Starting phenix.real_space_refine on Fri Feb 14 08:08:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfc_33785/02_2025/7yfc_33785.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfc_33785/02_2025/7yfc_33785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yfc_33785/02_2025/7yfc_33785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfc_33785/02_2025/7yfc_33785.map" model { file = "/net/cci-nas-00/data/ceres_data/7yfc_33785/02_2025/7yfc_33785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfc_33785/02_2025/7yfc_33785.cif" } resolution = 3.0 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 6294 2.51 5 N 1686 2.21 5 O 1843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9882 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1912 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1799 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2096 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'CLR': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.98, per 1000 atoms: 0.61 Number of scatterers: 9882 At special positions: 0 Unit cell: (88.88, 126.72, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1843 8.00 N 1686 7.00 C 6294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 229 " distance=2.03 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 87 " - pdb=" SG CYS R 164 " 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: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 34.9% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 4.004A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.592A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.567A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.287A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 4.087A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.522A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.503A pdb=" N SER C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 56 removed outlier: 3.938A pdb=" N GLY C 56 " --> pdb=" O SER C 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.990A pdb=" N VAL C 224 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.749A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.192A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 43 Processing helix chain 'R' and resid 48 through 76 removed outlier: 4.471A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 83 through 118 Processing helix chain 'R' and resid 118 through 124 Processing helix chain 'R' and resid 131 through 155 removed outlier: 3.570A pdb=" N TRP R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 171 through 181 Processing helix chain 'R' and resid 183 through 204 Processing helix chain 'R' and resid 300 through 329 removed outlier: 4.010A pdb=" N LEU R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 4.073A pdb=" N ILE R 324 " --> pdb=" O SER R 320 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 358 removed outlier: 3.796A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 359 through 362 removed outlier: 4.115A pdb=" N HIS R 362 " --> pdb=" O PRO R 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 359 through 362' Processing helix chain 'R' and resid 364 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.586A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.235A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.823A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.617A 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: 3.719A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A 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 153 removed outlier: 6.514A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.905A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.504A pdb=" N GLY B 244 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.687A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.769A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.407A pdb=" N PHE C 110 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 140 through 141 removed outlier: 3.567A pdb=" N ARG C 160 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 146 through 148 removed outlier: 3.653A pdb=" N GLU C 246 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 189 " --> pdb=" O TRP C 176 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 178 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU C 187 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.009A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1332 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: 3.10 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1590 1.27 - 1.40: 2602 1.40 - 1.54: 5747 1.54 - 1.68: 73 1.68 - 1.81: 85 Bond restraints: 10097 Sorted by residual: bond pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 1.503 1.132 0.371 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 1.492 1.218 0.274 5.00e-02 4.00e+02 2.99e+01 bond pdb=" N PRO R 355 " pdb=" CA PRO R 355 " ideal model delta sigma weight residual 1.471 1.521 -0.050 1.32e-02 5.74e+03 1.43e+01 bond pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.51e+00 bond pdb=" C3 CLR R 602 " pdb=" O1 CLR R 602 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.09e+00 ... (remaining 10092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.55: 13686 6.55 - 13.11: 4 13.11 - 19.66: 1 19.66 - 26.21: 0 26.21 - 32.77: 2 Bond angle restraints: 13693 Sorted by residual: angle pdb=" N PRO R 355 " pdb=" CD PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 103.20 74.58 28.62 1.50e+00 4.44e-01 3.64e+02 angle pdb=" CA PRO R 355 " pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 104.50 71.73 32.77 1.90e+00 2.77e-01 2.97e+02 angle pdb=" CA PRO R 355 " pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 112.00 102.69 9.31 1.40e+00 5.10e-01 4.42e+01 angle pdb=" N PRO R 355 " pdb=" CA PRO R 355 " pdb=" CB PRO R 355 " ideal model delta sigma weight residual 103.48 97.38 6.10 1.00e+00 1.00e+00 3.73e+01 angle pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 106.10 125.14 -19.04 3.20e+00 9.77e-02 3.54e+01 ... (remaining 13688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 5332 22.39 - 44.78: 585 44.78 - 67.17: 75 67.17 - 89.56: 22 89.56 - 111.95: 2 Dihedral angle restraints: 6016 sinusoidal: 2358 harmonic: 3658 Sorted by residual: dihedral pdb=" N PRO R 355 " pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " pdb=" CB PRO R 355 " ideal model delta sinusoidal sigma weight residual 30.00 91.78 -61.78 1 1.50e+01 4.44e-03 2.25e+01 dihedral pdb=" C2 CLR R 602 " pdb=" C3 CLR R 602 " pdb=" C4 CLR R 602 " pdb=" C5 CLR R 602 " ideal model delta sinusoidal sigma weight residual -55.03 56.92 -111.95 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C5 CLR R 602 " pdb=" C3 CLR R 602 " pdb=" C4 CLR R 602 " pdb=" O1 CLR R 602 " ideal model delta sinusoidal sigma weight residual 175.64 64.31 111.33 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 6013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1275 0.051 - 0.102: 224 0.102 - 0.153: 42 0.153 - 0.204: 1 0.204 - 0.255: 1 Chirality restraints: 1543 Sorted by residual: chirality pdb=" CB THR B 181 " pdb=" CA THR B 181 " pdb=" OG1 THR B 181 " pdb=" CG2 THR B 181 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA TYR C 235 " pdb=" N TYR C 235 " pdb=" C TYR C 235 " pdb=" CB TYR C 235 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CA THR B 181 " pdb=" N THR B 181 " pdb=" C THR B 181 " pdb=" CB THR B 181 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1540 not shown) Planarity restraints: 1731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 354 " 0.037 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO R 355 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 355 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 355 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 40 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO C 41 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 235 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO C 236 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.025 5.00e-02 4.00e+02 ... (remaining 1728 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 688 2.74 - 3.28: 9272 3.28 - 3.82: 16074 3.82 - 4.36: 18907 4.36 - 4.90: 34512 Nonbonded interactions: 79453 Sorted by model distance: nonbonded pdb=" NH1 ARG A 205 " pdb=" OD1 ASP B 186 " model vdw 2.198 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD2 ASP B 76 " model vdw 2.239 3.040 nonbonded pdb=" NE2 GLN A 52 " pdb=" O ASP A 335 " model vdw 2.273 3.120 nonbonded pdb=" OD1 ASP N 90 " pdb=" OH TYR N 94 " model vdw 2.279 3.040 nonbonded pdb=" NH2 ARG C 180 " pdb=" OE2 GLU C 222 " model vdw 2.297 3.120 ... (remaining 79448 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 24.800 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.005 0.371 10097 Z= 0.378 Angle : 0.658 32.766 13693 Z= 0.356 Chirality : 0.040 0.255 1543 Planarity : 0.004 0.054 1731 Dihedral : 18.014 111.951 3645 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.09 % Allowed : 31.36 % Favored : 68.54 % 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: 1.05 (0.24), residues: 1240 helix: 2.54 (0.26), residues: 394 sheet: 0.47 (0.29), residues: 316 loop : -0.57 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 316 HIS 0.003 0.001 HIS B 311 PHE 0.015 0.001 PHE A 189 TYR 0.021 0.001 TYR C 235 ARG 0.013 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 1.120 Fit side-chains REVERT: B 42 ARG cc_start: 0.7413 (mmp-170) cc_final: 0.7086 (tpp-160) REVERT: R 353 VAL cc_start: 0.6955 (t) cc_final: 0.6711 (p) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 1.2790 time to fit residues: 166.6192 Evaluate side-chains 109 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 349 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 0.0060 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120646 restraints weight = 12289.908| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.66 r_work: 0.3320 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10097 Z= 0.276 Angle : 0.589 11.618 13693 Z= 0.305 Chirality : 0.043 0.229 1543 Planarity : 0.004 0.048 1731 Dihedral : 5.617 41.020 1442 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.82 % Allowed : 27.70 % Favored : 66.48 % 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 (0.24), residues: 1240 helix: 2.21 (0.26), residues: 407 sheet: 0.31 (0.29), residues: 321 loop : -0.62 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS A 324 PHE 0.017 0.001 PHE A 189 TYR 0.030 0.002 TYR C 235 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 108 time to evaluate : 0.957 Fit side-chains REVERT: B 59 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: B 197 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6444 (mtp-110) REVERT: B 234 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7608 (t80) REVERT: B 336 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8185 (tt) REVERT: C 46 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: C 169 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8693 (m110) REVERT: R 75 HIS cc_start: 0.7542 (OUTLIER) cc_final: 0.7247 (t-170) REVERT: R 353 VAL cc_start: 0.6613 (t) cc_final: 0.6275 (p) outliers start: 62 outliers final: 23 residues processed: 151 average time/residue: 1.1653 time to fit residues: 190.5603 Evaluate side-chains 135 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 127 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.154791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123237 restraints weight = 12393.425| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.67 r_work: 0.3370 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10097 Z= 0.177 Angle : 0.507 9.117 13693 Z= 0.266 Chirality : 0.041 0.218 1543 Planarity : 0.004 0.047 1731 Dihedral : 4.879 39.638 1440 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.60 % Allowed : 28.73 % Favored : 66.67 % 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: 0.98 (0.24), residues: 1240 helix: 2.37 (0.26), residues: 407 sheet: 0.34 (0.29), residues: 322 loop : -0.54 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 PHE 0.033 0.001 PHE R 349 TYR 0.027 0.001 TYR C 235 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 1.173 Fit side-chains REVERT: B 59 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.6938 (m-80) REVERT: B 172 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7698 (tt0) REVERT: B 197 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6342 (mtp-110) REVERT: B 234 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7614 (t80) REVERT: B 311 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.5934 (t-90) REVERT: B 336 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8041 (tt) REVERT: C 38 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7688 (ttp-170) REVERT: C 169 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8599 (m110) REVERT: R 75 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.7269 (t-170) REVERT: R 353 VAL cc_start: 0.6666 (t) cc_final: 0.6325 (p) outliers start: 49 outliers final: 21 residues processed: 154 average time/residue: 1.1474 time to fit residues: 191.1176 Evaluate side-chains 137 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 123 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 183 GLN N 35 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.154260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123168 restraints weight = 12238.524| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.63 r_work: 0.3361 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10097 Z= 0.202 Angle : 0.519 10.018 13693 Z= 0.271 Chirality : 0.041 0.223 1543 Planarity : 0.004 0.051 1731 Dihedral : 4.849 38.002 1440 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 6.01 % Allowed : 28.26 % Favored : 65.73 % 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: 0.96 (0.24), residues: 1240 helix: 2.36 (0.26), residues: 407 sheet: 0.31 (0.29), residues: 324 loop : -0.55 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.004 0.001 HIS C 35 PHE 0.016 0.001 PHE A 189 TYR 0.029 0.001 TYR C 235 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 109 time to evaluate : 1.076 Fit side-chains REVERT: B 13 GLN cc_start: 0.7797 (tp40) cc_final: 0.7507 (mt0) REVERT: B 59 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.6964 (m-80) REVERT: B 172 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7673 (tt0) REVERT: B 197 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6373 (mtp-110) REVERT: B 234 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7591 (t80) REVERT: B 311 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.5885 (t-90) REVERT: B 336 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8070 (tt) REVERT: C 38 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7702 (ttp-170) REVERT: C 169 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8651 (m110) REVERT: C 214 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7442 (tp) REVERT: R 75 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.7345 (t-170) REVERT: R 353 VAL cc_start: 0.6632 (t) cc_final: 0.6295 (p) outliers start: 64 outliers final: 34 residues processed: 159 average time/residue: 1.1327 time to fit residues: 195.4552 Evaluate side-chains 152 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 185 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN C 183 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123506 restraints weight = 12284.783| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.62 r_work: 0.3366 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10097 Z= 0.193 Angle : 0.512 9.894 13693 Z= 0.267 Chirality : 0.041 0.215 1543 Planarity : 0.004 0.049 1731 Dihedral : 4.822 38.193 1440 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.45 % Allowed : 29.11 % Favored : 65.45 % 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: 0.98 (0.24), residues: 1240 helix: 2.39 (0.26), residues: 407 sheet: 0.31 (0.29), residues: 323 loop : -0.53 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 PHE 0.031 0.001 PHE R 349 TYR 0.030 0.001 TYR C 235 ARG 0.010 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 114 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 310 LYS cc_start: 0.7700 (tptt) cc_final: 0.7298 (tptt) REVERT: B 59 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: B 197 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6338 (mtp-110) REVERT: B 234 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.7604 (t80) REVERT: B 311 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.5801 (t-90) REVERT: B 336 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8048 (tt) REVERT: C 38 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7694 (ttp-170) REVERT: C 169 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8634 (m110) REVERT: R 75 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.7385 (t-170) REVERT: R 353 VAL cc_start: 0.6497 (t) cc_final: 0.6183 (p) outliers start: 58 outliers final: 36 residues processed: 158 average time/residue: 1.0665 time to fit residues: 183.0978 Evaluate side-chains 153 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 185 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 75 optimal weight: 0.0060 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 39 optimal weight: 4.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 183 GLN N 35 ASN R 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126666 restraints weight = 12314.690| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.63 r_work: 0.3404 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10097 Z= 0.136 Angle : 0.481 10.103 13693 Z= 0.252 Chirality : 0.040 0.215 1543 Planarity : 0.004 0.050 1731 Dihedral : 4.577 37.746 1440 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.79 % Allowed : 30.42 % Favored : 64.79 % 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: 1.12 (0.24), residues: 1240 helix: 2.51 (0.26), residues: 407 sheet: 0.42 (0.29), residues: 318 loop : -0.47 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 PHE 0.014 0.001 PHE A 189 TYR 0.027 0.001 TYR C 235 ARG 0.011 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: B 13 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: B 59 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: B 172 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7572 (tt0) REVERT: B 197 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6292 (mtp-110) REVERT: B 234 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7602 (t80) REVERT: B 311 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.5840 (t-90) REVERT: C 169 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8495 (m110) REVERT: N 4 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8551 (mt) REVERT: R 75 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.7335 (t-170) REVERT: R 353 VAL cc_start: 0.6462 (t) cc_final: 0.6215 (p) outliers start: 51 outliers final: 32 residues processed: 158 average time/residue: 1.0587 time to fit residues: 182.1163 Evaluate side-chains 155 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 185 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN ** N 35 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 = 0.3776 r_free = 0.3776 target = 0.151892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120119 restraints weight = 12484.597| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.66 r_work: 0.3314 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10097 Z= 0.314 Angle : 0.588 9.479 13693 Z= 0.307 Chirality : 0.043 0.247 1543 Planarity : 0.004 0.051 1731 Dihedral : 5.082 39.012 1440 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 6.29 % Allowed : 29.20 % Favored : 64.51 % 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: 0.85 (0.24), residues: 1240 helix: 2.30 (0.25), residues: 405 sheet: 0.29 (0.29), residues: 319 loop : -0.65 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.005 0.001 HIS A 324 PHE 0.034 0.002 PHE R 349 TYR 0.035 0.002 TYR C 235 ARG 0.012 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 116 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: B 13 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7378 (mt0) REVERT: B 59 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.6962 (m-80) REVERT: B 172 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7721 (tt0) REVERT: B 197 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6308 (mtp-110) REVERT: B 234 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.7660 (t80) REVERT: B 311 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.5977 (t-90) REVERT: B 336 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8237 (tt) REVERT: C 38 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7681 (ttp-170) REVERT: C 46 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6880 (tt0) REVERT: C 169 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8749 (m110) REVERT: G 47 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8042 (mt-10) REVERT: R 75 HIS cc_start: 0.7542 (OUTLIER) cc_final: 0.7222 (t-170) REVERT: R 301 LEU cc_start: 0.5904 (OUTLIER) cc_final: 0.5600 (tp) REVERT: R 353 VAL cc_start: 0.6650 (t) cc_final: 0.6319 (p) outliers start: 67 outliers final: 38 residues processed: 168 average time/residue: 1.0078 time to fit residues: 184.8699 Evaluate side-chains 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 301 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 0.0010 chunk 121 optimal weight: 0.0470 chunk 63 optimal weight: 0.0770 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 79 optimal weight: 0.0470 chunk 81 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 183 GLN N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.158297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128063 restraints weight = 12450.876| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.62 r_work: 0.3413 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10097 Z= 0.129 Angle : 0.489 10.277 13693 Z= 0.256 Chirality : 0.040 0.241 1543 Planarity : 0.004 0.051 1731 Dihedral : 4.572 38.353 1440 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.13 % Allowed : 31.46 % Favored : 64.41 % 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: 1.18 (0.24), residues: 1240 helix: 2.57 (0.26), residues: 407 sheet: 0.45 (0.29), residues: 318 loop : -0.45 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.002 0.001 HIS C 35 PHE 0.013 0.001 PHE A 189 TYR 0.027 0.001 TYR C 235 ARG 0.013 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 1.095 Fit side-chains REVERT: A 24 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: B 13 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7358 (mt0) REVERT: B 59 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: B 197 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6182 (mtp-110) REVERT: B 234 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7643 (t80) REVERT: B 311 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.5820 (t-90) REVERT: N 30 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8467 (p) REVERT: R 75 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.7323 (t-170) REVERT: R 301 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5508 (tp) outliers start: 44 outliers final: 27 residues processed: 148 average time/residue: 1.1088 time to fit residues: 178.9177 Evaluate side-chains 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 301 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 55 optimal weight: 0.0000 chunk 77 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125847 restraints weight = 12396.902| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.63 r_work: 0.3388 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10097 Z= 0.167 Angle : 0.511 9.883 13693 Z= 0.265 Chirality : 0.041 0.244 1543 Planarity : 0.004 0.058 1731 Dihedral : 4.651 38.452 1440 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.13 % Allowed : 31.55 % Favored : 64.32 % 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: 1.15 (0.24), residues: 1240 helix: 2.57 (0.26), residues: 407 sheet: 0.40 (0.29), residues: 318 loop : -0.46 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 PHE 0.046 0.001 PHE R 349 TYR 0.029 0.001 TYR C 235 ARG 0.014 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 1.148 Fit side-chains REVERT: A 24 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: B 59 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.7067 (m-80) REVERT: B 172 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7540 (tt0) REVERT: B 197 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6200 (mtp-110) REVERT: B 234 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.7578 (t80) REVERT: B 245 SER cc_start: 0.8758 (p) cc_final: 0.8294 (t) REVERT: B 311 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.5947 (t-90) REVERT: C 169 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8489 (m110) REVERT: C 230 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7602 (ttt) REVERT: N 30 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8486 (p) REVERT: N 48 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7919 (t) REVERT: R 75 HIS cc_start: 0.7553 (OUTLIER) cc_final: 0.7216 (t-170) REVERT: R 301 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5640 (tp) outliers start: 44 outliers final: 28 residues processed: 143 average time/residue: 1.0851 time to fit residues: 168.5708 Evaluate side-chains 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124721 restraints weight = 12315.257| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.62 r_work: 0.3380 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10097 Z= 0.181 Angle : 0.523 9.839 13693 Z= 0.273 Chirality : 0.041 0.249 1543 Planarity : 0.004 0.061 1731 Dihedral : 4.729 38.861 1440 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.85 % Allowed : 31.83 % Favored : 64.32 % 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: 1.12 (0.24), residues: 1240 helix: 2.55 (0.26), residues: 407 sheet: 0.38 (0.29), residues: 318 loop : -0.48 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 PHE 0.016 0.001 PHE A 189 TYR 0.030 0.001 TYR C 235 ARG 0.014 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 1.068 Fit side-chains REVERT: A 24 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: B 59 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: B 172 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7551 (tt0) REVERT: B 197 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6223 (mtp-110) REVERT: B 234 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7623 (t80) REVERT: B 245 SER cc_start: 0.8750 (p) cc_final: 0.8216 (t) REVERT: B 311 HIS cc_start: 0.7682 (OUTLIER) cc_final: 0.5902 (t-90) REVERT: C 169 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8534 (m110) REVERT: C 230 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7642 (ttt) REVERT: N 30 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8478 (p) REVERT: R 301 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5785 (tp) outliers start: 41 outliers final: 28 residues processed: 141 average time/residue: 1.1164 time to fit residues: 171.2817 Evaluate side-chains 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 18 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 5 optimal weight: 0.0000 chunk 87 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124831 restraints weight = 12280.582| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.67 r_work: 0.3366 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10097 Z= 0.180 Angle : 0.534 12.044 13693 Z= 0.276 Chirality : 0.041 0.246 1543 Planarity : 0.004 0.061 1731 Dihedral : 4.740 39.070 1440 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.85 % Allowed : 31.64 % Favored : 64.51 % 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: 1.10 (0.24), residues: 1240 helix: 2.52 (0.26), residues: 407 sheet: 0.36 (0.29), residues: 318 loop : -0.47 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.003 0.001 HIS C 35 PHE 0.050 0.001 PHE R 349 TYR 0.030 0.001 TYR C 235 ARG 0.015 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7045.83 seconds wall clock time: 125 minutes 8.01 seconds (7508.01 seconds total)