ILE R 23 " pdb=" C ILE R 23 " pdb=" CB ILE R 23 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1249 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 174 " 0.020 2.00e-02 2.50e+03 1.85e-02 8.59e+00 pdb=" CG TRP R 174 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP R 174 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 174 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 174 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP R 174 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 174 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 174 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 174 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 174 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 102 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C PHE R 102 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE R 102 " 0.011 2.00e-02 2.50e+03 pdb=" N SER R 103 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 857 2.75 - 3.28: 7297 3.28 - 3.82: 12011 3.82 - 4.36: 14062 4.36 - 4.90: 25387 Nonbonded interactions: 59614 Sorted by model distance: nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.207 3.040 nonbonded pdb=" O GLY A 52 " pdb=" OG1 THR A 55 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" O TYR A 339 " model vdw 2.244 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.275 3.040 nonbonded pdb=" O PHE N 29 " pdb=" NH2 ARG N 72 " model vdw 2.289 3.120 ... (remaining 59609 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: 0.010 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 0.304 7805 Z= 0.357 Angle : 0.686 11.449 10632 Z= 0.388 Chirality : 0.047 0.308 1252 Planarity : 0.004 0.040 1347 Dihedral : 13.617 79.821 2647 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.41 % Allowed : 1.09 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.27), residues: 1016 helix: 0.40 (0.27), residues: 406 sheet: -0.17 (0.35), residues: 220 loop : -1.34 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP R 174 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.002 PHE A 376 TYR 0.014 0.002 TYR R 130 ARG 0.012 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.13489 ( 375) hydrogen bonds : angle 5.91461 ( 1089) SS BOND : bond 0.00293 ( 3) SS BOND : angle 0.79110 ( 6) covalent geometry : bond 0.00722 ( 7802) covalent geometry : angle 0.68623 (10626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6084 (mm-30) REVERT: A 24 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7499 (ttmm) REVERT: A 31 GLN cc_start: 0.7654 (tp40) cc_final: 0.7199 (tp40) REVERT: A 33 ASP cc_start: 0.7117 (t0) cc_final: 0.6695 (t0) REVERT: A 36 VAL cc_start: 0.8318 (t) cc_final: 0.7857 (p) REVERT: A 211 LYS cc_start: 0.8501 (mttm) cc_final: 0.8258 (mttm) REVERT: A 274 ASP cc_start: 0.7488 (t70) cc_final: 0.7237 (t70) REVERT: A 343 ASP cc_start: 0.7752 (m-30) cc_final: 0.7477 (m-30) REVERT: B 13 GLN cc_start: 0.6733 (pp30) cc_final: 0.6448 (pp30) REVERT: B 14 LEU cc_start: 0.7508 (mt) cc_final: 0.7171 (mm) REVERT: B 19 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7294 (ttp80) REVERT: B 46 ARG cc_start: 0.6553 (mtp-110) cc_final: 0.6211 (mtp-110) REVERT: B 66 ASP cc_start: 0.7345 (p0) cc_final: 0.6961 (p0) REVERT: B 78 LYS cc_start: 0.8491 (tppt) cc_final: 0.8084 (mmtt) REVERT: B 155 ASN cc_start: 0.8550 (t0) cc_final: 0.8124 (t0) REVERT: B 189 SER cc_start: 0.8598 (p) cc_final: 0.7968 (m) REVERT: B 233 CYS cc_start: 0.7866 (t) cc_final: 0.7075 (t) REVERT: B 239 ASN cc_start: 0.7797 (m110) cc_final: 0.7532 (m-40) REVERT: B 243 THR cc_start: 0.8307 (m) cc_final: 0.8058 (t) REVERT: B 303 ASP cc_start: 0.7418 (m-30) cc_final: 0.7126 (m-30) REVERT: B 308 LEU cc_start: 0.8107 (mt) cc_final: 0.7722 (mp) REVERT: R 27 MET cc_start: 0.7413 (mtm) cc_final: 0.7175 (mtp) REVERT: R 30 PHE cc_start: 0.8307 (m-10) cc_final: 0.7729 (m-80) REVERT: R 72 VAL cc_start: 0.7528 (OUTLIER) cc_final: 0.7311 (p) REVERT: R 94 TYR cc_start: 0.7316 (t80) cc_final: 0.6968 (t80) REVERT: R 113 MET cc_start: 0.8073 (mtp) cc_final: 0.7837 (mtp) REVERT: R 184 TYR cc_start: 0.7886 (t80) cc_final: 0.6596 (t80) REVERT: R 327 TRP cc_start: 0.8880 (m100) cc_final: 0.8324 (m100) REVERT: R 331 LEU cc_start: 0.8210 (mt) cc_final: 0.7823 (mp) outliers start: 3 outliers final: 1 residues processed: 183 average time/residue: 0.2854 time to fit residues: 64.8152 Evaluate side-chains 160 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain R residue 72 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 119 ASN B 176 GLN B 183 HIS N 31 ASN R 321 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106530 restraints weight = 10775.748| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.36 r_work: 0.3142 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7805 Z= 0.154 Angle : 0.549 7.338 10632 Z= 0.299 Chirality : 0.043 0.158 1252 Planarity : 0.004 0.039 1347 Dihedral : 5.810 54.768 1155 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.96 % Allowed : 9.71 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.27), residues: 1016 helix: 0.75 (0.27), residues: 415 sheet: -0.04 (0.34), residues: 223 loop : -1.21 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 174 HIS 0.004 0.001 HIS B 225 PHE 0.018 0.002 PHE A 376 TYR 0.012 0.001 TYR R 130 ARG 0.003 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 375) hydrogen bonds : angle 4.46902 ( 1089) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.75072 ( 6) covalent geometry : bond 0.00361 ( 7802) covalent geometry : angle 0.54878 (10626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7926 (tp40) cc_final: 0.7614 (tp40) REVERT: A 33 ASP cc_start: 0.7451 (t0) cc_final: 0.7023 (t0) REVERT: A 46 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 211 LYS cc_start: 0.8814 (mttm) cc_final: 0.8594 (mttm) REVERT: A 274 ASP cc_start: 0.8159 (t70) cc_final: 0.7911 (t0) REVERT: A 279 ASN cc_start: 0.8263 (t0) cc_final: 0.8034 (t0) REVERT: A 317 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7422 (mpp-170) REVERT: A 343 ASP cc_start: 0.7902 (m-30) cc_final: 0.7676 (m-30) REVERT: A 347 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.7181 (ttp80) REVERT: A 390 GLN cc_start: 0.8636 (pt0) cc_final: 0.8323 (pt0) REVERT: B 13 GLN cc_start: 0.7141 (pp30) cc_final: 0.6794 (pp30) REVERT: B 14 LEU cc_start: 0.8295 (mt) cc_final: 0.7620 (mm) REVERT: B 19 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.8128 (ttp80) REVERT: B 46 ARG cc_start: 0.7559 (mtp-110) cc_final: 0.7350 (mtp-110) REVERT: B 66 ASP cc_start: 0.7341 (p0) cc_final: 0.6991 (p0) REVERT: B 78 LYS cc_start: 0.8331 (tppt) cc_final: 0.8062 (mmtt) REVERT: B 189 SER cc_start: 0.8537 (p) cc_final: 0.7952 (m) REVERT: B 239 ASN cc_start: 0.7884 (m110) cc_final: 0.7626 (m-40) REVERT: B 307 VAL cc_start: 0.8947 (t) cc_final: 0.8165 (p) REVERT: G 27 ARG cc_start: 0.8841 (mtt90) cc_final: 0.8537 (mtm180) REVERT: R 30 PHE cc_start: 0.8770 (m-10) cc_final: 0.8240 (m-80) REVERT: R 54 PHE cc_start: 0.8179 (t80) cc_final: 0.7898 (t80) REVERT: R 184 TYR cc_start: 0.8391 (t80) cc_final: 0.7378 (t80) REVERT: R 331 LEU cc_start: 0.8300 (mt) cc_final: 0.7888 (mp) outliers start: 7 outliers final: 4 residues processed: 165 average time/residue: 0.2500 time to fit residues: 52.8582 Evaluate side-chains 170 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 0.0010 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107426 restraints weight = 10933.448| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.38 r_work: 0.3144 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7805 Z= 0.129 Angle : 0.502 7.094 10632 Z= 0.273 Chirality : 0.041 0.146 1252 Planarity : 0.003 0.038 1347 Dihedral : 5.067 52.885 1152 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.50 % Allowed : 12.72 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.27), residues: 1016 helix: 1.07 (0.28), residues: 414 sheet: 0.12 (0.34), residues: 223 loop : -1.10 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 174 HIS 0.003 0.001 HIS B 183 PHE 0.017 0.002 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.007 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 375) hydrogen bonds : angle 4.17852 ( 1089) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.60497 ( 6) covalent geometry : bond 0.00297 ( 7802) covalent geometry : angle 0.50234 (10626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.922 Fit side-chains REVERT: A 25 LYS cc_start: 0.8070 (ttmm) cc_final: 0.7792 (tttt) REVERT: A 31 GLN cc_start: 0.7842 (tp40) cc_final: 0.7489 (tp40) REVERT: A 33 ASP cc_start: 0.7355 (t0) cc_final: 0.7059 (t0) REVERT: A 211 LYS cc_start: 0.8799 (mttm) cc_final: 0.8049 (mttm) REVERT: A 231 ARG cc_start: 0.8813 (ptp90) cc_final: 0.8431 (ptt180) REVERT: A 343 ASP cc_start: 0.7926 (m-30) cc_final: 0.7687 (m-30) REVERT: A 390 GLN cc_start: 0.8622 (pt0) cc_final: 0.8304 (pt0) REVERT: B 13 GLN cc_start: 0.7219 (pp30) cc_final: 0.6817 (pp30) REVERT: B 19 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8238 (ttp80) REVERT: B 25 CYS cc_start: 0.8252 (p) cc_final: 0.7858 (p) REVERT: B 46 ARG cc_start: 0.7534 (mtp-110) cc_final: 0.7330 (mtp-110) REVERT: B 66 ASP cc_start: 0.7304 (p0) cc_final: 0.6940 (p0) REVERT: B 78 LYS cc_start: 0.8442 (tppt) cc_final: 0.8083 (mmtt) REVERT: B 189 SER cc_start: 0.8580 (p) cc_final: 0.8013 (m) REVERT: B 307 VAL cc_start: 0.8951 (t) cc_final: 0.8266 (p) REVERT: R 30 PHE cc_start: 0.8776 (m-10) cc_final: 0.8212 (m-80) REVERT: R 94 TYR cc_start: 0.7905 (t80) cc_final: 0.7401 (t80) REVERT: R 184 TYR cc_start: 0.8394 (t80) cc_final: 0.7494 (t80) outliers start: 11 outliers final: 9 residues processed: 171 average time/residue: 0.2827 time to fit residues: 61.2094 Evaluate side-chains 172 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106832 restraints weight = 10918.092| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.39 r_work: 0.3181 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7805 Z= 0.132 Angle : 0.498 7.027 10632 Z= 0.271 Chirality : 0.042 0.154 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.902 52.033 1152 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.50 % Allowed : 15.18 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.27), residues: 1016 helix: 1.36 (0.27), residues: 405 sheet: 0.04 (0.34), residues: 229 loop : -0.86 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 174 HIS 0.004 0.001 HIS A 220 PHE 0.018 0.002 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.004 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 375) hydrogen bonds : angle 4.11207 ( 1089) SS BOND : bond 0.00222 ( 3) SS BOND : angle 0.58197 ( 6) covalent geometry : bond 0.00307 ( 7802) covalent geometry : angle 0.49789 (10626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.826 Fit side-chains REVERT: A 25 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7759 (tttt) REVERT: A 31 GLN cc_start: 0.7836 (tp40) cc_final: 0.7492 (tp40) REVERT: A 33 ASP cc_start: 0.7283 (t0) cc_final: 0.6964 (t0) REVERT: A 317 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7365 (mpp-170) REVERT: A 342 ARG cc_start: 0.8222 (ttt-90) cc_final: 0.7920 (ttt-90) REVERT: A 343 ASP cc_start: 0.7929 (m-30) cc_final: 0.7539 (m-30) REVERT: A 390 GLN cc_start: 0.8598 (pt0) cc_final: 0.8302 (pt0) REVERT: B 13 GLN cc_start: 0.7195 (pp30) cc_final: 0.6834 (pp30) REVERT: B 19 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8225 (ttp80) REVERT: B 25 CYS cc_start: 0.8264 (p) cc_final: 0.7838 (p) REVERT: B 66 ASP cc_start: 0.7288 (p0) cc_final: 0.6923 (p0) REVERT: B 78 LYS cc_start: 0.8470 (tppt) cc_final: 0.8107 (mmtt) REVERT: B 189 SER cc_start: 0.8569 (p) cc_final: 0.7984 (m) REVERT: B 239 ASN cc_start: 0.8216 (m-40) cc_final: 0.7969 (t0) REVERT: B 307 VAL cc_start: 0.8985 (t) cc_final: 0.8315 (p) REVERT: R 30 PHE cc_start: 0.8703 (m-10) cc_final: 0.8115 (m-80) REVERT: R 184 TYR cc_start: 0.8391 (t80) cc_final: 0.7587 (t80) outliers start: 11 outliers final: 8 residues processed: 169 average time/residue: 0.2699 time to fit residues: 57.4744 Evaluate side-chains 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.0870 chunk 69 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105675 restraints weight = 10907.868| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.39 r_work: 0.3151 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7805 Z= 0.141 Angle : 0.505 7.071 10632 Z= 0.274 Chirality : 0.042 0.159 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.842 49.726 1152 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.19 % Allowed : 15.87 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.27), residues: 1016 helix: 1.45 (0.27), residues: 405 sheet: -0.01 (0.34), residues: 229 loop : -0.84 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 174 HIS 0.005 0.001 HIS A 220 PHE 0.019 0.002 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.004 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 375) hydrogen bonds : angle 4.08231 ( 1089) SS BOND : bond 0.00211 ( 3) SS BOND : angle 0.59586 ( 6) covalent geometry : bond 0.00331 ( 7802) covalent geometry : angle 0.50515 (10626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7813 (tp40) cc_final: 0.7463 (tp40) REVERT: A 33 ASP cc_start: 0.7357 (t0) cc_final: 0.7053 (t0) REVERT: A 276 ILE cc_start: 0.8501 (mt) cc_final: 0.8112 (tt) REVERT: A 317 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7386 (mpp-170) REVERT: A 390 GLN cc_start: 0.8606 (pt0) cc_final: 0.8308 (pt0) REVERT: B 13 GLN cc_start: 0.7235 (pp30) cc_final: 0.6847 (pp30) REVERT: B 19 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8269 (ttp80) REVERT: B 25 CYS cc_start: 0.8236 (p) cc_final: 0.7858 (p) REVERT: B 66 ASP cc_start: 0.7269 (p0) cc_final: 0.6913 (p0) REVERT: B 78 LYS cc_start: 0.8396 (tppt) cc_final: 0.8138 (mmtt) REVERT: B 189 SER cc_start: 0.8586 (p) cc_final: 0.7977 (m) REVERT: B 307 VAL cc_start: 0.8970 (t) cc_final: 0.8351 (p) REVERT: R 30 PHE cc_start: 0.8679 (m-10) cc_final: 0.8080 (m-80) REVERT: R 184 TYR cc_start: 0.8339 (t80) cc_final: 0.7480 (t80) outliers start: 16 outliers final: 13 residues processed: 165 average time/residue: 0.2765 time to fit residues: 57.2200 Evaluate side-chains 172 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 283 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104106 restraints weight = 10970.215| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.40 r_work: 0.3159 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7805 Z= 0.184 Angle : 0.549 7.547 10632 Z= 0.297 Chirality : 0.043 0.170 1252 Planarity : 0.004 0.038 1347 Dihedral : 5.055 46.877 1152 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.87 % Allowed : 16.28 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.27), residues: 1016 helix: 1.28 (0.27), residues: 411 sheet: 0.08 (0.34), residues: 228 loop : -1.04 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 174 HIS 0.005 0.001 HIS R 129 PHE 0.021 0.002 PHE A 376 TYR 0.010 0.002 TYR R 118 ARG 0.003 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04443 ( 375) hydrogen bonds : angle 4.23758 ( 1089) SS BOND : bond 0.00258 ( 3) SS BOND : angle 0.61864 ( 6) covalent geometry : bond 0.00439 ( 7802) covalent geometry : angle 0.54896 (10626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.837 Fit side-chains REVERT: A 31 GLN cc_start: 0.7857 (tp40) cc_final: 0.7457 (tp40) REVERT: A 33 ASP cc_start: 0.7301 (t0) cc_final: 0.6968 (t0) REVERT: A 276 ILE cc_start: 0.8516 (mt) cc_final: 0.8099 (tt) REVERT: A 317 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7377 (mpp-170) REVERT: A 343 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: A 390 GLN cc_start: 0.8642 (pt0) cc_final: 0.8355 (pt0) REVERT: B 13 GLN cc_start: 0.7255 (pp30) cc_final: 0.6875 (pp30) REVERT: B 19 ARG cc_start: 0.8606 (ttm-80) cc_final: 0.8250 (ttp80) REVERT: B 25 CYS cc_start: 0.8335 (p) cc_final: 0.7929 (p) REVERT: B 66 ASP cc_start: 0.7253 (p0) cc_final: 0.6927 (p0) REVERT: B 78 LYS cc_start: 0.8454 (tppt) cc_final: 0.8139 (mmtt) REVERT: B 134 ARG cc_start: 0.7614 (mtp-110) cc_final: 0.7407 (mtp-110) REVERT: B 189 SER cc_start: 0.8562 (p) cc_final: 0.7956 (m) REVERT: B 307 VAL cc_start: 0.8961 (t) cc_final: 0.8443 (p) REVERT: R 30 PHE cc_start: 0.8485 (m-10) cc_final: 0.7886 (m-80) outliers start: 21 outliers final: 16 residues processed: 167 average time/residue: 0.2743 time to fit residues: 57.7259 Evaluate side-chains 175 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 283 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 64 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 17 optimal weight: 0.0670 chunk 82 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.122121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108929 restraints weight = 10776.209| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.36 r_work: 0.3189 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7805 Z= 0.104 Angle : 0.474 6.518 10632 Z= 0.258 Chirality : 0.041 0.162 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.678 49.750 1152 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.19 % Allowed : 17.51 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.28), residues: 1016 helix: 1.81 (0.28), residues: 405 sheet: 0.19 (0.35), residues: 214 loop : -0.94 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 129 PHE 0.011 0.001 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.002 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 375) hydrogen bonds : angle 3.96386 ( 1089) SS BOND : bond 0.00170 ( 3) SS BOND : angle 0.54294 ( 6) covalent geometry : bond 0.00235 ( 7802) covalent geometry : angle 0.47348 (10626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7830 (tp40) cc_final: 0.7477 (tp40) REVERT: A 33 ASP cc_start: 0.7343 (t0) cc_final: 0.6978 (t0) REVERT: A 267 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8619 (tp40) REVERT: A 276 ILE cc_start: 0.8461 (mt) cc_final: 0.8082 (tt) REVERT: A 317 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7373 (mpp-170) REVERT: A 390 GLN cc_start: 0.8565 (pt0) cc_final: 0.8292 (pt0) REVERT: B 13 GLN cc_start: 0.7225 (pp30) cc_final: 0.6831 (pp30) REVERT: B 19 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8299 (ttp80) REVERT: B 25 CYS cc_start: 0.8285 (p) cc_final: 0.7850 (p) REVERT: B 66 ASP cc_start: 0.7218 (p0) cc_final: 0.6869 (p0) REVERT: B 134 ARG cc_start: 0.7587 (mtp-110) cc_final: 0.7376 (mtp-110) REVERT: B 187 VAL cc_start: 0.6960 (t) cc_final: 0.6593 (t) REVERT: B 189 SER cc_start: 0.8558 (p) cc_final: 0.7939 (m) REVERT: B 307 VAL cc_start: 0.8938 (t) cc_final: 0.8375 (p) REVERT: R 30 PHE cc_start: 0.8479 (m-10) cc_final: 0.7896 (m-80) REVERT: R 184 TYR cc_start: 0.8296 (t80) cc_final: 0.7486 (t80) outliers start: 16 outliers final: 12 residues processed: 166 average time/residue: 0.2705 time to fit residues: 56.5833 Evaluate side-chains 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 283 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 24 optimal weight: 0.0040 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.107078 restraints weight = 10820.088| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.36 r_work: 0.3159 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7805 Z= 0.152 Angle : 0.516 7.093 10632 Z= 0.279 Chirality : 0.042 0.156 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.799 48.469 1152 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.60 % Allowed : 17.51 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.27), residues: 1016 helix: 1.68 (0.27), residues: 415 sheet: 0.16 (0.35), residues: 213 loop : -1.05 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 174 HIS 0.004 0.001 HIS R 129 PHE 0.020 0.002 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.002 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 375) hydrogen bonds : angle 4.06423 ( 1089) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.62484 ( 6) covalent geometry : bond 0.00359 ( 7802) covalent geometry : angle 0.51599 (10626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.849 Fit side-chains REVERT: A 25 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7734 (tttt) REVERT: A 31 GLN cc_start: 0.7908 (tp40) cc_final: 0.7542 (tp40) REVERT: A 33 ASP cc_start: 0.7137 (t0) cc_final: 0.6830 (t0) REVERT: A 276 ILE cc_start: 0.8466 (mt) cc_final: 0.8099 (tt) REVERT: A 317 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7389 (mpp-170) REVERT: A 343 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: A 390 GLN cc_start: 0.8617 (pt0) cc_final: 0.8340 (pt0) REVERT: B 13 GLN cc_start: 0.7243 (pp30) cc_final: 0.6852 (pp30) REVERT: B 19 ARG cc_start: 0.8594 (ttm-80) cc_final: 0.8238 (ttp80) REVERT: B 25 CYS cc_start: 0.8349 (p) cc_final: 0.7893 (p) REVERT: B 66 ASP cc_start: 0.7226 (p0) cc_final: 0.6898 (p0) REVERT: B 189 SER cc_start: 0.8570 (p) cc_final: 0.7974 (m) REVERT: B 307 VAL cc_start: 0.8936 (t) cc_final: 0.8449 (p) REVERT: R 30 PHE cc_start: 0.8484 (m-10) cc_final: 0.7862 (m-80) outliers start: 19 outliers final: 16 residues processed: 165 average time/residue: 0.2807 time to fit residues: 57.9970 Evaluate side-chains 175 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 283 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 96 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 239 ASN ** 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 = 0.3468 r_free = 0.3468 target = 0.121450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108302 restraints weight = 10933.159| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.36 r_work: 0.3170 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7805 Z= 0.127 Angle : 0.497 7.048 10632 Z= 0.268 Chirality : 0.041 0.154 1252 Planarity : 0.003 0.038 1347 Dihedral : 4.724 49.669 1152 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.46 % Allowed : 17.78 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.28), residues: 1016 helix: 1.90 (0.27), residues: 409 sheet: 0.17 (0.35), residues: 213 loop : -0.89 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 174 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.002 0.000 ARG R 316 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 375) hydrogen bonds : angle 3.99090 ( 1089) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.55300 ( 6) covalent geometry : bond 0.00298 ( 7802) covalent geometry : angle 0.49663 (10626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7720 (tttt) REVERT: A 31 GLN cc_start: 0.7891 (tp40) cc_final: 0.7527 (tp40) REVERT: A 33 ASP cc_start: 0.7192 (t0) cc_final: 0.6911 (t0) REVERT: A 317 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7403 (mpp-170) REVERT: A 390 GLN cc_start: 0.8591 (pt0) cc_final: 0.8332 (pt0) REVERT: B 13 GLN cc_start: 0.7235 (pp30) cc_final: 0.6839 (pp30) REVERT: B 19 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8283 (ttp80) REVERT: B 25 CYS cc_start: 0.8346 (p) cc_final: 0.7899 (p) REVERT: B 66 ASP cc_start: 0.7229 (p0) cc_final: 0.6904 (p0) REVERT: B 187 VAL cc_start: 0.6956 (t) cc_final: 0.6584 (t) REVERT: B 189 SER cc_start: 0.8569 (p) cc_final: 0.7950 (m) REVERT: B 307 VAL cc_start: 0.8924 (t) cc_final: 0.8449 (p) REVERT: R 30 PHE cc_start: 0.8483 (m-10) cc_final: 0.7861 (m-80) REVERT: R 184 TYR cc_start: 0.8316 (t80) cc_final: 0.7571 (t80) outliers start: 18 outliers final: 16 residues processed: 163 average time/residue: 0.2868 time to fit residues: 59.1610 Evaluate side-chains 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 219 ARG Chi-restraints excluded: chain R residue 283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 0.0970 chunk 71 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.107934 restraints weight = 10858.362| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.35 r_work: 0.3166 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7805 Z= 0.138 Angle : 0.507 7.024 10632 Z= 0.274 Chirality : 0.042 0.152 1252 Planarity : 0.003 0.038 1347 Dihedral : 4.752 49.367 1152 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.46 % Allowed : 17.92 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.27), residues: 1016 helix: 1.88 (0.27), residues: 409 sheet: 0.17 (0.35), residues: 212 loop : -0.89 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 174 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.002 PHE R 191 TYR 0.009 0.001 TYR R 130 ARG 0.002 0.000 ARG R 316 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 375) hydrogen bonds : angle 4.03017 ( 1089) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.54489 ( 6) covalent geometry : bond 0.00326 ( 7802) covalent geometry : angle 0.50718 (10626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8068 (ttmm) cc_final: 0.7733 (tttt) REVERT: A 31 GLN cc_start: 0.7883 (tp40) cc_final: 0.7518 (tp40) REVERT: A 33 ASP cc_start: 0.7187 (t0) cc_final: 0.6898 (t0) REVERT: A 317 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7441 (mpp-170) REVERT: A 390 GLN cc_start: 0.8594 (pt0) cc_final: 0.8317 (pt0) REVERT: B 13 GLN cc_start: 0.7227 (pp30) cc_final: 0.6827 (pp30) REVERT: B 19 ARG cc_start: 0.8606 (ttm-80) cc_final: 0.8257 (ttp80) REVERT: B 25 CYS cc_start: 0.8352 (p) cc_final: 0.7911 (p) REVERT: B 66 ASP cc_start: 0.7224 (p0) cc_final: 0.6900 (p0) REVERT: B 187 VAL cc_start: 0.6957 (t) cc_final: 0.6582 (t) REVERT: B 189 SER cc_start: 0.8579 (p) cc_final: 0.7959 (m) REVERT: B 307 VAL cc_start: 0.8909 (t) cc_final: 0.8444 (p) REVERT: R 30 PHE cc_start: 0.8478 (m-10) cc_final: 0.7853 (m-80) outliers start: 18 outliers final: 15 residues processed: 161 average time/residue: 0.2581 time to fit residues: 52.5432 Evaluate side-chains 168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 69 optimal weight: 0.0870 chunk 77 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 67 optimal weight: 0.0980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108835 restraints weight = 10828.699| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.35 r_work: 0.3207 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7805 Z= 0.112 Angle : 0.484 6.618 10632 Z= 0.261 Chirality : 0.041 0.143 1252 Planarity : 0.003 0.038 1347 Dihedral : 4.636 50.464 1152 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.33 % Allowed : 18.60 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.28), residues: 1016 helix: 2.03 (0.27), residues: 409 sheet: 0.18 (0.35), residues: 213 loop : -0.82 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 220 PHE 0.011 0.001 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.002 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 375) hydrogen bonds : angle 3.92844 ( 1089) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.52810 ( 6) covalent geometry : bond 0.00259 ( 7802) covalent geometry : angle 0.48415 (10626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4725.41 seconds wall clock time: 81 minutes 12.75 seconds (4872.75 seconds total)