Starting phenix.real_space_refine on Tue Jul 29 04:11:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ao8_11837/07_2025/7ao8_11837_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ao8_11837/07_2025/7ao8_11837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ao8_11837/07_2025/7ao8_11837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ao8_11837/07_2025/7ao8_11837.map" model { file = "/net/cci-nas-00/data/ceres_data/7ao8_11837/07_2025/7ao8_11837_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ao8_11837/07_2025/7ao8_11837_neut.cif" } resolution = 4.5 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= 0.001 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 Zn 2 6.06 5 P 12 5.49 5 S 59 5.16 5 C 6897 2.51 5 N 1837 2.21 5 O 2094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10905 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 487 Classifications: {'peptide': 64} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2206 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 266} Chain breaks: 4 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2206 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 266} Chain breaks: 4 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2964 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2964 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 IHP D 801 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP D 801 " occ=0.70 residue: pdb=" C1 IHP A 801 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP A 801 " occ=0.70 Time building chain proxies: 7.02, per 1000 atoms: 0.64 Number of scatterers: 10905 At special positions: 0 Unit cell: (206.01, 85.02, 92.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 K 4 19.00 S 59 16.00 P 12 15.00 O 2094 8.00 N 1837 7.00 C 6897 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=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 178 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" ND1 HIS E 178 " 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 43.5% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'C' and resid 189 through 198 Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 206 through 227 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 247 through 261 Processing helix chain 'D' and resid 264 through 273 removed outlier: 3.791A pdb=" N SER D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 288 Processing helix chain 'D' and resid 289 through 304 removed outlier: 3.620A pdb=" N GLU D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 319 through 331 Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 206 through 227 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 264 through 273 removed outlier: 3.792A pdb=" N SER A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.620A pdb=" N GLU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.847A pdb=" N GLY E 20 " --> pdb=" O GLY E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 45 removed outlier: 4.142A pdb=" N ARG E 36 " --> pdb=" O PRO E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 69 through 79 Processing helix chain 'E' and resid 83 through 94 removed outlier: 3.595A pdb=" N SER E 88 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN E 90 " --> pdb=" O GLU E 86 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 126 Processing helix chain 'E' and resid 154 through 164 Processing helix chain 'E' and resid 180 through 187 removed outlier: 3.556A pdb=" N PHE E 187 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 220 Processing helix chain 'E' and resid 233 through 253 Proline residue: E 243 - end of helix Processing helix chain 'E' and resid 277 through 291 removed outlier: 3.646A pdb=" N CYS E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 320 Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 355 through 372 removed outlier: 3.527A pdb=" N ILE E 362 " --> pdb=" O TYR E 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.848A pdb=" N GLY B 20 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 45 removed outlier: 4.143A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.594A pdb=" N SER B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 126 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 180 through 187 removed outlier: 3.556A pdb=" N PHE B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'B' and resid 233 through 253 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.646A pdb=" N CYS B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 285 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 320 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 355 through 372 removed outlier: 3.527A pdb=" N ILE B 362 " --> pdb=" O TYR B 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AA2, first strand: chain 'D' and resid 146 through 149 removed outlier: 4.238A pdb=" N TYR D 11 " --> pdb=" O CYS D 126 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 23 " --> pdb=" O PHE D 14 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG D 25 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE D 45 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE D 27 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 43 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLN D 113 " --> pdb=" O CYS D 44 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR D 46 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER D 111 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU D 110 " --> pdb=" O TYR D 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 195 through 199 removed outlier: 6.268A pdb=" N ILE E 53 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL E 11 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR E 54 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR E 13 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS E 12 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL E 257 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU E 298 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 259 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU E 171 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLN E 260 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE E 173 " --> pdb=" O GLN E 260 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL E 224 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR E 195 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N TYR E 226 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER E 197 " --> pdb=" O TYR E 226 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU E 228 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS E 199 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 149 removed outlier: 4.237A pdb=" N TYR A 11 " --> pdb=" O CYS A 126 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 23 " --> pdb=" O PHE A 14 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG A 25 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 45 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE A 27 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 43 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLN A 113 " --> pdb=" O CYS A 44 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR A 46 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 111 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU A 110 " --> pdb=" O TYR A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 195 through 199 removed outlier: 6.270A pdb=" N ILE B 53 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL B 11 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR B 54 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR B 13 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS B 12 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 257 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU B 298 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 259 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 171 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLN B 260 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 173 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL B 224 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TYR B 226 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER B 197 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU B 228 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS B 199 " --> pdb=" O LEU B 228 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 3.14 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: 1815 1.31 - 1.44: 3183 1.44 - 1.57: 6036 1.57 - 1.70: 23 1.70 - 1.83: 95 Bond restraints: 11152 Sorted by residual: bond pdb=" CA ILE A 51 " pdb=" C ILE A 51 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.27e-02 6.20e+03 2.74e+01 bond pdb=" CA ILE D 51 " pdb=" C ILE D 51 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.27e-02 6.20e+03 2.71e+01 bond pdb=" CA ILE D 51 " pdb=" CB ILE D 51 " ideal model delta sigma weight residual 1.540 1.472 0.068 1.36e-02 5.41e+03 2.47e+01 bond pdb=" CA ILE A 51 " pdb=" CB ILE A 51 " ideal model delta sigma weight residual 1.540 1.473 0.067 1.36e-02 5.41e+03 2.44e+01 bond pdb=" C GLY E 299 " pdb=" O GLY E 299 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.35e-02 5.49e+03 1.79e+01 ... (remaining 11147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 13033 2.08 - 4.16: 1712 4.16 - 6.24: 289 6.24 - 8.32: 45 8.32 - 10.40: 17 Bond angle restraints: 15096 Sorted by residual: angle pdb=" CA ASN A 31 " pdb=" CB ASN A 31 " pdb=" CG ASN A 31 " ideal model delta sigma weight residual 112.60 105.88 6.72 1.00e+00 1.00e+00 4.52e+01 angle pdb=" CA ASN D 31 " pdb=" CB ASN D 31 " pdb=" CG ASN D 31 " ideal model delta sigma weight residual 112.60 105.91 6.69 1.00e+00 1.00e+00 4.47e+01 angle pdb=" C ARG D 143 " pdb=" N GLU D 144 " pdb=" CA GLU D 144 " ideal model delta sigma weight residual 120.28 129.61 -9.33 1.44e+00 4.82e-01 4.20e+01 angle pdb=" C ARG A 143 " pdb=" N GLU A 144 " pdb=" CA GLU A 144 " ideal model delta sigma weight residual 120.28 129.46 -9.18 1.44e+00 4.82e-01 4.07e+01 angle pdb=" C GLY D 36 " pdb=" N ASN D 37 " pdb=" CA ASN D 37 " ideal model delta sigma weight residual 120.71 129.68 -8.97 1.42e+00 4.96e-01 3.99e+01 ... (remaining 15091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 6195 24.14 - 48.28: 372 48.28 - 72.42: 59 72.42 - 96.56: 26 96.56 - 120.70: 12 Dihedral angle restraints: 6664 sinusoidal: 2718 harmonic: 3946 Sorted by residual: dihedral pdb=" C SER D 52 " pdb=" N SER D 52 " pdb=" CA SER D 52 " pdb=" CB SER D 52 " ideal model delta harmonic sigma weight residual -122.60 -138.48 15.88 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" C SER A 52 " pdb=" N SER A 52 " pdb=" CA SER A 52 " pdb=" CB SER A 52 " ideal model delta harmonic sigma weight residual -122.60 -138.42 15.82 0 2.50e+00 1.60e-01 4.01e+01 dihedral pdb=" C HIS A 101 " pdb=" N HIS A 101 " pdb=" CA HIS A 101 " pdb=" CB HIS A 101 " ideal model delta harmonic sigma weight residual -122.60 -135.95 13.35 0 2.50e+00 1.60e-01 2.85e+01 ... (remaining 6661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 1592 1.007 - 2.013: 0 2.013 - 3.020: 0 3.020 - 4.027: 0 4.027 - 5.034: 4 Chirality restraints: 1596 Sorted by residual: chirality pdb=" C2 IHP D 801 " pdb=" C1 IHP D 801 " pdb=" C3 IHP D 801 " pdb=" O12 IHP D 801 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C2 IHP A 801 " pdb=" C1 IHP A 801 " pdb=" C3 IHP A 801 " pdb=" O12 IHP A 801 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C3 IHP D 801 " pdb=" C2 IHP D 801 " pdb=" C4 IHP D 801 " pdb=" O13 IHP D 801 " both_signs ideal model delta sigma weight residual False -2.34 2.39 -4.73 2.00e-01 2.50e+01 5.60e+02 ... (remaining 1593 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 109 " 0.271 2.00e-02 2.50e+03 1.86e-01 6.05e+02 pdb=" CG PHE D 109 " -0.115 2.00e-02 2.50e+03 pdb=" CD1 PHE D 109 " -0.147 2.00e-02 2.50e+03 pdb=" CD2 PHE D 109 " -0.260 2.00e-02 2.50e+03 pdb=" CE1 PHE D 109 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 PHE D 109 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE D 109 " 0.249 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 109 " -0.271 2.00e-02 2.50e+03 1.86e-01 6.04e+02 pdb=" CG PHE A 109 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE A 109 " 0.147 2.00e-02 2.50e+03 pdb=" CD2 PHE A 109 " 0.260 2.00e-02 2.50e+03 pdb=" CE1 PHE A 109 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 PHE A 109 " -0.047 2.00e-02 2.50e+03 pdb=" CZ PHE A 109 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 153 " -0.085 2.00e-02 2.50e+03 5.85e-02 6.85e+01 pdb=" CG TYR A 153 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 153 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 153 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 153 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR A 153 " 0.047 2.00e-02 2.50e+03 pdb=" CZ TYR A 153 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR A 153 " -0.110 2.00e-02 2.50e+03 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 1.22 - 2.00: 13 2.00 - 2.79: 2213 2.79 - 3.57: 17734 3.57 - 4.36: 34180 4.36 - 5.14: 56741 Nonbonded interactions: 110881 Sorted by model distance: nonbonded pdb=" OD1 ASP D 163 " pdb=" OE1 GLN E 353 " model vdw 1.219 3.040 nonbonded pdb=" CB PRO C 153 " pdb=" SD MET B 84 " model vdw 1.235 3.800 nonbonded pdb=" CG ASP D 163 " pdb=" OE1 GLN E 353 " model vdw 1.299 3.270 nonbonded pdb=" OE1 GLU D 135 " pdb=" NZ LYS E 361 " model vdw 1.611 3.120 nonbonded pdb=" CG1 ILE C 165 " pdb=" O GLU A 301 " model vdw 1.766 3.440 ... (remaining 110876 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.130 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.200 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3308 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 : 0.011 0.191 11154 Z= 0.720 Angle : 1.515 10.400 15096 Z= 0.983 Chirality : 0.259 5.034 1596 Planarity : 0.011 0.186 1946 Dihedral : 17.193 120.702 4142 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.87 % Favored : 92.52 % Rotamer: Outliers : 4.18 % Allowed : 7.06 % Favored : 88.76 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.19), residues: 1324 helix: -2.91 (0.16), residues: 544 sheet: -1.04 (0.36), residues: 180 loop : -1.95 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP C 159 HIS 0.009 0.002 HIS D 121 PHE 0.271 0.012 PHE A 109 TYR 0.110 0.008 TYR D 153 ARG 0.031 0.003 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.22740 ( 426) hydrogen bonds : angle 8.80789 ( 1218) metal coordination : bond 0.19074 ( 2) covalent geometry : bond 0.01094 (11152) covalent geometry : angle 1.51470 (15096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 VAL cc_start: 0.3628 (OUTLIER) cc_final: 0.3321 (m) REVERT: A 269 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6423 (tp) REVERT: E 47 LEU cc_start: 0.8178 (mt) cc_final: 0.7760 (mm) REVERT: E 82 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: B 45 TYR cc_start: 0.6913 (m-80) cc_final: 0.6487 (m-80) REVERT: B 82 ASP cc_start: 0.4851 (OUTLIER) cc_final: 0.4416 (m-30) REVERT: B 313 THR cc_start: 0.7810 (m) cc_final: 0.7439 (m) outliers start: 48 outliers final: 2 residues processed: 187 average time/residue: 0.2617 time to fit residues: 67.3205 Evaluate side-chains 88 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 103 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 197 GLN D 261 ASN A 197 GLN A 253 HIS A 261 ASN E 26 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN E 57 HIS E 128 GLN ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 354 ASN B 375 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.073431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.054696 restraints weight = 92142.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.055814 restraints weight = 74503.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.056675 restraints weight = 62919.184| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11154 Z= 0.206 Angle : 0.774 10.176 15096 Z= 0.400 Chirality : 0.047 0.361 1596 Planarity : 0.005 0.046 1946 Dihedral : 6.486 49.265 1580 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.22), residues: 1324 helix: -0.36 (0.21), residues: 540 sheet: -0.76 (0.36), residues: 184 loop : -0.97 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 312 HIS 0.012 0.002 HIS E 199 PHE 0.022 0.003 PHE E 198 TYR 0.026 0.003 TYR E 303 ARG 0.007 0.001 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 426) hydrogen bonds : angle 5.41048 ( 1218) metal coordination : bond 0.00092 ( 2) covalent geometry : bond 0.00427 (11152) covalent geometry : angle 0.77414 (15096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 285 MET cc_start: 0.6845 (tmm) cc_final: 0.6172 (tmm) REVERT: D 329 MET cc_start: 0.8927 (mtp) cc_final: 0.8664 (ptp) REVERT: A 329 MET cc_start: 0.8934 (mpp) cc_final: 0.8704 (mpp) REVERT: E 51 MET cc_start: 0.8181 (pmm) cc_final: 0.7811 (pmm) REVERT: E 249 MET cc_start: 0.7861 (tpt) cc_final: 0.7651 (tpt) REVERT: E 324 ILE cc_start: 0.8054 (pt) cc_final: 0.7568 (pt) REVERT: B 91 MET cc_start: 0.2218 (tpp) cc_final: 0.1955 (tpp) REVERT: B 226 TYR cc_start: 0.7419 (t80) cc_final: 0.6428 (t80) REVERT: B 241 PHE cc_start: 0.8289 (t80) cc_final: 0.8085 (t80) REVERT: B 259 LEU cc_start: 0.8226 (tp) cc_final: 0.7595 (tp) REVERT: B 289 LYS cc_start: 0.8649 (tttm) cc_final: 0.8200 (tptt) REVERT: B 311 CYS cc_start: 0.8751 (t) cc_final: 0.8375 (t) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.2341 time to fit residues: 35.5103 Evaluate side-chains 75 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 0.0040 chunk 65 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 26 optimal weight: 0.2980 chunk 38 optimal weight: 30.0000 chunk 103 optimal weight: 0.0980 chunk 130 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS E 33 HIS ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.074548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.055388 restraints weight = 92103.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.056623 restraints weight = 73118.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.057269 restraints weight = 61177.161| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3992 r_free = 0.3992 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11154 Z= 0.103 Angle : 0.565 7.530 15096 Z= 0.292 Chirality : 0.042 0.334 1596 Planarity : 0.004 0.037 1946 Dihedral : 5.998 55.477 1580 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.19 (0.23), residues: 1324 helix: 0.74 (0.23), residues: 546 sheet: -0.57 (0.39), residues: 184 loop : -0.71 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 312 HIS 0.003 0.001 HIS E 178 PHE 0.015 0.001 PHE E 187 TYR 0.021 0.001 TYR E 237 ARG 0.004 0.000 ARG C 188 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 426) hydrogen bonds : angle 4.71043 ( 1218) metal coordination : bond 0.00048 ( 2) covalent geometry : bond 0.00218 (11152) covalent geometry : angle 0.56537 (15096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 285 MET cc_start: 0.6740 (tmm) cc_final: 0.6194 (tmm) REVERT: D 329 MET cc_start: 0.8819 (mtp) cc_final: 0.8612 (ptp) REVERT: E 51 MET cc_start: 0.7980 (pmm) cc_final: 0.7437 (pmm) REVERT: E 316 THR cc_start: 0.9176 (m) cc_final: 0.8818 (m) REVERT: E 324 ILE cc_start: 0.7844 (pt) cc_final: 0.6952 (pt) REVERT: B 64 MET cc_start: 0.3803 (mtt) cc_final: 0.3445 (mtt) REVERT: B 241 PHE cc_start: 0.8186 (t80) cc_final: 0.7815 (t80) REVERT: B 259 LEU cc_start: 0.8192 (tp) cc_final: 0.7871 (tp) REVERT: B 289 LYS cc_start: 0.8625 (tttm) cc_final: 0.8263 (tptt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2557 time to fit residues: 36.4762 Evaluate side-chains 75 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 97 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 127 optimal weight: 0.0670 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN E 353 GLN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN B 281 HIS B 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.061861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.044315 restraints weight = 100824.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.045133 restraints weight = 77988.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.046009 restraints weight = 65525.546| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.8151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 11154 Z= 0.244 Angle : 0.782 9.848 15096 Z= 0.414 Chirality : 0.047 0.348 1596 Planarity : 0.006 0.054 1946 Dihedral : 6.985 59.422 1580 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.22), residues: 1324 helix: -0.31 (0.21), residues: 547 sheet: -1.01 (0.39), residues: 170 loop : -0.91 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 312 HIS 0.010 0.002 HIS A 202 PHE 0.030 0.003 PHE B 337 TYR 0.022 0.003 TYR E 72 ARG 0.007 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.05083 ( 426) hydrogen bonds : angle 5.43288 ( 1218) metal coordination : bond 0.00383 ( 2) covalent geometry : bond 0.00499 (11152) covalent geometry : angle 0.78247 (15096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 285 MET cc_start: 0.7022 (tmm) cc_final: 0.6746 (tmm) REVERT: D 329 MET cc_start: 0.9152 (mtp) cc_final: 0.8769 (ptp) REVERT: A 329 MET cc_start: 0.9060 (mpp) cc_final: 0.8785 (mpp) REVERT: E 51 MET cc_start: 0.8448 (pmm) cc_final: 0.7860 (pmm) REVERT: E 140 HIS cc_start: 0.7386 (p90) cc_final: 0.7015 (p90) REVERT: B 64 MET cc_start: 0.5286 (mtt) cc_final: 0.4954 (mtt) REVERT: B 91 MET cc_start: 0.3233 (tpp) cc_final: 0.2940 (tpp) REVERT: B 237 TYR cc_start: 0.8923 (t80) cc_final: 0.8485 (t80) REVERT: B 289 LYS cc_start: 0.8746 (tttm) cc_final: 0.8421 (tptt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2342 time to fit residues: 26.8819 Evaluate side-chains 59 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 191 GLN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS E 225 ASN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.058666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.041716 restraints weight = 107413.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.042717 restraints weight = 81253.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.043465 restraints weight = 66169.910| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.9650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11154 Z= 0.202 Angle : 0.697 7.928 15096 Z= 0.369 Chirality : 0.044 0.237 1596 Planarity : 0.005 0.040 1946 Dihedral : 7.022 59.099 1580 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 0.09 % Allowed : 2.87 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.14 (0.22), residues: 1324 helix: -0.05 (0.22), residues: 537 sheet: -1.05 (0.41), residues: 160 loop : -1.24 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 288 HIS 0.010 0.002 HIS E 33 PHE 0.017 0.002 PHE E 150 TYR 0.034 0.002 TYR E 45 ARG 0.010 0.001 ARG D 282 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 426) hydrogen bonds : angle 5.17172 ( 1218) metal coordination : bond 0.00442 ( 2) covalent geometry : bond 0.00415 (11152) covalent geometry : angle 0.69700 (15096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 285 MET cc_start: 0.6711 (tmm) cc_final: 0.6327 (tmm) REVERT: D 329 MET cc_start: 0.8930 (mtp) cc_final: 0.8684 (ptt) REVERT: B 64 MET cc_start: 0.6345 (mtt) cc_final: 0.5943 (mtt) REVERT: B 278 ILE cc_start: 0.9304 (mt) cc_final: 0.9004 (tt) REVERT: B 289 LYS cc_start: 0.8963 (tttm) cc_final: 0.8672 (tptt) outliers start: 1 outliers final: 1 residues processed: 71 average time/residue: 0.2107 time to fit residues: 22.7591 Evaluate side-chains 59 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 50.0000 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.059157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.041843 restraints weight = 107220.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.042979 restraints weight = 79596.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.043761 restraints weight = 63705.806| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.9957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11154 Z= 0.136 Angle : 0.590 8.532 15096 Z= 0.313 Chirality : 0.041 0.205 1596 Planarity : 0.004 0.040 1946 Dihedral : 6.559 57.463 1580 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.22), residues: 1324 helix: 0.33 (0.22), residues: 553 sheet: -1.02 (0.41), residues: 160 loop : -1.19 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 330 HIS 0.006 0.001 HIS E 39 PHE 0.014 0.001 PHE A 213 TYR 0.018 0.002 TYR E 45 ARG 0.004 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 426) hydrogen bonds : angle 4.94810 ( 1218) metal coordination : bond 0.00170 ( 2) covalent geometry : bond 0.00285 (11152) covalent geometry : angle 0.58978 (15096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 285 MET cc_start: 0.6724 (tmm) cc_final: 0.6377 (tmm) REVERT: D 329 MET cc_start: 0.8978 (mtp) cc_final: 0.8743 (ptt) REVERT: E 350 MET cc_start: 0.5736 (ppp) cc_final: 0.5481 (ppp) REVERT: B 64 MET cc_start: 0.6361 (mtt) cc_final: 0.5868 (mtt) REVERT: B 237 TYR cc_start: 0.9110 (t80) cc_final: 0.8809 (t80) REVERT: B 278 ILE cc_start: 0.9279 (mt) cc_final: 0.9008 (tt) REVERT: B 289 LYS cc_start: 0.8991 (tttm) cc_final: 0.8703 (tptt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2208 time to fit residues: 23.1053 Evaluate side-chains 58 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 102 GLN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.052886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.037339 restraints weight = 119207.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.038262 restraints weight = 87990.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.038896 restraints weight = 71244.274| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 1.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 11154 Z= 0.349 Angle : 0.938 15.313 15096 Z= 0.504 Chirality : 0.051 0.220 1596 Planarity : 0.007 0.064 1946 Dihedral : 7.971 54.685 1580 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 32.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.23 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -2.05 (0.21), residues: 1324 helix: -0.87 (0.21), residues: 525 sheet: -1.24 (0.45), residues: 137 loop : -1.75 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP B 135 HIS 0.013 0.003 HIS E 199 PHE 0.023 0.003 PHE B 75 TYR 0.029 0.004 TYR A 328 ARG 0.016 0.001 ARG B 229 Details of bonding type rmsd hydrogen bonds : bond 0.06221 ( 426) hydrogen bonds : angle 6.16834 ( 1218) metal coordination : bond 0.00500 ( 2) covalent geometry : bond 0.00704 (11152) covalent geometry : angle 0.93755 (15096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 240 MET cc_start: 0.7030 (ttt) cc_final: 0.6703 (ptp) REVERT: A 329 MET cc_start: 0.9443 (mmp) cc_final: 0.9242 (mmm) REVERT: E 350 MET cc_start: 0.6883 (ppp) cc_final: 0.6678 (ppp) REVERT: B 64 MET cc_start: 0.7179 (mtt) cc_final: 0.6610 (mtt) REVERT: B 91 MET cc_start: 0.3928 (tpp) cc_final: 0.3479 (tpt) REVERT: B 289 LYS cc_start: 0.9138 (tttm) cc_final: 0.8775 (tptt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2159 time to fit residues: 20.4065 Evaluate side-chains 49 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 30.0000 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 26 GLN E 68 HIS E 225 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** 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 = 0.4102 r_free = 0.4102 target = 0.056503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.039759 restraints weight = 109154.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.040856 restraints weight = 79206.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.041563 restraints weight = 63170.822| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 1.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11154 Z= 0.130 Angle : 0.635 8.460 15096 Z= 0.333 Chirality : 0.043 0.176 1596 Planarity : 0.004 0.040 1946 Dihedral : 6.999 54.474 1580 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.23 (0.22), residues: 1324 helix: 0.18 (0.23), residues: 526 sheet: -1.50 (0.40), residues: 163 loop : -1.45 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 199 HIS 0.004 0.001 HIS E 33 PHE 0.026 0.002 PHE E 150 TYR 0.025 0.002 TYR E 45 ARG 0.006 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 426) hydrogen bonds : angle 5.33396 ( 1218) metal coordination : bond 0.00129 ( 2) covalent geometry : bond 0.00279 (11152) covalent geometry : angle 0.63477 (15096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: D 240 MET cc_start: 0.6829 (ttt) cc_final: 0.6585 (ptp) REVERT: D 329 MET cc_start: 0.9372 (tpp) cc_final: 0.9093 (ptp) REVERT: B 37 MET cc_start: 0.8296 (mmm) cc_final: 0.7271 (mmm) REVERT: B 64 MET cc_start: 0.7335 (mtt) cc_final: 0.6836 (mtt) REVERT: B 187 PHE cc_start: 0.6214 (m-80) cc_final: 0.5597 (m-80) REVERT: B 278 ILE cc_start: 0.9219 (mt) cc_final: 0.8931 (tt) REVERT: B 289 LYS cc_start: 0.9077 (tttm) cc_final: 0.8776 (tptt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2259 time to fit residues: 21.5767 Evaluate side-chains 54 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 2 optimal weight: 0.0370 chunk 119 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 86 optimal weight: 30.0000 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 HIS ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.055616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.039038 restraints weight = 111648.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.039895 restraints weight = 81834.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.040883 restraints weight = 66286.546| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 1.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11154 Z= 0.141 Angle : 0.619 8.199 15096 Z= 0.329 Chirality : 0.042 0.175 1596 Planarity : 0.004 0.042 1946 Dihedral : 6.736 51.313 1580 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.08 (0.23), residues: 1324 helix: 0.30 (0.23), residues: 539 sheet: -1.48 (0.40), residues: 163 loop : -1.37 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 330 HIS 0.005 0.001 HIS E 39 PHE 0.021 0.002 PHE B 367 TYR 0.023 0.002 TYR E 45 ARG 0.003 0.001 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 426) hydrogen bonds : angle 5.18429 ( 1218) metal coordination : bond 0.00199 ( 2) covalent geometry : bond 0.00297 (11152) covalent geometry : angle 0.61909 (15096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: D 329 MET cc_start: 0.9428 (tpp) cc_final: 0.9102 (ptp) REVERT: B 37 MET cc_start: 0.8293 (mmm) cc_final: 0.7235 (mmm) REVERT: B 64 MET cc_start: 0.7457 (mtt) cc_final: 0.6975 (mtt) REVERT: B 278 ILE cc_start: 0.9184 (mt) cc_final: 0.8882 (tt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2014 time to fit residues: 18.1180 Evaluate side-chains 50 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 81 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 HIS E 364 GLN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS ** B 141 HIS ** 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 = 0.4087 r_free = 0.4087 target = 0.055790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.039203 restraints weight = 110217.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.040060 restraints weight = 81206.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.041040 restraints weight = 65883.972| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 1.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11154 Z= 0.131 Angle : 0.591 8.363 15096 Z= 0.312 Chirality : 0.041 0.182 1596 Planarity : 0.004 0.045 1946 Dihedral : 6.554 50.535 1580 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.87 (0.23), residues: 1324 helix: 0.52 (0.23), residues: 541 sheet: -1.39 (0.40), residues: 163 loop : -1.29 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 199 HIS 0.005 0.001 HIS E 199 PHE 0.015 0.001 PHE B 367 TYR 0.020 0.002 TYR E 45 ARG 0.004 0.000 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 426) hydrogen bonds : angle 5.05738 ( 1218) metal coordination : bond 0.00165 ( 2) covalent geometry : bond 0.00277 (11152) covalent geometry : angle 0.59087 (15096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: D 329 MET cc_start: 0.9438 (tpp) cc_final: 0.9119 (ptp) REVERT: E 350 MET cc_start: 0.6093 (ppp) cc_final: 0.5785 (ppp) REVERT: B 37 MET cc_start: 0.8312 (mmm) cc_final: 0.7257 (mmm) REVERT: B 64 MET cc_start: 0.7414 (mtt) cc_final: 0.7019 (mtt) REVERT: B 278 ILE cc_start: 0.9151 (mt) cc_final: 0.8871 (tt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1948 time to fit residues: 17.8410 Evaluate side-chains 51 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.053673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.037926 restraints weight = 113747.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.038921 restraints weight = 84513.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.039680 restraints weight = 68185.089| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 1.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11154 Z= 0.202 Angle : 0.690 9.417 15096 Z= 0.367 Chirality : 0.044 0.169 1596 Planarity : 0.005 0.043 1946 Dihedral : 7.011 52.404 1580 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.19 (0.22), residues: 1324 helix: 0.08 (0.22), residues: 542 sheet: -1.40 (0.42), residues: 147 loop : -1.36 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 135 HIS 0.007 0.002 HIS E 199 PHE 0.022 0.002 PHE E 252 TYR 0.025 0.002 TYR E 45 ARG 0.006 0.001 ARG E 192 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 426) hydrogen bonds : angle 5.47891 ( 1218) metal coordination : bond 0.00233 ( 2) covalent geometry : bond 0.00415 (11152) covalent geometry : angle 0.68966 (15096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4106.77 seconds wall clock time: 73 minutes 52.74 seconds (4432.74 seconds total)