Starting phenix.real_space_refine on Fri Aug 22 23:38:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zje_60142/08_2025/8zje_60142_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zje_60142/08_2025/8zje_60142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zje_60142/08_2025/8zje_60142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zje_60142/08_2025/8zje_60142.map" model { file = "/net/cci-nas-00/data/ceres_data/8zje_60142/08_2025/8zje_60142_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zje_60142/08_2025/8zje_60142_neut.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.069 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 56 5.16 5 C 5571 2.51 5 N 1504 2.21 5 O 1612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8743 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1810 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2570 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2142 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 263} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "S" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1726 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Unusual residues: {'ACY': 1, 'XZA': 1} Classifications: {'peptide': 8, 'undetermined': 2} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 6, None: 3} Not linked: pdbres="ACY C 1 " pdbres="DTY C 2 " Not linked: pdbres="PHE C 6 " pdbres="XZA C 7 " Not linked: pdbres="XZA C 7 " pdbres="LEU C 8 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'ACY:plan-1': 1, 'HYP:plan-1': 1, 'XZA:plan-1': 1, 'NMM:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.42, per 1000 atoms: 0.28 Number of scatterers: 8743 At special positions: 0 Unit cell: (94.9, 115.34, 129.21, 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 56 16.00 O 1612 8.00 N 1504 7.00 C 5571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 337.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTY C 2 " Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 39.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 6 through 27 Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.695A pdb=" N GLN A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.549A pdb=" N LEU A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 10 through 31 removed outlier: 4.355A pdb=" N GLN B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.838A pdb=" N ILE G 24 " --> pdb=" O MET G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 44 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 54 through 58 removed outlier: 4.243A pdb=" N ASN G 58 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 68 removed outlier: 4.592A pdb=" N LEU R 47 " --> pdb=" O TRP R 43 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA R 51 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU R 52 " --> pdb=" O PHE R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 95 Processing helix chain 'R' and resid 97 through 103 removed outlier: 4.143A pdb=" N LEU R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 146 removed outlier: 3.626A pdb=" N ASN R 119 " --> pdb=" O CYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 174 Processing helix chain 'R' and resid 175 through 180 removed outlier: 4.060A pdb=" N ALA R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 213 Processing helix chain 'R' and resid 213 through 234 Processing helix chain 'R' and resid 242 through 253 Processing helix chain 'R' and resid 253 through 289 removed outlier: 3.871A pdb=" N ARG R 258 " --> pdb=" O ALA R 254 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG R 263 " --> pdb=" O ALA R 259 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 298 through 324 removed outlier: 3.523A pdb=" N SER R 316 " --> pdb=" O SER R 312 " (cutoff:3.500A) Proline residue: R 320 - end of helix Processing helix chain 'R' and resid 327 through 336 Processing helix chain 'S' and resid 27 through 31 Processing helix chain 'S' and resid 52 through 55 removed outlier: 4.015A pdb=" N GLY S 55 " --> pdb=" O SER S 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 52 through 55' Processing helix chain 'S' and resid 86 through 90 removed outlier: 3.603A pdb=" N THR S 90 " --> pdb=" O SER S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 removed outlier: 6.405A pdb=" N LEU A 34 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 206 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 36 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 9.820A pdb=" N SER A 227 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LYS A 35 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N MET A 229 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 37 " --> pdb=" O MET A 229 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU A 231 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 228 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 274 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE A 230 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN A 276 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 232 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57 removed outlier: 3.626A pdb=" N LEU B 341 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.537A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.806A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.327A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.678A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 239 removed outlier: 3.656A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.309A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'S' and resid 2 through 5 Processing sheet with id=AB2, first strand: chain 'S' and resid 9 through 11 removed outlier: 6.018A pdb=" N ARG S 37 " --> pdb=" O TRP S 46 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP S 46 " --> pdb=" O ARG S 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.771A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1409 1.31 - 1.43: 2489 1.43 - 1.56: 4943 1.56 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 8924 Sorted by residual: bond pdb=" CA ARG A 29 " pdb=" C ARG A 29 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.28e-02 6.10e+03 2.96e+01 bond pdb=" CA VAL A 201 " pdb=" CB VAL A 201 " ideal model delta sigma weight residual 1.548 1.479 0.068 1.46e-02 4.69e+03 2.19e+01 bond pdb=" N VAL A 201 " pdb=" CA VAL A 201 " ideal model delta sigma weight residual 1.458 1.413 0.045 1.17e-02 7.31e+03 1.47e+01 bond pdb=" CA GLU A 33 " pdb=" C GLU A 33 " ideal model delta sigma weight residual 1.521 1.477 0.044 1.17e-02 7.31e+03 1.44e+01 bond pdb=" CA GLU A 28 " pdb=" C GLU A 28 " ideal model delta sigma weight residual 1.522 1.474 0.047 1.25e-02 6.40e+03 1.43e+01 ... (remaining 8919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 11896 2.38 - 4.76: 186 4.76 - 7.13: 21 7.13 - 9.51: 4 9.51 - 11.89: 3 Bond angle restraints: 12110 Sorted by residual: angle pdb=" N ARG A 29 " pdb=" CA ARG A 29 " pdb=" C ARG A 29 " ideal model delta sigma weight residual 112.94 102.00 10.94 1.41e+00 5.03e-01 6.02e+01 angle pdb=" N GLU A 28 " pdb=" CA GLU A 28 " pdb=" C GLU A 28 " ideal model delta sigma weight residual 114.09 102.20 11.89 1.55e+00 4.16e-01 5.89e+01 angle pdb=" N ARG A 31 " pdb=" CA ARG A 31 " pdb=" C ARG A 31 " ideal model delta sigma weight residual 113.41 104.83 8.58 1.22e+00 6.72e-01 4.94e+01 angle pdb=" N HYP C 3 " pdb=" CA HYP C 3 " pdb=" CB HYP C 3 " ideal model delta sigma weight residual 103.00 109.27 -6.27 1.10e+00 8.26e-01 3.25e+01 angle pdb=" N PHE A 222 " pdb=" CA PHE A 222 " pdb=" C PHE A 222 " ideal model delta sigma weight residual 111.55 105.34 6.21 1.37e+00 5.33e-01 2.06e+01 ... (remaining 12105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4738 17.96 - 35.92: 410 35.92 - 53.87: 96 53.87 - 71.83: 11 71.83 - 89.79: 11 Dihedral angle restraints: 5266 sinusoidal: 1973 harmonic: 3293 Sorted by residual: dihedral pdb=" CA THR B 254 " pdb=" C THR B 254 " pdb=" N CYS B 255 " pdb=" CA CYS B 255 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LYS B 83 " pdb=" C LYS B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA THR B 170 " pdb=" C THR B 170 " pdb=" N CYS B 171 " pdb=" CA CYS B 171 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1331 0.103 - 0.207: 50 0.207 - 0.310: 2 0.310 - 0.414: 2 0.414 - 0.517: 1 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA HYP C 3 " pdb=" N HYP C 3 " pdb=" C HYP C 3 " pdb=" CB HYP C 3 " both_signs ideal model delta sigma weight residual False 2.72 2.20 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA THR A 226 " pdb=" N THR A 226 " pdb=" C THR A 226 " pdb=" CB THR A 226 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 1383 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD NMM C 9 " -0.066 2.00e-02 2.50e+03 1.51e-01 3.41e+02 pdb=" NE NMM C 9 " 0.223 2.00e-02 2.50e+03 pdb=" CZ NMM C 9 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 NMM C 9 " -0.088 2.00e-02 2.50e+03 pdb=" NH2 NMM C 9 " -0.212 2.00e-02 2.50e+03 pdb=" CAA NMM C 9 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 197 " 0.027 2.00e-02 2.50e+03 5.60e-02 3.14e+01 pdb=" C ASP A 197 " -0.097 2.00e-02 2.50e+03 pdb=" O ASP A 197 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU A 198 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 319 " 0.060 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO R 320 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO R 320 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 320 " 0.050 5.00e-02 4.00e+02 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 912 2.74 - 3.28: 8882 3.28 - 3.82: 14382 3.82 - 4.36: 17199 4.36 - 4.90: 30801 Nonbonded interactions: 72176 Sorted by model distance: nonbonded pdb=" O THR B 91 " pdb=" OG1 THR B 92 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR B 279 " pdb=" O VAL B 320 " model vdw 2.223 3.040 nonbonded pdb=" OG SER B 286 " pdb=" OD2 ASP G 47 " model vdw 2.251 3.040 nonbonded pdb=" O ALA R 128 " pdb=" OG1 THR R 132 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR B 70 " pdb=" O PRO B 112 " model vdw 2.257 3.040 ... (remaining 72171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 0.079 8928 Z= 0.338 Angle : 0.714 11.891 12110 Z= 0.417 Chirality : 0.047 0.517 1386 Planarity : 0.006 0.151 1530 Dihedral : 14.594 89.791 3138 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.33 % Allowed : 14.46 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.27), residues: 1104 helix: 2.42 (0.26), residues: 393 sheet: -0.05 (0.32), residues: 288 loop : -0.06 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 218 TYR 0.022 0.001 TYR S 190 PHE 0.022 0.001 PHE A 222 TRP 0.019 0.001 TRP C 10 HIS 0.004 0.001 HIS R 309 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 8924) covalent geometry : angle 0.71447 (12110) hydrogen bonds : bond 0.16336 ( 450) hydrogen bonds : angle 6.58847 ( 1266) Misc. bond : bond 0.07222 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.342 Fit side-chains REVERT: A 28 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7892 (pt0) REVERT: A 310 PHE cc_start: 0.8285 (t80) cc_final: 0.8058 (t80) REVERT: A 325 ILE cc_start: 0.8491 (tp) cc_final: 0.8271 (tt) REVERT: A 358 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: B 64 TYR cc_start: 0.9036 (m-80) cc_final: 0.8749 (m-80) REVERT: B 231 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7634 (mp0) REVERT: B 267 MET cc_start: 0.8377 (ttm) cc_final: 0.7934 (ttm) REVERT: B 306 LYS cc_start: 0.8289 (mmmm) cc_final: 0.8016 (mmtt) REVERT: S 5 GLU cc_start: 0.8598 (mp0) cc_final: 0.7707 (mp0) REVERT: S 67 PHE cc_start: 0.8173 (m-10) cc_final: 0.7833 (m-10) REVERT: S 81 GLN cc_start: 0.8106 (tp-100) cc_final: 0.7138 (tp40) REVERT: S 223 ASP cc_start: 0.7616 (m-30) cc_final: 0.7307 (m-30) REVERT: C 10 TRP cc_start: 0.7882 (OUTLIER) cc_final: 0.7582 (p90) outliers start: 3 outliers final: 0 residues processed: 153 average time/residue: 0.1262 time to fit residues: 25.3377 Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain C residue 10 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS B 18 GLN B 22 GLN R 122 GLN R 208 ASN R 295 HIS S 183 GLN S 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116498 restraints weight = 10447.532| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.12 r_work: 0.3268 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8928 Z= 0.117 Angle : 0.538 6.380 12110 Z= 0.288 Chirality : 0.041 0.171 1386 Planarity : 0.004 0.057 1530 Dihedral : 5.367 58.978 1239 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.64 % Allowed : 13.58 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.27), residues: 1104 helix: 2.42 (0.26), residues: 398 sheet: 0.10 (0.32), residues: 276 loop : 0.04 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 26 TYR 0.019 0.001 TYR S 190 PHE 0.018 0.001 PHE A 49 TRP 0.017 0.001 TRP B 174 HIS 0.004 0.001 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8924) covalent geometry : angle 0.53777 (12110) hydrogen bonds : bond 0.03711 ( 450) hydrogen bonds : angle 4.97420 ( 1266) Misc. bond : bond 0.00042 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.342 Fit side-chains REVERT: A 259 THR cc_start: 0.8000 (m) cc_final: 0.7767 (p) REVERT: A 358 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: B 194 SER cc_start: 0.8154 (m) cc_final: 0.7860 (p) REVERT: B 231 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7425 (mp0) REVERT: R 53 MET cc_start: 0.7168 (tpt) cc_final: 0.6961 (tpt) REVERT: R 336 ARG cc_start: 0.5406 (OUTLIER) cc_final: 0.5173 (ttt180) REVERT: S 42 LYS cc_start: 0.7771 (mtpp) cc_final: 0.7393 (mptt) REVERT: S 81 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7159 (tp40) REVERT: S 92 MET cc_start: 0.8076 (ttm) cc_final: 0.7608 (tpp) REVERT: C 10 TRP cc_start: 0.8418 (OUTLIER) cc_final: 0.7935 (p90) outliers start: 15 outliers final: 4 residues processed: 158 average time/residue: 0.1083 time to fit residues: 23.2061 Evaluate side-chains 146 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain C residue 10 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 53 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.164820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111457 restraints weight = 10469.804| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.10 r_work: 0.3204 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8928 Z= 0.181 Angle : 0.550 7.130 12110 Z= 0.294 Chirality : 0.042 0.162 1386 Planarity : 0.004 0.054 1530 Dihedral : 5.276 58.145 1239 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.52 % Allowed : 15.12 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.26), residues: 1104 helix: 2.34 (0.25), residues: 396 sheet: -0.13 (0.31), residues: 288 loop : 0.03 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 202 TYR 0.025 0.002 TYR S 190 PHE 0.018 0.002 PHE A 49 TRP 0.013 0.001 TRP B 174 HIS 0.005 0.001 HIS R 309 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8924) covalent geometry : angle 0.54995 (12110) hydrogen bonds : bond 0.03879 ( 450) hydrogen bonds : angle 4.77454 ( 1266) Misc. bond : bond 0.00018 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7103 (pt0) REVERT: A 305 GLN cc_start: 0.7182 (tp-100) cc_final: 0.6818 (tp40) REVERT: A 358 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: B 202 ARG cc_start: 0.7631 (tpp80) cc_final: 0.7418 (ttm-80) REVERT: B 231 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7465 (mp0) REVERT: B 234 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8062 (mp) REVERT: R 325 PHE cc_start: 0.7075 (m-10) cc_final: 0.6646 (m-10) REVERT: R 336 ARG cc_start: 0.5417 (OUTLIER) cc_final: 0.5066 (ttt180) REVERT: S 42 LYS cc_start: 0.7768 (mtpp) cc_final: 0.7323 (mptt) REVERT: S 81 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7058 (tp40) REVERT: S 92 MET cc_start: 0.8068 (ttm) cc_final: 0.7592 (tpp) REVERT: C 10 TRP cc_start: 0.8554 (OUTLIER) cc_final: 0.7877 (p90) outliers start: 23 outliers final: 11 residues processed: 164 average time/residue: 0.1095 time to fit residues: 24.4795 Evaluate side-chains 156 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain C residue 10 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 0.0870 chunk 64 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS B 22 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 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 = 0.4011 r_free = 0.4011 target = 0.167765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114654 restraints weight = 10758.457| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.08 r_work: 0.3273 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8928 Z= 0.102 Angle : 0.482 6.360 12110 Z= 0.256 Chirality : 0.040 0.147 1386 Planarity : 0.004 0.055 1530 Dihedral : 4.949 55.379 1239 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.08 % Allowed : 16.32 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.26), residues: 1104 helix: 2.42 (0.25), residues: 397 sheet: -0.07 (0.31), residues: 279 loop : 0.07 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 224 TYR 0.013 0.001 TYR A 237 PHE 0.014 0.001 PHE A 49 TRP 0.015 0.001 TRP B 174 HIS 0.003 0.001 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8924) covalent geometry : angle 0.48225 (12110) hydrogen bonds : bond 0.03257 ( 450) hydrogen bonds : angle 4.51807 ( 1266) Misc. bond : bond 0.00011 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.226 Fit side-chains REVERT: A 25 GLU cc_start: 0.7392 (tt0) cc_final: 0.6801 (tm-30) REVERT: A 259 THR cc_start: 0.8198 (m) cc_final: 0.7988 (p) REVERT: A 358 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: B 194 SER cc_start: 0.8270 (m) cc_final: 0.7969 (p) REVERT: B 231 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7533 (mp0) REVERT: B 234 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7986 (mp) REVERT: B 308 ASP cc_start: 0.7326 (m-30) cc_final: 0.6643 (p0) REVERT: R 336 ARG cc_start: 0.5509 (OUTLIER) cc_final: 0.5166 (ttt180) REVERT: S 42 LYS cc_start: 0.7903 (mtpp) cc_final: 0.7468 (mptt) REVERT: S 81 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7110 (tp-100) REVERT: S 92 MET cc_start: 0.8070 (ttm) cc_final: 0.7588 (tpp) REVERT: C 10 TRP cc_start: 0.8532 (OUTLIER) cc_final: 0.7912 (p90) outliers start: 19 outliers final: 7 residues processed: 163 average time/residue: 0.1024 time to fit residues: 22.2542 Evaluate side-chains 155 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain C residue 10 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110009 restraints weight = 10732.293| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.13 r_work: 0.3182 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8928 Z= 0.220 Angle : 0.579 7.640 12110 Z= 0.306 Chirality : 0.043 0.167 1386 Planarity : 0.004 0.057 1530 Dihedral : 5.246 56.176 1239 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.74 % Allowed : 17.09 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.26), residues: 1104 helix: 2.33 (0.26), residues: 396 sheet: -0.13 (0.31), residues: 282 loop : -0.10 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 71 TYR 0.026 0.002 TYR S 190 PHE 0.022 0.002 PHE S 28 TRP 0.011 0.001 TRP B 87 HIS 0.005 0.001 HIS R 309 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 8924) covalent geometry : angle 0.57898 (12110) hydrogen bonds : bond 0.03878 ( 450) hydrogen bonds : angle 4.60695 ( 1266) Misc. bond : bond 0.00019 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.341 Fit side-chains REVERT: A 25 GLU cc_start: 0.7184 (tt0) cc_final: 0.6560 (tm-30) REVERT: A 358 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: B 24 ARG cc_start: 0.8158 (tmm-80) cc_final: 0.7883 (tmm-80) REVERT: B 225 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.6708 (mm-40) REVERT: B 231 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7448 (mp0) REVERT: B 234 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8052 (mp) REVERT: R 336 ARG cc_start: 0.5378 (OUTLIER) cc_final: 0.4974 (ttt180) REVERT: S 42 LYS cc_start: 0.7719 (mtpp) cc_final: 0.7285 (mptt) REVERT: S 81 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7003 (tp-100) REVERT: C 10 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.8313 (p90) outliers start: 25 outliers final: 13 residues processed: 156 average time/residue: 0.1114 time to fit residues: 23.4173 Evaluate side-chains 154 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain C residue 10 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114321 restraints weight = 10594.012| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.16 r_work: 0.3235 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8928 Z= 0.119 Angle : 0.508 7.934 12110 Z= 0.267 Chirality : 0.041 0.165 1386 Planarity : 0.004 0.053 1530 Dihedral : 4.936 54.394 1239 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.19 % Allowed : 17.85 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.26), residues: 1104 helix: 2.38 (0.25), residues: 397 sheet: -0.23 (0.30), residues: 285 loop : -0.06 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 97 TYR 0.014 0.001 TYR S 190 PHE 0.017 0.001 PHE S 28 TRP 0.015 0.001 TRP B 87 HIS 0.002 0.001 HIS S 34 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8924) covalent geometry : angle 0.50821 (12110) hydrogen bonds : bond 0.03362 ( 450) hydrogen bonds : angle 4.41277 ( 1266) Misc. bond : bond 0.00010 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.370 Fit side-chains REVERT: A 25 GLU cc_start: 0.7240 (tt0) cc_final: 0.6630 (tm-30) REVERT: A 29 ARG cc_start: 0.8265 (mtm110) cc_final: 0.8037 (mtm110) REVERT: A 239 GLN cc_start: 0.7999 (mm110) cc_final: 0.7674 (mm110) REVERT: A 259 THR cc_start: 0.8077 (m) cc_final: 0.7834 (p) REVERT: A 289 HIS cc_start: 0.7421 (m-70) cc_final: 0.7150 (m90) REVERT: A 358 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: B 24 ARG cc_start: 0.8206 (tmm-80) cc_final: 0.7911 (tmm-80) REVERT: B 225 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.6825 (mm-40) REVERT: B 231 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7457 (mp0) REVERT: B 234 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7969 (mp) REVERT: B 267 MET cc_start: 0.8100 (mmm) cc_final: 0.7723 (ttm) REVERT: R 190 TYR cc_start: 0.6064 (m-80) cc_final: 0.5410 (m-80) REVERT: R 336 ARG cc_start: 0.5396 (OUTLIER) cc_final: 0.5076 (ttt180) REVERT: S 42 LYS cc_start: 0.7844 (mtpp) cc_final: 0.7410 (mptt) REVERT: S 81 GLN cc_start: 0.7869 (tp-100) cc_final: 0.6959 (tp-100) outliers start: 20 outliers final: 14 residues processed: 159 average time/residue: 0.1157 time to fit residues: 24.5628 Evaluate side-chains 157 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.169098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115923 restraints weight = 10667.798| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.15 r_work: 0.3258 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8928 Z= 0.109 Angle : 0.506 9.094 12110 Z= 0.264 Chirality : 0.040 0.180 1386 Planarity : 0.004 0.055 1530 Dihedral : 4.729 55.219 1237 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.52 % Allowed : 18.40 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.26), residues: 1104 helix: 2.50 (0.26), residues: 396 sheet: -0.17 (0.30), residues: 285 loop : -0.10 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 202 TYR 0.021 0.001 TYR A 237 PHE 0.021 0.001 PHE S 67 TRP 0.014 0.001 TRP B 87 HIS 0.002 0.000 HIS R 309 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8924) covalent geometry : angle 0.50638 (12110) hydrogen bonds : bond 0.03252 ( 450) hydrogen bonds : angle 4.30540 ( 1266) Misc. bond : bond 0.00005 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.338 Fit side-chains REVERT: A 25 GLU cc_start: 0.7152 (tt0) cc_final: 0.6560 (tm-30) REVERT: A 29 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7969 (mtm110) REVERT: A 259 THR cc_start: 0.8035 (m) cc_final: 0.7796 (p) REVERT: A 286 MET cc_start: 0.8115 (mmm) cc_final: 0.7548 (mtt) REVERT: A 289 HIS cc_start: 0.7357 (m-70) cc_final: 0.7098 (m90) REVERT: B 24 ARG cc_start: 0.8155 (tmm-80) cc_final: 0.7846 (tmm-80) REVERT: B 225 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.6769 (mm-40) REVERT: B 231 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7440 (mp0) REVERT: B 234 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7851 (mp) REVERT: B 274 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6108 (pp) REVERT: B 308 ASP cc_start: 0.7171 (m-30) cc_final: 0.6457 (p0) REVERT: R 190 TYR cc_start: 0.6066 (m-80) cc_final: 0.5473 (m-80) REVERT: R 336 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.5089 (ttt180) REVERT: S 42 LYS cc_start: 0.7766 (mtpp) cc_final: 0.7336 (mptt) REVERT: S 81 GLN cc_start: 0.7860 (tp-100) cc_final: 0.6959 (tp-100) outliers start: 23 outliers final: 16 residues processed: 160 average time/residue: 0.1008 time to fit residues: 21.7320 Evaluate side-chains 161 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 20 SER Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 20.0000 chunk 99 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.116940 restraints weight = 10563.691| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.16 r_work: 0.3270 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8928 Z= 0.104 Angle : 0.501 7.686 12110 Z= 0.260 Chirality : 0.040 0.182 1386 Planarity : 0.004 0.054 1530 Dihedral : 4.656 55.344 1237 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.74 % Allowed : 17.85 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.26), residues: 1104 helix: 2.52 (0.26), residues: 396 sheet: -0.08 (0.31), residues: 274 loop : -0.08 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 74 TYR 0.013 0.001 TYR S 190 PHE 0.015 0.001 PHE A 310 TRP 0.013 0.001 TRP B 174 HIS 0.002 0.001 HIS S 34 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8924) covalent geometry : angle 0.50115 (12110) hydrogen bonds : bond 0.03211 ( 450) hydrogen bonds : angle 4.20276 ( 1266) Misc. bond : bond 0.00006 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.357 Fit side-chains REVERT: A 25 GLU cc_start: 0.7170 (tt0) cc_final: 0.6596 (tm-30) REVERT: A 29 ARG cc_start: 0.8182 (mtm110) cc_final: 0.7959 (mtm110) REVERT: A 239 GLN cc_start: 0.8014 (mm110) cc_final: 0.7713 (mm110) REVERT: A 259 THR cc_start: 0.7998 (m) cc_final: 0.7760 (p) REVERT: A 289 HIS cc_start: 0.7380 (m-70) cc_final: 0.7126 (m90) REVERT: A 357 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8091 (tt0) REVERT: B 225 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6816 (mm-40) REVERT: B 231 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7438 (mp0) REVERT: B 234 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7864 (mp) REVERT: B 274 ILE cc_start: 0.6532 (OUTLIER) cc_final: 0.6067 (pp) REVERT: B 308 ASP cc_start: 0.7160 (m-30) cc_final: 0.6472 (p0) REVERT: G 24 ILE cc_start: 0.6395 (OUTLIER) cc_final: 0.6142 (mp) REVERT: R 190 TYR cc_start: 0.6101 (m-80) cc_final: 0.5541 (m-80) REVERT: R 336 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.5225 (ttt180) REVERT: S 81 GLN cc_start: 0.7850 (tp-100) cc_final: 0.6942 (tp-100) REVERT: S 92 MET cc_start: 0.7979 (ttm) cc_final: 0.7228 (tpp) REVERT: S 153 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7604 (mm-30) outliers start: 25 outliers final: 18 residues processed: 172 average time/residue: 0.1049 time to fit residues: 24.3174 Evaluate side-chains 165 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 20 SER Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 153 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 105 optimal weight: 0.0670 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.170481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117796 restraints weight = 10552.293| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.13 r_work: 0.3310 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8928 Z= 0.100 Angle : 0.516 9.364 12110 Z= 0.263 Chirality : 0.040 0.191 1386 Planarity : 0.004 0.055 1530 Dihedral : 4.599 55.395 1237 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.85 % Allowed : 17.85 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.26), residues: 1104 helix: 2.47 (0.26), residues: 401 sheet: 0.02 (0.31), residues: 273 loop : -0.02 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 160 TYR 0.021 0.001 TYR A 237 PHE 0.015 0.001 PHE A 310 TRP 0.013 0.001 TRP B 87 HIS 0.002 0.000 HIS S 34 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8924) covalent geometry : angle 0.51550 (12110) hydrogen bonds : bond 0.03226 ( 450) hydrogen bonds : angle 4.16545 ( 1266) Misc. bond : bond 0.00005 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.335 Fit side-chains REVERT: A 25 GLU cc_start: 0.7218 (tt0) cc_final: 0.6653 (tm-30) REVERT: A 29 ARG cc_start: 0.8210 (mtm110) cc_final: 0.8002 (mtm110) REVERT: A 239 GLN cc_start: 0.8074 (mm110) cc_final: 0.7778 (mm110) REVERT: A 259 THR cc_start: 0.8073 (m) cc_final: 0.7831 (p) REVERT: A 286 MET cc_start: 0.8212 (mmm) cc_final: 0.7618 (mtt) REVERT: A 289 HIS cc_start: 0.7445 (m-70) cc_final: 0.7183 (m90) REVERT: A 357 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8129 (tt0) REVERT: B 24 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7806 (ttp-170) REVERT: B 225 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.6901 (mm-40) REVERT: B 231 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7439 (mp0) REVERT: B 234 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7898 (mp) REVERT: B 267 MET cc_start: 0.8195 (tpp) cc_final: 0.7643 (mtp) REVERT: B 274 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6113 (pp) REVERT: B 308 ASP cc_start: 0.7113 (m-30) cc_final: 0.6503 (p0) REVERT: G 24 ILE cc_start: 0.6440 (OUTLIER) cc_final: 0.6170 (mp) REVERT: R 190 TYR cc_start: 0.6188 (m-80) cc_final: 0.5656 (m-80) REVERT: R 336 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.5269 (ttt180) REVERT: S 37 ARG cc_start: 0.7639 (ptt180) cc_final: 0.7223 (ptt90) REVERT: S 81 GLN cc_start: 0.7899 (tp-100) cc_final: 0.6975 (tp-100) REVERT: S 92 MET cc_start: 0.8030 (ttm) cc_final: 0.7295 (tpp) REVERT: S 153 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7582 (mm-30) outliers start: 26 outliers final: 19 residues processed: 166 average time/residue: 0.1105 time to fit residues: 24.7377 Evaluate side-chains 167 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 20 SER Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 153 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.116964 restraints weight = 10560.714| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.15 r_work: 0.3296 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8928 Z= 0.107 Angle : 0.522 9.517 12110 Z= 0.265 Chirality : 0.040 0.177 1386 Planarity : 0.004 0.055 1530 Dihedral : 4.602 55.604 1237 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.74 % Allowed : 17.74 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.26), residues: 1104 helix: 2.58 (0.26), residues: 395 sheet: -0.04 (0.30), residues: 286 loop : -0.01 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 54 TYR 0.014 0.001 TYR A 237 PHE 0.015 0.001 PHE S 28 TRP 0.012 0.001 TRP B 87 HIS 0.003 0.000 HIS S 34 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8924) covalent geometry : angle 0.52232 (12110) hydrogen bonds : bond 0.03211 ( 450) hydrogen bonds : angle 4.21206 ( 1266) Misc. bond : bond 0.00005 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.337 Fit side-chains REVERT: A 25 GLU cc_start: 0.7211 (tt0) cc_final: 0.6635 (tm-30) REVERT: A 29 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7946 (mtm110) REVERT: A 239 GLN cc_start: 0.8069 (mm110) cc_final: 0.7761 (mm110) REVERT: A 259 THR cc_start: 0.8064 (m) cc_final: 0.7822 (p) REVERT: A 286 MET cc_start: 0.8245 (mmm) cc_final: 0.7663 (mtt) REVERT: A 289 HIS cc_start: 0.7406 (m-70) cc_final: 0.7152 (m90) REVERT: B 24 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7808 (ttp-170) REVERT: B 225 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.6887 (mm-40) REVERT: B 231 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7416 (mp0) REVERT: B 234 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7865 (mp) REVERT: B 267 MET cc_start: 0.8181 (tpp) cc_final: 0.7748 (mtp) REVERT: B 274 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6117 (pp) REVERT: B 308 ASP cc_start: 0.7080 (m-30) cc_final: 0.6484 (p0) REVERT: G 24 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.6194 (mp) REVERT: R 190 TYR cc_start: 0.6160 (m-80) cc_final: 0.5649 (m-80) REVERT: R 336 ARG cc_start: 0.5425 (OUTLIER) cc_final: 0.5174 (ttt180) REVERT: S 2 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7848 (mm-40) REVERT: S 37 ARG cc_start: 0.7585 (ptt180) cc_final: 0.7178 (ptt90) REVERT: S 81 GLN cc_start: 0.7936 (tp-100) cc_final: 0.6986 (tp-100) REVERT: S 153 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7611 (mm-30) outliers start: 25 outliers final: 19 residues processed: 165 average time/residue: 0.1106 time to fit residues: 24.4862 Evaluate side-chains 167 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 20 SER Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 153 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 0.0050 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.169191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116408 restraints weight = 10504.112| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.12 r_work: 0.3290 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8928 Z= 0.117 Angle : 0.526 9.360 12110 Z= 0.268 Chirality : 0.040 0.176 1386 Planarity : 0.004 0.055 1530 Dihedral : 4.608 55.904 1237 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.85 % Allowed : 17.63 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.26), residues: 1104 helix: 2.54 (0.26), residues: 396 sheet: -0.08 (0.31), residues: 280 loop : -0.06 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 74 TYR 0.015 0.001 TYR A 237 PHE 0.015 0.001 PHE S 28 TRP 0.012 0.001 TRP B 174 HIS 0.002 0.001 HIS S 34 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8924) covalent geometry : angle 0.52604 (12110) hydrogen bonds : bond 0.03256 ( 450) hydrogen bonds : angle 4.18661 ( 1266) Misc. bond : bond 0.00007 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2523.93 seconds wall clock time: 44 minutes 0.89 seconds (2640.89 seconds total)