Starting phenix.real_space_refine on Sat Nov 16 21:04:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/11_2024/8gda_29944_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/11_2024/8gda_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/11_2024/8gda_29944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/11_2024/8gda_29944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/11_2024/8gda_29944_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/11_2024/8gda_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-5513/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: 4.72, per 1000 atoms: 0.62 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: 1.98 Conformation dependent library (CDL) restraints added in 935.8 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: 2.19 Time building geometry restraints manager: 2.26 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: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.960 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.910 ------------------------------------------------------------------------------- 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 7802 Z= 0.455 Angle : 0.686 11.449 10626 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 *********************** 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 : 0.883 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: 0.2836 time to fit residues: 64.2022 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 : 0.789 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 7802 Z= 0.237 Angle : 0.549 7.338 10626 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 *********************** 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 : 0.856 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.6632 (mm-30) cc_final: 0.6428 (mm-30) REVERT: A 24 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7668 (ttmm) REVERT: A 31 GLN cc_start: 0.7553 (tp40) cc_final: 0.7173 (tp40) REVERT: A 33 ASP cc_start: 0.6935 (t0) cc_final: 0.6544 (t0) REVERT: A 46 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8282 (mp) REVERT: A 211 LYS cc_start: 0.8706 (mttm) cc_final: 0.8415 (mttm) REVERT: A 274 ASP cc_start: 0.7381 (t70) cc_final: 0.7149 (t0) REVERT: A 279 ASN cc_start: 0.8163 (t0) cc_final: 0.7859 (t0) REVERT: A 286 SER cc_start: 0.8979 (m) cc_final: 0.8695 (t) REVERT: A 317 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7115 (mpp-170) REVERT: A 343 ASP cc_start: 0.7602 (m-30) cc_final: 0.7354 (m-30) REVERT: A 347 ARG cc_start: 0.6588 (ttm-80) cc_final: 0.6248 (ttp80) REVERT: A 390 GLN cc_start: 0.8614 (pt0) cc_final: 0.8283 (pt0) REVERT: B 13 GLN cc_start: 0.6685 (pp30) cc_final: 0.6401 (pp30) REVERT: B 14 LEU cc_start: 0.7642 (mt) cc_final: 0.6906 (mm) REVERT: B 19 ARG cc_start: 0.7660 (ttm-80) cc_final: 0.7275 (ttp80) REVERT: B 66 ASP cc_start: 0.7261 (p0) cc_final: 0.6926 (p0) REVERT: B 78 LYS cc_start: 0.8247 (tppt) cc_final: 0.7969 (mmtt) REVERT: B 155 ASN cc_start: 0.8497 (t0) cc_final: 0.8272 (t0) REVERT: B 189 SER cc_start: 0.8448 (p) cc_final: 0.7882 (m) REVERT: B 239 ASN cc_start: 0.7747 (m110) cc_final: 0.7476 (m-40) REVERT: B 307 VAL cc_start: 0.8818 (t) cc_final: 0.8074 (p) REVERT: G 27 ARG cc_start: 0.8838 (mtt90) cc_final: 0.8528 (mtm180) REVERT: R 30 PHE cc_start: 0.8379 (m-10) cc_final: 0.7868 (m-80) REVERT: R 54 PHE cc_start: 0.7832 (t80) cc_final: 0.7578 (t80) REVERT: R 72 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7226 (p) REVERT: R 113 MET cc_start: 0.8193 (mtp) cc_final: 0.7963 (mtp) REVERT: R 184 TYR cc_start: 0.7803 (t80) cc_final: 0.6636 (t80) REVERT: R 331 LEU cc_start: 0.8250 (mt) cc_final: 0.7855 (mp) outliers start: 7 outliers final: 4 residues processed: 165 average time/residue: 0.2477 time to fit residues: 52.0498 Evaluate side-chains 170 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 72 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 176 GLN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7802 Z= 0.256 Angle : 0.539 7.644 10626 Z= 0.293 Chirality : 0.043 0.153 1252 Planarity : 0.004 0.038 1347 Dihedral : 5.293 53.443 1153 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.64 % Allowed : 13.00 % Favored : 85.36 % 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: -0.07 (0.27), residues: 1016 helix: 1.02 (0.27), residues: 409 sheet: -0.09 (0.34), residues: 229 loop : -1.13 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 174 HIS 0.004 0.001 HIS B 183 PHE 0.019 0.002 PHE A 376 TYR 0.010 0.001 TYR R 118 ARG 0.006 0.000 ARG A 265 *********************** 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: 12 poor density : 167 time to evaluate : 0.812 Fit side-chains REVERT: A 24 LYS cc_start: 0.7906 (ttmm) cc_final: 0.7703 (ttmm) REVERT: A 31 GLN cc_start: 0.7414 (tp40) cc_final: 0.7000 (tp40) REVERT: A 33 ASP cc_start: 0.6784 (t0) cc_final: 0.6531 (t0) REVERT: A 46 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8302 (mp) REVERT: A 211 LYS cc_start: 0.8644 (mttm) cc_final: 0.7822 (mttm) REVERT: A 286 SER cc_start: 0.8967 (m) cc_final: 0.8674 (t) REVERT: A 343 ASP cc_start: 0.7674 (m-30) cc_final: 0.7387 (m-30) REVERT: A 390 GLN cc_start: 0.8618 (pt0) cc_final: 0.8276 (pt0) REVERT: B 13 GLN cc_start: 0.6785 (pp30) cc_final: 0.6448 (pp30) REVERT: B 19 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.7272 (ttp80) REVERT: B 25 CYS cc_start: 0.7378 (p) cc_final: 0.6915 (p) REVERT: B 66 ASP cc_start: 0.7218 (p0) cc_final: 0.6898 (p0) REVERT: B 78 LYS cc_start: 0.8367 (tppt) cc_final: 0.7998 (mmtt) REVERT: B 189 SER cc_start: 0.8484 (p) cc_final: 0.7933 (m) REVERT: B 307 VAL cc_start: 0.8868 (t) cc_final: 0.8231 (p) REVERT: R 30 PHE cc_start: 0.8007 (m-10) cc_final: 0.7467 (m-80) REVERT: R 113 MET cc_start: 0.8262 (mtp) cc_final: 0.7968 (mtp) REVERT: R 331 LEU cc_start: 0.8276 (mt) cc_final: 0.7869 (mp) outliers start: 12 outliers final: 10 residues processed: 169 average time/residue: 0.2626 time to fit residues: 55.8414 Evaluate side-chains 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 317 ARG 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 71 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 0.0570 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7802 Z= 0.228 Angle : 0.514 7.376 10626 Z= 0.280 Chirality : 0.042 0.157 1252 Planarity : 0.003 0.038 1347 Dihedral : 5.067 53.278 1152 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.64 % Allowed : 15.73 % Favored : 82.63 % 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: 0.09 (0.27), residues: 1016 helix: 1.14 (0.27), residues: 411 sheet: -0.06 (0.34), residues: 229 loop : -1.00 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 174 HIS 0.004 0.001 HIS R 129 PHE 0.020 0.002 PHE A 315 TYR 0.009 0.001 TYR R 130 ARG 0.004 0.000 ARG A 265 *********************** 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 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.864 Fit side-chains REVERT: A 24 LYS cc_start: 0.7921 (ttmm) cc_final: 0.7718 (ttmm) REVERT: A 31 GLN cc_start: 0.7381 (tp40) cc_final: 0.6986 (tp40) REVERT: A 33 ASP cc_start: 0.6786 (t0) cc_final: 0.6525 (t0) REVERT: A 46 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8276 (mp) REVERT: A 211 LYS cc_start: 0.8520 (mttm) cc_final: 0.8286 (mttm) REVERT: A 267 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8460 (tp40) REVERT: A 286 SER cc_start: 0.8963 (m) cc_final: 0.8672 (t) REVERT: A 343 ASP cc_start: 0.7708 (m-30) cc_final: 0.7284 (m-30) REVERT: A 390 GLN cc_start: 0.8597 (pt0) cc_final: 0.8282 (pt0) REVERT: B 13 GLN cc_start: 0.6737 (pp30) cc_final: 0.6462 (pp30) REVERT: B 19 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.7196 (ttp80) REVERT: B 25 CYS cc_start: 0.7285 (p) cc_final: 0.6829 (p) REVERT: B 66 ASP cc_start: 0.7185 (p0) cc_final: 0.6864 (p0) REVERT: B 78 LYS cc_start: 0.8320 (tppt) cc_final: 0.8042 (mmtt) REVERT: B 189 SER cc_start: 0.8500 (p) cc_final: 0.7927 (m) REVERT: B 239 ASN cc_start: 0.8020 (m-40) cc_final: 0.7742 (m-40) REVERT: B 307 VAL cc_start: 0.8832 (t) cc_final: 0.8220 (p) REVERT: R 30 PHE cc_start: 0.7724 (m-10) cc_final: 0.7206 (m-80) REVERT: R 113 MET cc_start: 0.8253 (mtp) cc_final: 0.8014 (mtp) REVERT: R 296 GLN cc_start: 0.8094 (tp40) cc_final: 0.7877 (tp40) outliers start: 12 outliers final: 10 residues processed: 164 average time/residue: 0.2762 time to fit residues: 56.9364 Evaluate side-chains 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 46 LEU 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 Chi-restraints excluded: chain R residue 174 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7802 Z= 0.247 Angle : 0.525 7.453 10626 Z= 0.284 Chirality : 0.042 0.163 1252 Planarity : 0.003 0.038 1347 Dihedral : 5.006 50.501 1152 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.74 % Allowed : 15.05 % Favored : 82.22 % 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: 0.18 (0.27), residues: 1016 helix: 1.23 (0.27), residues: 411 sheet: -0.02 (0.34), residues: 228 loop : -0.97 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 174 HIS 0.005 0.001 HIS A 220 PHE 0.019 0.002 PHE A 376 TYR 0.010 0.001 TYR R 130 ARG 0.004 0.000 ARG N 38 *********************** 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 183 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.846 Fit side-chains REVERT: A 24 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7724 (ttmm) REVERT: A 31 GLN cc_start: 0.7349 (tp40) cc_final: 0.6934 (tp40) REVERT: A 33 ASP cc_start: 0.6799 (t0) cc_final: 0.6519 (t0) REVERT: A 46 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8257 (mp) REVERT: A 276 ILE cc_start: 0.8104 (mt) cc_final: 0.7772 (tt) REVERT: A 286 SER cc_start: 0.8933 (m) cc_final: 0.8684 (t) REVERT: A 317 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7011 (mpp-170) REVERT: A 343 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: A 390 GLN cc_start: 0.8600 (pt0) cc_final: 0.8272 (pt0) REVERT: B 13 GLN cc_start: 0.6728 (pp30) cc_final: 0.6429 (pp30) REVERT: B 19 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7257 (ttp80) REVERT: B 25 CYS cc_start: 0.7334 (p) cc_final: 0.6861 (p) REVERT: B 66 ASP cc_start: 0.7165 (p0) cc_final: 0.6863 (p0) REVERT: B 78 LYS cc_start: 0.8332 (tppt) cc_final: 0.8049 (mmtt) REVERT: B 189 SER cc_start: 0.8476 (p) cc_final: 0.7900 (m) REVERT: B 239 ASN cc_start: 0.7972 (m-40) cc_final: 0.7716 (m-40) REVERT: B 307 VAL cc_start: 0.8830 (t) cc_final: 0.8245 (p) REVERT: R 30 PHE cc_start: 0.7713 (m-10) cc_final: 0.7195 (m-80) REVERT: R 296 GLN cc_start: 0.8127 (tp40) cc_final: 0.7887 (tp40) outliers start: 20 outliers final: 14 residues processed: 170 average time/residue: 0.2807 time to fit residues: 60.1467 Evaluate side-chains 178 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 LEU 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 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 87 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.0030 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7802 Z= 0.217 Angle : 0.505 7.129 10626 Z= 0.274 Chirality : 0.042 0.167 1252 Planarity : 0.003 0.038 1347 Dihedral : 4.902 49.842 1152 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.46 % Allowed : 16.42 % Favored : 81.12 % 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: 0.39 (0.27), residues: 1016 helix: 1.46 (0.27), residues: 405 sheet: 0.04 (0.34), residues: 228 loop : -0.85 (0.32), residues: 383 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 0.003 0.000 ARG N 38 *********************** 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 179 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7919 (ttmm) cc_final: 0.7711 (ttmm) REVERT: A 25 LYS cc_start: 0.7469 (ttmm) cc_final: 0.7227 (tttt) REVERT: A 31 GLN cc_start: 0.7378 (tp40) cc_final: 0.6928 (tp40) REVERT: A 33 ASP cc_start: 0.6780 (t0) cc_final: 0.6504 (t0) REVERT: A 46 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 267 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8421 (tp40) REVERT: A 276 ILE cc_start: 0.8091 (mt) cc_final: 0.7758 (tt) REVERT: A 286 SER cc_start: 0.8915 (m) cc_final: 0.8677 (t) REVERT: A 317 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7016 (mpp-170) REVERT: A 390 GLN cc_start: 0.8580 (pt0) cc_final: 0.8270 (pt0) REVERT: B 13 GLN cc_start: 0.6724 (pp30) cc_final: 0.6440 (pp30) REVERT: B 19 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.7278 (ttp80) REVERT: B 25 CYS cc_start: 0.7273 (p) cc_final: 0.6799 (p) REVERT: B 66 ASP cc_start: 0.7167 (p0) cc_final: 0.6855 (p0) REVERT: B 78 LYS cc_start: 0.8315 (tppt) cc_final: 0.8040 (mmtt) REVERT: B 189 SER cc_start: 0.8476 (p) cc_final: 0.7899 (m) REVERT: B 239 ASN cc_start: 0.7990 (m-40) cc_final: 0.7707 (m-40) REVERT: B 307 VAL cc_start: 0.8817 (t) cc_final: 0.8253 (p) REVERT: R 30 PHE cc_start: 0.7719 (m-10) cc_final: 0.7195 (m-80) REVERT: R 296 GLN cc_start: 0.8131 (tp40) cc_final: 0.7900 (tp40) outliers start: 18 outliers final: 14 residues processed: 167 average time/residue: 0.2682 time to fit residues: 56.3962 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 : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG 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 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 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 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 11 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.0670 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7802 Z= 0.269 Angle : 0.536 7.509 10626 Z= 0.289 Chirality : 0.043 0.172 1252 Planarity : 0.004 0.039 1347 Dihedral : 5.003 48.700 1152 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.42 % Allowed : 16.28 % 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: 0.31 (0.27), residues: 1016 helix: 1.35 (0.27), residues: 415 sheet: 0.08 (0.34), residues: 228 loop : -0.96 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 174 HIS 0.004 0.001 HIS R 129 PHE 0.020 0.002 PHE A 376 TYR 0.010 0.001 TYR R 130 ARG 0.004 0.000 ARG N 38 *********************** 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 185 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.806 Fit side-chains REVERT: A 31 GLN cc_start: 0.7373 (tp40) cc_final: 0.6915 (tp40) REVERT: A 33 ASP cc_start: 0.6790 (t0) cc_final: 0.6485 (t0) REVERT: A 46 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 211 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8398 (mtmm) REVERT: A 276 ILE cc_start: 0.8121 (mt) cc_final: 0.7772 (tt) REVERT: A 286 SER cc_start: 0.8900 (m) cc_final: 0.8671 (t) REVERT: A 317 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7080 (mpp-170) REVERT: A 343 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7252 (m-30) REVERT: A 390 GLN cc_start: 0.8608 (pt0) cc_final: 0.8292 (pt0) REVERT: B 13 GLN cc_start: 0.6707 (pp30) cc_final: 0.6427 (pp30) REVERT: B 19 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.7256 (ttp80) REVERT: B 25 CYS cc_start: 0.7280 (p) cc_final: 0.6817 (p) REVERT: B 66 ASP cc_start: 0.7159 (p0) cc_final: 0.6890 (p0) REVERT: B 78 LYS cc_start: 0.8316 (tppt) cc_final: 0.8037 (mmtt) REVERT: B 189 SER cc_start: 0.8464 (p) cc_final: 0.7892 (m) REVERT: B 239 ASN cc_start: 0.7950 (m-40) cc_final: 0.7689 (m-40) REVERT: B 307 VAL cc_start: 0.8819 (t) cc_final: 0.8335 (p) REVERT: R 30 PHE cc_start: 0.7701 (m-10) cc_final: 0.7181 (m-80) REVERT: R 296 GLN cc_start: 0.8159 (tp40) cc_final: 0.7940 (tp40) outliers start: 25 outliers final: 16 residues processed: 168 average time/residue: 0.2670 time to fit residues: 56.1545 Evaluate side-chains 179 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 211 LYS 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 18 LEU 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 29 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.0470 chunk 9 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 chunk 88 optimal weight: 0.1980 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7802 Z= 0.124 Angle : 0.454 5.926 10626 Z= 0.247 Chirality : 0.040 0.151 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.524 51.221 1152 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.05 % Allowed : 18.06 % 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: 0.81 (0.28), residues: 1016 helix: 1.96 (0.28), residues: 409 sheet: 0.10 (0.34), residues: 224 loop : -0.73 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS A 220 PHE 0.010 0.001 PHE R 102 TYR 0.009 0.001 TYR R 130 ARG 0.003 0.000 ARG N 38 *********************** 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 183 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7350 (tp40) cc_final: 0.6913 (tp40) REVERT: A 33 ASP cc_start: 0.6799 (t0) cc_final: 0.6458 (t0) REVERT: A 211 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8377 (mtmm) REVERT: A 267 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8477 (tp40) REVERT: A 286 SER cc_start: 0.8789 (m) cc_final: 0.8568 (t) REVERT: A 390 GLN cc_start: 0.8494 (pt0) cc_final: 0.8217 (pt0) REVERT: B 13 GLN cc_start: 0.6708 (pp30) cc_final: 0.6340 (pp30) REVERT: B 14 LEU cc_start: 0.7589 (mt) cc_final: 0.6769 (mm) REVERT: B 19 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7294 (ttp80) REVERT: B 25 CYS cc_start: 0.7162 (p) cc_final: 0.6687 (p) REVERT: B 66 ASP cc_start: 0.7119 (p0) cc_final: 0.6796 (p0) REVERT: B 78 LYS cc_start: 0.8255 (tppt) cc_final: 0.8032 (mmtt) REVERT: B 187 VAL cc_start: 0.6464 (t) cc_final: 0.6127 (t) REVERT: B 189 SER cc_start: 0.8427 (p) cc_final: 0.7866 (m) REVERT: B 239 ASN cc_start: 0.7958 (m-40) cc_final: 0.7695 (m-40) REVERT: B 307 VAL cc_start: 0.8752 (t) cc_final: 0.8225 (p) outliers start: 15 outliers final: 9 residues processed: 172 average time/residue: 0.2760 time to fit residues: 59.6826 Evaluate side-chains 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 211 LYS 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 B 183 HIS G 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7802 Z= 0.244 Angle : 0.523 10.416 10626 Z= 0.279 Chirality : 0.042 0.143 1252 Planarity : 0.003 0.038 1347 Dihedral : 4.764 48.944 1152 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.60 % Allowed : 18.06 % Favored : 79.34 % 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: 0.67 (0.28), residues: 1016 helix: 1.78 (0.27), residues: 415 sheet: 0.20 (0.34), residues: 224 loop : -0.89 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 174 HIS 0.004 0.001 HIS R 129 PHE 0.021 0.002 PHE R 194 TYR 0.009 0.001 TYR R 130 ARG 0.003 0.000 ARG N 38 *********************** 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 180 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.823 Fit side-chains REVERT: A 31 GLN cc_start: 0.7375 (tp40) cc_final: 0.6915 (tp40) REVERT: A 33 ASP cc_start: 0.6788 (t0) cc_final: 0.6508 (t0) REVERT: A 211 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8413 (mtmm) REVERT: A 267 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8415 (tp40) REVERT: A 286 SER cc_start: 0.8832 (m) cc_final: 0.8604 (t) REVERT: A 343 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7107 (m-30) REVERT: A 390 GLN cc_start: 0.8590 (pt0) cc_final: 0.8285 (pt0) REVERT: B 13 GLN cc_start: 0.6746 (pp30) cc_final: 0.6435 (pp30) REVERT: B 19 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.7231 (ttp80) REVERT: B 25 CYS cc_start: 0.7266 (p) cc_final: 0.6760 (p) REVERT: B 66 ASP cc_start: 0.7121 (p0) cc_final: 0.6860 (p0) REVERT: B 78 LYS cc_start: 0.8295 (tppt) cc_final: 0.8035 (mmtt) REVERT: B 187 VAL cc_start: 0.6438 (t) cc_final: 0.6046 (t) REVERT: B 189 SER cc_start: 0.8490 (p) cc_final: 0.7881 (m) REVERT: B 239 ASN cc_start: 0.7965 (m-40) cc_final: 0.7704 (m-40) REVERT: B 307 VAL cc_start: 0.8788 (t) cc_final: 0.8324 (p) REVERT: R 30 PHE cc_start: 0.7700 (m-10) cc_final: 0.7155 (m-80) outliers start: 19 outliers final: 11 residues processed: 170 average time/residue: 0.2507 time to fit residues: 54.0155 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 : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 211 LYS 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 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 45 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 80 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 24 optimal weight: 0.0060 overall best weight: 0.2796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7802 Z= 0.144 Angle : 0.473 6.494 10626 Z= 0.255 Chirality : 0.040 0.143 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.577 51.390 1152 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.37 % Allowed : 19.97 % Favored : 78.66 % 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: 0.91 (0.28), residues: 1016 helix: 2.08 (0.28), residues: 409 sheet: 0.29 (0.34), residues: 213 loop : -0.79 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 174 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.001 PHE R 194 TYR 0.009 0.001 TYR R 130 ARG 0.003 0.000 ARG N 38 ********************** 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 166 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7340 (tp40) cc_final: 0.6911 (tp40) REVERT: A 33 ASP cc_start: 0.6781 (t0) cc_final: 0.6482 (t0) REVERT: A 211 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8397 (mtmm) REVERT: A 267 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8398 (tp40) REVERT: A 286 SER cc_start: 0.8782 (m) cc_final: 0.8566 (t) REVERT: A 390 GLN cc_start: 0.8527 (pt0) cc_final: 0.8231 (pt0) REVERT: B 13 GLN cc_start: 0.6719 (pp30) cc_final: 0.6345 (pp30) REVERT: B 14 LEU cc_start: 0.7597 (mt) cc_final: 0.6775 (mm) REVERT: B 19 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.7293 (ttp80) REVERT: B 25 CYS cc_start: 0.7180 (p) cc_final: 0.6704 (p) REVERT: B 66 ASP cc_start: 0.7111 (p0) cc_final: 0.6844 (p0) REVERT: B 78 LYS cc_start: 0.8277 (tppt) cc_final: 0.8036 (mmtt) REVERT: B 187 VAL cc_start: 0.6437 (t) cc_final: 0.6070 (t) REVERT: B 189 SER cc_start: 0.8463 (p) cc_final: 0.7885 (m) REVERT: B 239 ASN cc_start: 0.7977 (m-40) cc_final: 0.7726 (m-40) REVERT: B 307 VAL cc_start: 0.8763 (t) cc_final: 0.8317 (p) outliers start: 10 outliers final: 9 residues processed: 159 average time/residue: 0.2690 time to fit residues: 53.7838 Evaluate side-chains 166 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 183 HIS 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 83 MET Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.0030 chunk 11 optimal weight: 0.0050 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.122204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109323 restraints weight = 10740.935| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.33 r_work: 0.3201 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7802 Z= 0.181 Angle : 0.488 7.025 10626 Z= 0.262 Chirality : 0.041 0.139 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.614 50.821 1152 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.64 % Allowed : 20.11 % Favored : 78.25 % 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: 0.80 (0.27), residues: 1016 helix: 1.97 (0.27), residues: 415 sheet: 0.31 (0.34), residues: 213 loop : -0.93 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 174 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.002 PHE R 194 TYR 0.009 0.001 TYR R 130 ARG 0.003 0.000 ARG N 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2117.25 seconds wall clock time: 39 minutes 17.20 seconds (2357.20 seconds total)