Starting phenix.real_space_refine on Sun Jan 19 00:18:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yx6_39648/01_2025/8yx6_39648.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yx6_39648/01_2025/8yx6_39648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yx6_39648/01_2025/8yx6_39648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yx6_39648/01_2025/8yx6_39648.map" model { file = "/net/cci-nas-00/data/ceres_data/8yx6_39648/01_2025/8yx6_39648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yx6_39648/01_2025/8yx6_39648.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 55 5.16 5 C 8485 2.51 5 N 2190 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13080 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' ZN': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: F, I, H, J, C, B, E, D Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" C1 NAG F 2 " occ=0.63 ... (12 atoms not shown) pdb=" O7 NAG F 2 " occ=0.63 residue: pdb=" C1 NAG G 2 " occ=0.63 ... (12 atoms not shown) pdb=" O7 NAG G 2 " occ=0.63 residue: pdb=" C1 NAG H 2 " occ=0.63 ... (12 atoms not shown) pdb=" O7 NAG H 2 " occ=0.63 residue: pdb=" C1 NAG I 2 " occ=0.63 ... (12 atoms not shown) pdb=" O7 NAG I 2 " occ=0.63 residue: pdb=" C1 NAG J 2 " occ=0.63 ... (12 atoms not shown) pdb=" O7 NAG J 2 " occ=0.63 Time building chain proxies: 5.75, per 1000 atoms: 0.44 Number of scatterers: 13080 At special positions: 0 Unit cell: (93, 92.07, 121.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 10 29.99 S 55 16.00 O 2340 8.00 N 2190 7.00 C 8485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 394 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 501 " - " ASN A 170 " " NAG B 501 " - " ASN B 170 " " NAG C 501 " - " ASN C 170 " " NAG D 501 " - " ASN D 170 " " NAG E 501 " - " ASN E 170 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN B 55 " " NAG H 1 " - " ASN C 55 " " NAG I 1 " - " ASN D 55 " " NAG J 1 " - " ASN E 55 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 163 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 168 " pdb=" ZN A 503 " pdb="ZN ZN A 503 " - pdb=" ND1 HIS A 144 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 163 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 168 " pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" ND1 HIS B 144 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 163 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 168 " pdb=" ZN C 503 " pdb="ZN ZN C 503 " - pdb=" ND1 HIS C 144 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 163 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 168 " pdb=" ZN D 503 " pdb="ZN ZN D 503 " - pdb=" ND1 HIS D 144 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 163 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 168 " pdb=" ZN E 503 " pdb="ZN ZN E 503 " - pdb=" ND1 HIS E 144 " 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 39.5% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.524A pdb=" N ILE A 50 " --> pdb=" O GLN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 160 through 164 removed outlier: 4.384A pdb=" N HIS A 163 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.516A pdb=" N VAL A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 258 through 282 removed outlier: 4.246A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 320 removed outlier: 4.066A pdb=" N TYR A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 391 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.524A pdb=" N ILE B 50 " --> pdb=" O GLN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 160 through 164 removed outlier: 4.384A pdb=" N HIS B 163 " --> pdb=" O GLU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.516A pdb=" N VAL B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 258 through 282 removed outlier: 4.246A pdb=" N ILE B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 320 removed outlier: 4.066A pdb=" N TYR B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 391 Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.524A pdb=" N ILE C 50 " --> pdb=" O GLN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 160 through 164 removed outlier: 4.384A pdb=" N HIS C 163 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.516A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 258 through 282 removed outlier: 4.246A pdb=" N ILE C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 320 removed outlier: 4.065A pdb=" N TYR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 391 Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.523A pdb=" N ILE D 50 " --> pdb=" O GLN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 160 through 164 removed outlier: 4.384A pdb=" N HIS D 163 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 252 removed outlier: 4.516A pdb=" N VAL D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 258 through 282 removed outlier: 4.246A pdb=" N ILE D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 320 removed outlier: 4.066A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 391 Processing helix chain 'D' and resid 399 through 404 Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.524A pdb=" N ILE E 50 " --> pdb=" O GLN E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 160 through 164 removed outlier: 4.384A pdb=" N HIS E 163 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 252 removed outlier: 4.515A pdb=" N VAL E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 258 through 282 removed outlier: 4.246A pdb=" N ILE E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 320 removed outlier: 4.066A pdb=" N TYR E 295 " --> pdb=" O PRO E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 391 Processing helix chain 'E' and resid 399 through 404 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA A 150 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP A 130 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA A 152 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL A 128 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A 154 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN A 73 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET A 84 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL A 71 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU A 86 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER A 69 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG A 88 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE A 67 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER A 90 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ARG A 65 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU A 92 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N ASP A 63 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 removed outlier: 6.751A pdb=" N GLN A 221 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR A 209 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A 223 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A 207 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG A 225 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA B 150 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP B 130 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 152 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL B 128 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU B 154 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN B 73 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET B 84 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL B 71 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU B 86 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER B 69 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG B 88 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE B 67 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER B 90 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG B 65 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU B 92 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N ASP B 63 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 122 removed outlier: 6.751A pdb=" N GLN B 221 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B 209 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR B 223 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 207 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG B 225 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA C 150 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP C 130 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA C 152 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL C 128 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU C 154 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN C 73 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET C 84 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL C 71 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU C 86 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER C 69 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG C 88 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE C 67 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER C 90 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG C 65 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU C 92 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N ASP C 63 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.751A pdb=" N GLN C 221 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR C 209 " --> pdb=" O GLN C 221 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR C 223 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU C 207 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG C 225 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA D 150 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TRP D 130 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA D 152 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL D 128 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU D 154 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 73 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET D 84 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL D 71 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU D 86 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER D 69 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG D 88 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE D 67 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER D 90 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG D 65 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU D 92 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N ASP D 63 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 121 through 122 removed outlier: 6.751A pdb=" N GLN D 221 " --> pdb=" O THR D 209 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR D 209 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR D 223 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU D 207 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG D 225 " --> pdb=" O TYR D 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA E 150 " --> pdb=" O TRP E 130 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP E 130 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA E 152 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL E 128 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU E 154 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN E 73 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET E 84 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL E 71 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU E 86 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER E 69 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG E 88 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE E 67 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N SER E 90 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG E 65 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU E 92 " --> pdb=" O ASP E 63 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N ASP E 63 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 121 through 122 removed outlier: 6.751A pdb=" N GLN E 221 " --> pdb=" O THR E 209 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR E 209 " --> pdb=" O GLN E 221 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR E 223 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU E 207 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG E 225 " --> pdb=" O TYR E 205 " (cutoff:3.500A) 705 hydrogen bonds defined for protein. 2040 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: 4.77 Time building geometry restraints manager: 3.62 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: 2020 1.31 - 1.44: 3605 1.44 - 1.56: 7685 1.56 - 1.69: 0 1.69 - 1.82: 75 Bond restraints: 13385 Sorted by residual: bond pdb=" C7 NAG C 501 " pdb=" N2 NAG C 501 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C7 NAG G 2 " pdb=" N2 NAG G 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C7 NAG F 2 " pdb=" N2 NAG F 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C7 NAG H 2 " pdb=" N2 NAG H 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01 ... (remaining 13380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 17764 1.19 - 2.39: 306 2.39 - 3.58: 161 3.58 - 4.77: 29 4.77 - 5.96: 45 Bond angle restraints: 18305 Sorted by residual: angle pdb=" C4 NAG J 2 " pdb=" C5 NAG J 2 " pdb=" C6 NAG J 2 " ideal model delta sigma weight residual 113.89 108.73 5.16 3.00e+00 1.11e-01 2.96e+00 angle pdb=" C4 NAG G 2 " pdb=" C5 NAG G 2 " pdb=" C6 NAG G 2 " ideal model delta sigma weight residual 113.89 108.75 5.14 3.00e+00 1.11e-01 2.93e+00 angle pdb=" C4 NAG I 2 " pdb=" C5 NAG I 2 " pdb=" C6 NAG I 2 " ideal model delta sigma weight residual 113.89 108.75 5.14 3.00e+00 1.11e-01 2.93e+00 angle pdb=" C4 NAG F 2 " pdb=" C5 NAG F 2 " pdb=" C6 NAG F 2 " ideal model delta sigma weight residual 113.89 108.76 5.13 3.00e+00 1.11e-01 2.93e+00 angle pdb=" C4 NAG H 2 " pdb=" C5 NAG H 2 " pdb=" C6 NAG H 2 " ideal model delta sigma weight residual 113.89 108.77 5.12 3.00e+00 1.11e-01 2.92e+00 ... (remaining 18300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.72: 7354 8.72 - 17.43: 518 17.43 - 26.15: 171 26.15 - 34.86: 88 34.86 - 43.58: 25 Dihedral angle restraints: 8156 sinusoidal: 3361 harmonic: 4795 Sorted by residual: dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 394 " pdb=" CB CYS A 394 " ideal model delta sinusoidal sigma weight residual -86.00 -114.87 28.87 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" N PHE A 72 " pdb=" CA PHE A 72 " ideal model delta harmonic sigma weight residual -180.00 -166.52 -13.48 0 5.00e+00 4.00e-02 7.26e+00 dihedral pdb=" CA VAL C 71 " pdb=" C VAL C 71 " pdb=" N PHE C 72 " pdb=" CA PHE C 72 " ideal model delta harmonic sigma weight residual -180.00 -166.55 -13.45 0 5.00e+00 4.00e-02 7.24e+00 ... (remaining 8153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1417 0.029 - 0.058: 569 0.058 - 0.087: 116 0.087 - 0.115: 85 0.115 - 0.144: 48 Chirality restraints: 2235 Sorted by residual: chirality pdb=" C5 NAG A 501 " pdb=" C4 NAG A 501 " pdb=" C6 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.41 -2.55 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C5 NAG E 501 " pdb=" C4 NAG E 501 " pdb=" C6 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.41 -2.55 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" C5 NAG B 501 " pdb=" C4 NAG B 501 " pdb=" C6 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.41 -2.55 0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 2232 not shown) Planarity restraints: 2260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 283 " 0.014 5.00e-02 4.00e+02 2.14e-02 7.33e-01 pdb=" N PRO B 284 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 283 " -0.014 5.00e-02 4.00e+02 2.14e-02 7.29e-01 pdb=" N PRO D 284 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO D 284 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO D 284 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 283 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.26e-01 pdb=" N PRO C 284 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 284 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 284 " 0.012 5.00e-02 4.00e+02 ... (remaining 2257 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 118 2.55 - 3.14: 9971 3.14 - 3.73: 20530 3.73 - 4.31: 28467 4.31 - 4.90: 48927 Nonbonded interactions: 108013 Sorted by model distance: nonbonded pdb=" OD1 ASP A 142 " pdb=" ND1 HIS A 144 " model vdw 1.968 3.120 nonbonded pdb=" OD1 ASP D 142 " pdb=" ND1 HIS D 144 " model vdw 1.968 3.120 nonbonded pdb=" OD1 ASP E 142 " pdb=" ND1 HIS E 144 " model vdw 1.968 3.120 nonbonded pdb=" OD1 ASP B 142 " pdb=" ND1 HIS B 144 " model vdw 1.968 3.120 nonbonded pdb=" OD1 ASP C 142 " pdb=" ND1 HIS C 144 " model vdw 1.968 3.120 ... (remaining 108008 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: 0.09 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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=0.63 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.670 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 13385 Z= 0.410 Angle : 0.552 5.963 18305 Z= 0.250 Chirality : 0.040 0.144 2235 Planarity : 0.003 0.021 2250 Dihedral : 8.161 43.577 5010 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.41 (0.22), residues: 1600 helix: 3.29 (0.20), residues: 530 sheet: 1.37 (0.25), residues: 450 loop : 0.29 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 112 HIS 0.001 0.000 HIS D 190 PHE 0.008 0.001 PHE E 220 TYR 0.009 0.001 TYR B 272 ARG 0.001 0.000 ARG E 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8018 (t0) cc_final: 0.7274 (t0) REVERT: A 77 LEU cc_start: 0.9366 (mt) cc_final: 0.9136 (mm) REVERT: A 146 LYS cc_start: 0.8427 (mttt) cc_final: 0.8101 (mttp) REVERT: A 364 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7995 (mt-10) REVERT: B 75 ASP cc_start: 0.7961 (t0) cc_final: 0.7302 (t0) REVERT: B 78 ARG cc_start: 0.8735 (mtp180) cc_final: 0.8514 (mtm110) REVERT: B 124 GLU cc_start: 0.8556 (mp0) cc_final: 0.8277 (mp0) REVERT: B 146 LYS cc_start: 0.8405 (mttt) cc_final: 0.8129 (mtmm) REVERT: B 223 THR cc_start: 0.8877 (m) cc_final: 0.8658 (p) REVERT: B 232 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8632 (ttmt) REVERT: B 272 TYR cc_start: 0.8592 (t80) cc_final: 0.8343 (t80) REVERT: B 390 MET cc_start: 0.8050 (mmm) cc_final: 0.7797 (mmt) REVERT: C 75 ASP cc_start: 0.7891 (t0) cc_final: 0.7390 (t0) REVERT: C 124 GLU cc_start: 0.8620 (mp0) cc_final: 0.8385 (mp0) REVERT: C 146 LYS cc_start: 0.8475 (mttt) cc_final: 0.8223 (mtmm) REVERT: C 223 THR cc_start: 0.8891 (m) cc_final: 0.8624 (p) REVERT: C 306 LEU cc_start: 0.8836 (tp) cc_final: 0.8589 (tp) REVERT: D 75 ASP cc_start: 0.8063 (t0) cc_final: 0.7402 (t0) REVERT: D 129 ASP cc_start: 0.8421 (t0) cc_final: 0.8191 (t0) REVERT: D 146 LYS cc_start: 0.8507 (mttt) cc_final: 0.8254 (mttp) REVERT: D 176 TYR cc_start: 0.8695 (m-80) cc_final: 0.8405 (m-80) REVERT: D 223 THR cc_start: 0.8900 (m) cc_final: 0.8653 (p) REVERT: D 246 LEU cc_start: 0.8897 (tp) cc_final: 0.8681 (tp) REVERT: D 272 TYR cc_start: 0.8604 (t80) cc_final: 0.8250 (t80) REVERT: E 75 ASP cc_start: 0.7959 (t0) cc_final: 0.7318 (t0) REVERT: E 78 ARG cc_start: 0.8782 (mtp180) cc_final: 0.8460 (mtp85) REVERT: E 146 LYS cc_start: 0.8554 (mttt) cc_final: 0.8234 (mttp) REVERT: E 206 ASP cc_start: 0.7832 (t0) cc_final: 0.7594 (t0) outliers start: 0 outliers final: 1 residues processed: 403 average time/residue: 1.2220 time to fit residues: 538.3373 Evaluate side-chains 242 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 215 GLN B 215 GLN C 210 GLN C 214 GLN C 215 GLN C 290 ASN D 210 GLN D 215 GLN E 214 GLN E 215 GLN E 221 GLN E 382 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.084001 restraints weight = 18231.184| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.68 r_work: 0.2893 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13385 Z= 0.247 Angle : 0.552 9.258 18305 Z= 0.277 Chirality : 0.040 0.141 2235 Planarity : 0.004 0.031 2250 Dihedral : 4.583 33.877 2062 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.31 % Allowed : 13.01 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.28 (0.22), residues: 1600 helix: 3.31 (0.20), residues: 530 sheet: 0.96 (0.24), residues: 450 loop : 0.40 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 112 HIS 0.002 0.001 HIS A 144 PHE 0.012 0.002 PHE B 385 TYR 0.021 0.002 TYR B 176 ARG 0.007 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 291 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8190 (t0) cc_final: 0.7685 (t0) REVERT: A 77 LEU cc_start: 0.9243 (mt) cc_final: 0.9022 (mm) REVERT: A 112 TRP cc_start: 0.8519 (OUTLIER) cc_final: 0.8103 (t-100) REVERT: A 124 GLU cc_start: 0.8754 (mp0) cc_final: 0.8430 (mp0) REVERT: A 136 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.8853 (mt0) REVERT: A 146 LYS cc_start: 0.8474 (mttt) cc_final: 0.8173 (mtmm) REVERT: A 160 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7141 (tm-30) REVERT: A 201 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7671 (mp0) REVERT: A 223 THR cc_start: 0.8953 (m) cc_final: 0.8724 (p) REVERT: A 272 TYR cc_start: 0.8558 (t80) cc_final: 0.8114 (t80) REVERT: A 364 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8194 (mt-10) REVERT: B 75 ASP cc_start: 0.7877 (t0) cc_final: 0.7063 (t0) REVERT: B 78 ARG cc_start: 0.8921 (mtp180) cc_final: 0.8560 (mtp-110) REVERT: B 112 TRP cc_start: 0.8539 (OUTLIER) cc_final: 0.8157 (t-100) REVERT: B 124 GLU cc_start: 0.8810 (mp0) cc_final: 0.8590 (mp0) REVERT: B 146 LYS cc_start: 0.8491 (mttt) cc_final: 0.8153 (mtmm) REVERT: B 160 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7021 (tm-30) REVERT: B 201 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7849 (mp0) REVERT: B 272 TYR cc_start: 0.8755 (t80) cc_final: 0.8397 (t80) REVERT: B 390 MET cc_start: 0.8537 (mmm) cc_final: 0.8079 (mmt) REVERT: C 75 ASP cc_start: 0.8086 (t0) cc_final: 0.7418 (t0) REVERT: C 112 TRP cc_start: 0.8453 (OUTLIER) cc_final: 0.8018 (t-100) REVERT: C 146 LYS cc_start: 0.8413 (mttt) cc_final: 0.8085 (mtmm) REVERT: C 201 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7756 (mp0) REVERT: C 227 LYS cc_start: 0.8159 (ptpt) cc_final: 0.7615 (tttm) REVERT: C 306 LEU cc_start: 0.8673 (tp) cc_final: 0.8426 (tp) REVERT: D 75 ASP cc_start: 0.8138 (t0) cc_final: 0.7615 (t0) REVERT: D 129 ASP cc_start: 0.8719 (t0) cc_final: 0.8320 (t0) REVERT: D 146 LYS cc_start: 0.8538 (mttt) cc_final: 0.8265 (mttp) REVERT: D 201 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7699 (mp0) REVERT: D 223 THR cc_start: 0.8915 (m) cc_final: 0.8644 (p) REVERT: D 246 LEU cc_start: 0.8662 (tp) cc_final: 0.8457 (tp) REVERT: D 272 TYR cc_start: 0.8742 (t80) cc_final: 0.8165 (t80) REVERT: D 297 PHE cc_start: 0.8945 (m-80) cc_final: 0.8497 (m-80) REVERT: E 75 ASP cc_start: 0.7933 (t0) cc_final: 0.7154 (t0) REVERT: E 78 ARG cc_start: 0.8983 (mtp180) cc_final: 0.8460 (mtp85) REVERT: E 146 LYS cc_start: 0.8536 (mttt) cc_final: 0.8132 (mttp) REVERT: E 201 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7751 (mp0) REVERT: E 206 ASP cc_start: 0.8043 (t0) cc_final: 0.7638 (t0) REVERT: E 227 LYS cc_start: 0.8177 (ttpt) cc_final: 0.7249 (ttmm) outliers start: 33 outliers final: 6 residues processed: 310 average time/residue: 1.0441 time to fit residues: 358.7364 Evaluate side-chains 279 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 269 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 384 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 102 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 123 optimal weight: 0.0060 chunk 112 optimal weight: 3.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN C 214 GLN D 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.085866 restraints weight = 18592.284| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.74 r_work: 0.2905 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13385 Z= 0.176 Angle : 0.518 10.188 18305 Z= 0.258 Chirality : 0.040 0.137 2235 Planarity : 0.003 0.025 2250 Dihedral : 4.103 18.908 2060 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.54 % Allowed : 16.43 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.27 (0.22), residues: 1600 helix: 3.54 (0.20), residues: 500 sheet: 0.91 (0.24), residues: 440 loop : 0.37 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.001 0.000 HIS C 276 PHE 0.013 0.001 PHE B 385 TYR 0.028 0.002 TYR B 176 ARG 0.004 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 1.452 Fit side-chains REVERT: A 75 ASP cc_start: 0.8044 (t0) cc_final: 0.7453 (t0) REVERT: A 77 LEU cc_start: 0.9178 (mt) cc_final: 0.8887 (mm) REVERT: A 136 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8844 (mt0) REVERT: A 146 LYS cc_start: 0.8361 (mttt) cc_final: 0.7941 (mttp) REVERT: A 160 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6807 (tm-30) REVERT: A 201 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7599 (mp0) REVERT: A 223 THR cc_start: 0.8828 (m) cc_final: 0.8577 (p) REVERT: A 260 GLU cc_start: 0.8505 (pt0) cc_final: 0.8246 (mt-10) REVERT: A 272 TYR cc_start: 0.8513 (t80) cc_final: 0.8146 (t80) REVERT: A 364 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8130 (mt-10) REVERT: B 75 ASP cc_start: 0.7631 (t0) cc_final: 0.6809 (t0) REVERT: B 78 ARG cc_start: 0.8870 (mtp180) cc_final: 0.8507 (mtp-110) REVERT: B 146 LYS cc_start: 0.8347 (mttt) cc_final: 0.7995 (mtmm) REVERT: B 201 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7746 (mp0) REVERT: B 206 ASP cc_start: 0.7949 (t0) cc_final: 0.7730 (t0) REVERT: B 260 GLU cc_start: 0.8713 (pt0) cc_final: 0.8445 (mt-10) REVERT: B 272 TYR cc_start: 0.8649 (t80) cc_final: 0.8348 (t80) REVERT: B 390 MET cc_start: 0.8518 (mmm) cc_final: 0.8054 (mmt) REVERT: C 75 ASP cc_start: 0.7911 (t0) cc_final: 0.7210 (t0) REVERT: C 112 TRP cc_start: 0.8371 (OUTLIER) cc_final: 0.7927 (t-100) REVERT: C 146 LYS cc_start: 0.8278 (mttt) cc_final: 0.7941 (mtmm) REVERT: C 201 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7685 (mp0) REVERT: C 227 LYS cc_start: 0.7987 (ptpt) cc_final: 0.7463 (tttm) REVERT: C 306 LEU cc_start: 0.8530 (tp) cc_final: 0.8295 (tp) REVERT: D 75 ASP cc_start: 0.8000 (t0) cc_final: 0.7517 (t0) REVERT: D 90 SER cc_start: 0.8780 (m) cc_final: 0.8493 (t) REVERT: D 129 ASP cc_start: 0.8683 (t0) cc_final: 0.8286 (t0) REVERT: D 141 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8634 (pm20) REVERT: D 146 LYS cc_start: 0.8412 (mttt) cc_final: 0.8189 (mttp) REVERT: D 201 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7676 (mp0) REVERT: D 272 TYR cc_start: 0.8628 (t80) cc_final: 0.8014 (t80) REVERT: D 280 VAL cc_start: 0.8542 (t) cc_final: 0.8226 (m) REVERT: D 297 PHE cc_start: 0.8809 (m-80) cc_final: 0.8356 (m-80) REVERT: E 75 ASP cc_start: 0.7764 (t0) cc_final: 0.6955 (t0) REVERT: E 78 ARG cc_start: 0.8957 (mtp180) cc_final: 0.8427 (mtp85) REVERT: E 81 MET cc_start: 0.8692 (ttp) cc_final: 0.8474 (ttp) REVERT: E 141 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8600 (pm20) REVERT: E 146 LYS cc_start: 0.8396 (mttt) cc_final: 0.8002 (mttp) REVERT: E 201 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7618 (mp0) REVERT: E 206 ASP cc_start: 0.8064 (t0) cc_final: 0.7645 (t0) REVERT: E 227 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7097 (ttmm) outliers start: 22 outliers final: 3 residues processed: 283 average time/residue: 0.9752 time to fit residues: 308.3316 Evaluate side-chains 247 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 240 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 259 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 113 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN C 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.081992 restraints weight = 18970.137| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.74 r_work: 0.2848 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13385 Z= 0.350 Angle : 0.566 9.784 18305 Z= 0.283 Chirality : 0.042 0.140 2235 Planarity : 0.003 0.024 2250 Dihedral : 4.039 17.894 2060 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.24 % Allowed : 16.78 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.09 (0.21), residues: 1600 helix: 3.31 (0.20), residues: 500 sheet: 0.75 (0.24), residues: 450 loop : 0.37 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 112 HIS 0.003 0.001 HIS D 168 PHE 0.016 0.002 PHE A 72 TYR 0.028 0.002 TYR B 176 ARG 0.003 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 1.387 Fit side-chains REVERT: A 75 ASP cc_start: 0.8054 (t0) cc_final: 0.7503 (t0) REVERT: A 77 LEU cc_start: 0.9223 (mt) cc_final: 0.8969 (mm) REVERT: A 112 TRP cc_start: 0.8536 (OUTLIER) cc_final: 0.7655 (t-100) REVERT: A 146 LYS cc_start: 0.8346 (mttt) cc_final: 0.8084 (mttp) REVERT: A 160 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6881 (tm-30) REVERT: A 201 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7593 (mp0) REVERT: A 214 GLN cc_start: 0.8551 (mm-40) cc_final: 0.7929 (pp30) REVERT: A 272 TYR cc_start: 0.8568 (t80) cc_final: 0.8114 (t80) REVERT: A 364 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8117 (mt-10) REVERT: B 75 ASP cc_start: 0.7753 (t0) cc_final: 0.6853 (t0) REVERT: B 78 ARG cc_start: 0.8918 (mtp180) cc_final: 0.8494 (mtp-110) REVERT: B 112 TRP cc_start: 0.8457 (OUTLIER) cc_final: 0.7878 (t-100) REVERT: B 146 LYS cc_start: 0.8394 (mttt) cc_final: 0.8058 (mtmp) REVERT: B 201 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7721 (mp0) REVERT: B 206 ASP cc_start: 0.8025 (t0) cc_final: 0.7784 (t0) REVERT: B 260 GLU cc_start: 0.8694 (pt0) cc_final: 0.8454 (mt-10) REVERT: B 390 MET cc_start: 0.8499 (mmm) cc_final: 0.8004 (mmt) REVERT: C 75 ASP cc_start: 0.7932 (t0) cc_final: 0.7139 (t0) REVERT: C 77 LEU cc_start: 0.9208 (mt) cc_final: 0.8977 (mm) REVERT: C 112 TRP cc_start: 0.8633 (OUTLIER) cc_final: 0.8173 (t-100) REVERT: C 146 LYS cc_start: 0.8228 (mttt) cc_final: 0.7791 (mttp) REVERT: C 201 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7711 (mp0) REVERT: C 214 GLN cc_start: 0.8630 (mm-40) cc_final: 0.7742 (pp30) REVERT: C 260 GLU cc_start: 0.8812 (pt0) cc_final: 0.8607 (mt-10) REVERT: C 306 LEU cc_start: 0.8567 (tp) cc_final: 0.8352 (tp) REVERT: D 75 ASP cc_start: 0.8068 (t0) cc_final: 0.7491 (t0) REVERT: D 112 TRP cc_start: 0.8494 (OUTLIER) cc_final: 0.8291 (t-100) REVERT: D 129 ASP cc_start: 0.8570 (t0) cc_final: 0.8153 (t0) REVERT: D 146 LYS cc_start: 0.8391 (mttt) cc_final: 0.8060 (mtmp) REVERT: D 201 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7653 (mp0) REVERT: D 206 ASP cc_start: 0.7905 (t0) cc_final: 0.7660 (t0) REVERT: D 272 TYR cc_start: 0.8666 (t80) cc_final: 0.8051 (t80) REVERT: E 75 ASP cc_start: 0.7846 (t0) cc_final: 0.7068 (t0) REVERT: E 78 ARG cc_start: 0.8986 (mtp180) cc_final: 0.8488 (mtp-110) REVERT: E 81 MET cc_start: 0.8752 (ttp) cc_final: 0.8464 (ttp) REVERT: E 146 LYS cc_start: 0.8343 (mttt) cc_final: 0.7944 (mttp) REVERT: E 201 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7650 (mp0) REVERT: E 206 ASP cc_start: 0.8136 (t0) cc_final: 0.7672 (t0) REVERT: E 280 VAL cc_start: 0.8600 (t) cc_final: 0.8329 (m) outliers start: 32 outliers final: 8 residues processed: 270 average time/residue: 1.0157 time to fit residues: 305.1600 Evaluate side-chains 253 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 241 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 259 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.084371 restraints weight = 19074.399| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.70 r_work: 0.2895 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13385 Z= 0.183 Angle : 0.511 7.863 18305 Z= 0.254 Chirality : 0.040 0.147 2235 Planarity : 0.003 0.022 2250 Dihedral : 3.855 19.236 2060 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.75 % Allowed : 18.25 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.26 (0.22), residues: 1600 helix: 3.34 (0.20), residues: 500 sheet: 0.62 (0.24), residues: 500 loop : 0.79 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.001 0.000 HIS D 168 PHE 0.016 0.001 PHE C 305 TYR 0.029 0.002 TYR B 176 ARG 0.003 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 1.542 Fit side-chains REVERT: A 75 ASP cc_start: 0.8044 (t0) cc_final: 0.7497 (t0) REVERT: A 77 LEU cc_start: 0.9211 (mt) cc_final: 0.8973 (mm) REVERT: A 146 LYS cc_start: 0.8348 (mttt) cc_final: 0.7928 (mttp) REVERT: A 160 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6893 (tm-30) REVERT: A 201 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7558 (mp0) REVERT: A 272 TYR cc_start: 0.8557 (t80) cc_final: 0.8154 (t80) REVERT: A 364 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8190 (mt-10) REVERT: B 75 ASP cc_start: 0.7783 (t0) cc_final: 0.6825 (t0) REVERT: B 78 ARG cc_start: 0.8908 (mtp180) cc_final: 0.8419 (mtp85) REVERT: B 129 ASP cc_start: 0.8583 (t0) cc_final: 0.8143 (t0) REVERT: B 146 LYS cc_start: 0.8404 (mttt) cc_final: 0.8068 (mtmp) REVERT: B 201 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7664 (mp0) REVERT: B 206 ASP cc_start: 0.8048 (t0) cc_final: 0.7825 (t0) REVERT: B 214 GLN cc_start: 0.8484 (mm-40) cc_final: 0.7905 (pp30) REVERT: B 259 ILE cc_start: 0.9453 (pt) cc_final: 0.8987 (mm) REVERT: B 260 GLU cc_start: 0.8723 (pt0) cc_final: 0.8508 (mt-10) REVERT: B 272 TYR cc_start: 0.8624 (t80) cc_final: 0.8363 (t80) REVERT: B 390 MET cc_start: 0.8502 (mmm) cc_final: 0.8033 (mmt) REVERT: C 75 ASP cc_start: 0.7922 (t0) cc_final: 0.7143 (t0) REVERT: C 77 LEU cc_start: 0.9175 (mt) cc_final: 0.8956 (mm) REVERT: C 112 TRP cc_start: 0.8453 (OUTLIER) cc_final: 0.8050 (t-100) REVERT: C 146 LYS cc_start: 0.8224 (mttt) cc_final: 0.7922 (mtmm) REVERT: C 201 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7757 (mp0) REVERT: C 214 GLN cc_start: 0.8586 (mm-40) cc_final: 0.7729 (pp30) REVERT: C 305 PHE cc_start: 0.8386 (m-80) cc_final: 0.7763 (t80) REVERT: C 306 LEU cc_start: 0.8544 (tp) cc_final: 0.8313 (tp) REVERT: D 75 ASP cc_start: 0.8067 (t0) cc_final: 0.7543 (t0) REVERT: D 90 SER cc_start: 0.8728 (m) cc_final: 0.8465 (t) REVERT: D 129 ASP cc_start: 0.8637 (t0) cc_final: 0.8164 (t0) REVERT: D 146 LYS cc_start: 0.8447 (mttt) cc_final: 0.8141 (mtmp) REVERT: D 201 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7644 (mp0) REVERT: D 206 ASP cc_start: 0.7938 (t0) cc_final: 0.7638 (t0) REVERT: D 272 TYR cc_start: 0.8605 (t80) cc_final: 0.7990 (t80) REVERT: D 297 PHE cc_start: 0.8812 (m-80) cc_final: 0.8366 (m-80) REVERT: E 75 ASP cc_start: 0.7824 (t0) cc_final: 0.6984 (t0) REVERT: E 78 ARG cc_start: 0.8982 (mtp180) cc_final: 0.8442 (mtp85) REVERT: E 81 MET cc_start: 0.8716 (ttp) cc_final: 0.8436 (ttp) REVERT: E 146 LYS cc_start: 0.8377 (mttt) cc_final: 0.7997 (mttp) REVERT: E 201 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7641 (mp0) REVERT: E 206 ASP cc_start: 0.8129 (t0) cc_final: 0.7673 (t0) outliers start: 25 outliers final: 6 residues processed: 268 average time/residue: 1.0252 time to fit residues: 306.2054 Evaluate side-chains 233 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 226 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 259 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 83 optimal weight: 0.0050 chunk 30 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.084604 restraints weight = 19251.289| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.78 r_work: 0.2899 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13385 Z= 0.177 Angle : 0.502 6.950 18305 Z= 0.250 Chirality : 0.039 0.136 2235 Planarity : 0.003 0.048 2250 Dihedral : 3.758 19.409 2060 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.54 % Allowed : 18.95 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.30 (0.22), residues: 1600 helix: 3.17 (0.19), residues: 530 sheet: 0.61 (0.24), residues: 490 loop : 0.92 (0.29), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 112 HIS 0.001 0.000 HIS A 168 PHE 0.012 0.001 PHE B 305 TYR 0.030 0.002 TYR B 176 ARG 0.008 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 1.526 Fit side-chains REVERT: A 75 ASP cc_start: 0.8050 (t0) cc_final: 0.7501 (t0) REVERT: A 77 LEU cc_start: 0.9189 (mt) cc_final: 0.8953 (mm) REVERT: A 146 LYS cc_start: 0.8339 (mttt) cc_final: 0.7940 (mttp) REVERT: A 201 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7554 (mp0) REVERT: A 260 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8464 (mp0) REVERT: A 272 TYR cc_start: 0.8590 (t80) cc_final: 0.8188 (t80) REVERT: A 364 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8180 (mt-10) REVERT: B 75 ASP cc_start: 0.7758 (t0) cc_final: 0.6790 (t0) REVERT: B 78 ARG cc_start: 0.8921 (mtp180) cc_final: 0.8420 (mtp85) REVERT: B 129 ASP cc_start: 0.8600 (t0) cc_final: 0.8111 (t0) REVERT: B 146 LYS cc_start: 0.8385 (mttt) cc_final: 0.8021 (mttp) REVERT: B 201 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7652 (mp0) REVERT: B 206 ASP cc_start: 0.8072 (t0) cc_final: 0.7720 (t0) REVERT: B 214 GLN cc_start: 0.8518 (mm-40) cc_final: 0.7890 (pp30) REVERT: B 259 ILE cc_start: 0.9444 (pt) cc_final: 0.8984 (mm) REVERT: B 260 GLU cc_start: 0.8716 (pt0) cc_final: 0.8505 (mt-10) REVERT: B 272 TYR cc_start: 0.8623 (t80) cc_final: 0.8320 (t80) REVERT: B 390 MET cc_start: 0.8501 (mmm) cc_final: 0.8034 (mmt) REVERT: C 75 ASP cc_start: 0.7907 (t0) cc_final: 0.7116 (t0) REVERT: C 77 LEU cc_start: 0.9162 (mt) cc_final: 0.8946 (mm) REVERT: C 112 TRP cc_start: 0.8430 (OUTLIER) cc_final: 0.8007 (t-100) REVERT: C 146 LYS cc_start: 0.8210 (mttt) cc_final: 0.7829 (mttp) REVERT: C 201 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7764 (mp0) REVERT: C 214 GLN cc_start: 0.8624 (mm-40) cc_final: 0.7742 (pp30) REVERT: C 227 LYS cc_start: 0.8034 (ptpt) cc_final: 0.7521 (tttm) REVERT: C 305 PHE cc_start: 0.8328 (m-80) cc_final: 0.7672 (t80) REVERT: C 306 LEU cc_start: 0.8523 (tp) cc_final: 0.8302 (tp) REVERT: D 75 ASP cc_start: 0.8045 (t0) cc_final: 0.7498 (t0) REVERT: D 90 SER cc_start: 0.8738 (m) cc_final: 0.8505 (t) REVERT: D 129 ASP cc_start: 0.8625 (t0) cc_final: 0.8142 (t0) REVERT: D 146 LYS cc_start: 0.8423 (mttt) cc_final: 0.8128 (mtmp) REVERT: D 201 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7587 (mp0) REVERT: D 206 ASP cc_start: 0.8007 (t0) cc_final: 0.7660 (t0) REVERT: D 272 TYR cc_start: 0.8574 (t80) cc_final: 0.7938 (t80) REVERT: D 297 PHE cc_start: 0.8803 (m-80) cc_final: 0.8314 (m-80) REVERT: E 75 ASP cc_start: 0.7817 (t0) cc_final: 0.6998 (t0) REVERT: E 78 ARG cc_start: 0.8986 (mtp180) cc_final: 0.8502 (mtp-110) REVERT: E 81 MET cc_start: 0.8710 (ttp) cc_final: 0.8417 (ttp) REVERT: E 90 SER cc_start: 0.8618 (m) cc_final: 0.8388 (t) REVERT: E 146 LYS cc_start: 0.8355 (mttt) cc_final: 0.7992 (mttp) REVERT: E 201 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7634 (mp0) REVERT: E 206 ASP cc_start: 0.8108 (t0) cc_final: 0.7666 (t0) outliers start: 22 outliers final: 11 residues processed: 257 average time/residue: 0.9532 time to fit residues: 274.8654 Evaluate side-chains 240 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 235 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 102 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.081652 restraints weight = 19109.302| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.76 r_work: 0.2851 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13385 Z= 0.304 Angle : 0.546 6.335 18305 Z= 0.274 Chirality : 0.041 0.140 2235 Planarity : 0.003 0.041 2250 Dihedral : 3.872 18.608 2060 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.38 % Allowed : 18.11 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.22 (0.21), residues: 1600 helix: 3.05 (0.20), residues: 530 sheet: 0.56 (0.24), residues: 485 loop : 0.95 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 112 HIS 0.003 0.001 HIS A 168 PHE 0.017 0.002 PHE A 72 TYR 0.031 0.002 TYR B 176 ARG 0.010 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 1.609 Fit side-chains REVERT: A 75 ASP cc_start: 0.8082 (t0) cc_final: 0.7530 (t0) REVERT: A 77 LEU cc_start: 0.9252 (mt) cc_final: 0.9002 (mm) REVERT: A 112 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.7854 (t-100) REVERT: A 146 LYS cc_start: 0.8382 (mttt) cc_final: 0.8066 (mttp) REVERT: A 201 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7534 (mp0) REVERT: A 260 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8477 (mp0) REVERT: A 272 TYR cc_start: 0.8609 (t80) cc_final: 0.8174 (t80) REVERT: A 364 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 75 ASP cc_start: 0.7879 (t0) cc_final: 0.6915 (t0) REVERT: B 78 ARG cc_start: 0.8998 (mtp180) cc_final: 0.8524 (mtp-110) REVERT: B 112 TRP cc_start: 0.8399 (OUTLIER) cc_final: 0.7973 (t-100) REVERT: B 129 ASP cc_start: 0.8599 (t0) cc_final: 0.8115 (t0) REVERT: B 146 LYS cc_start: 0.8388 (mttt) cc_final: 0.8004 (mttp) REVERT: B 160 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6608 (tm-30) REVERT: B 186 GLU cc_start: 0.7970 (tt0) cc_final: 0.7728 (tt0) REVERT: B 201 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7618 (mp0) REVERT: B 214 GLN cc_start: 0.8494 (mm-40) cc_final: 0.7908 (pp30) REVERT: B 260 GLU cc_start: 0.8663 (pt0) cc_final: 0.8455 (mt-10) REVERT: B 272 TYR cc_start: 0.8668 (t80) cc_final: 0.8309 (t80) REVERT: B 390 MET cc_start: 0.8496 (mmm) cc_final: 0.8019 (mmt) REVERT: C 75 ASP cc_start: 0.7953 (t0) cc_final: 0.7122 (t0) REVERT: C 77 LEU cc_start: 0.9210 (mt) cc_final: 0.8981 (mm) REVERT: C 112 TRP cc_start: 0.8585 (OUTLIER) cc_final: 0.8019 (t-100) REVERT: C 146 LYS cc_start: 0.8234 (mttt) cc_final: 0.7948 (mtmm) REVERT: C 201 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7708 (mp0) REVERT: C 259 ILE cc_start: 0.9447 (pt) cc_final: 0.8973 (mm) REVERT: C 306 LEU cc_start: 0.8594 (tp) cc_final: 0.8386 (tp) REVERT: D 75 ASP cc_start: 0.8092 (t0) cc_final: 0.7472 (t0) REVERT: D 90 SER cc_start: 0.8786 (m) cc_final: 0.8527 (t) REVERT: D 129 ASP cc_start: 0.8603 (t0) cc_final: 0.8122 (t0) REVERT: D 141 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8595 (pm20) REVERT: D 146 LYS cc_start: 0.8448 (mttt) cc_final: 0.8099 (mttp) REVERT: D 201 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7537 (mp0) REVERT: D 206 ASP cc_start: 0.8047 (t0) cc_final: 0.7630 (t0) REVERT: D 259 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9142 (mm) REVERT: D 272 TYR cc_start: 0.8632 (t80) cc_final: 0.8010 (t80) REVERT: E 75 ASP cc_start: 0.7887 (t0) cc_final: 0.7086 (t0) REVERT: E 78 ARG cc_start: 0.9011 (mtp180) cc_final: 0.8504 (mtp-110) REVERT: E 146 LYS cc_start: 0.8377 (mttt) cc_final: 0.8004 (mttp) REVERT: E 201 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7626 (mp0) REVERT: E 206 ASP cc_start: 0.8124 (t0) cc_final: 0.7694 (t0) outliers start: 34 outliers final: 14 residues processed: 269 average time/residue: 1.0237 time to fit residues: 306.5654 Evaluate side-chains 260 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 293 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 37 optimal weight: 0.0470 chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.084070 restraints weight = 18974.905| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.75 r_work: 0.2873 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13385 Z= 0.182 Angle : 0.526 7.396 18305 Z= 0.260 Chirality : 0.040 0.135 2235 Planarity : 0.003 0.032 2250 Dihedral : 3.757 19.143 2060 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.10 % Allowed : 18.95 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.21 (0.22), residues: 1600 helix: 3.12 (0.20), residues: 530 sheet: 0.49 (0.24), residues: 490 loop : 0.93 (0.29), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 112 HIS 0.002 0.000 HIS C 276 PHE 0.015 0.001 PHE C 305 TYR 0.031 0.002 TYR B 176 ARG 0.012 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 1.523 Fit side-chains REVERT: A 75 ASP cc_start: 0.8077 (t0) cc_final: 0.7526 (t0) REVERT: A 77 LEU cc_start: 0.9217 (mt) cc_final: 0.8985 (mm) REVERT: A 146 LYS cc_start: 0.8408 (mttt) cc_final: 0.8090 (mttp) REVERT: A 201 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7548 (mp0) REVERT: A 206 ASP cc_start: 0.8056 (t0) cc_final: 0.7842 (t0) REVERT: A 259 ILE cc_start: 0.9499 (pt) cc_final: 0.8996 (mm) REVERT: A 260 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: A 272 TYR cc_start: 0.8577 (t80) cc_final: 0.8234 (t80) REVERT: A 297 PHE cc_start: 0.8832 (m-80) cc_final: 0.8627 (m-80) REVERT: A 364 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8225 (mt-10) REVERT: B 75 ASP cc_start: 0.7802 (t0) cc_final: 0.6881 (t0) REVERT: B 78 ARG cc_start: 0.8953 (mtp180) cc_final: 0.8553 (mtp-110) REVERT: B 129 ASP cc_start: 0.8610 (t0) cc_final: 0.8095 (t0) REVERT: B 146 LYS cc_start: 0.8437 (mttt) cc_final: 0.8052 (mttp) REVERT: B 201 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7611 (mp0) REVERT: B 206 ASP cc_start: 0.8103 (t0) cc_final: 0.7785 (t0) REVERT: B 272 TYR cc_start: 0.8661 (t80) cc_final: 0.8337 (t80) REVERT: B 390 MET cc_start: 0.8491 (mmm) cc_final: 0.8005 (mmt) REVERT: C 75 ASP cc_start: 0.7969 (t0) cc_final: 0.7132 (t0) REVERT: C 77 LEU cc_start: 0.9184 (mt) cc_final: 0.8965 (mm) REVERT: C 112 TRP cc_start: 0.8429 (OUTLIER) cc_final: 0.8068 (t-100) REVERT: C 146 LYS cc_start: 0.8255 (mttt) cc_final: 0.7970 (mtmm) REVERT: C 201 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7737 (mp0) REVERT: C 259 ILE cc_start: 0.9456 (pt) cc_final: 0.9011 (mm) REVERT: C 260 GLU cc_start: 0.8685 (pt0) cc_final: 0.8479 (mt-10) REVERT: C 306 LEU cc_start: 0.8546 (tp) cc_final: 0.8314 (tp) REVERT: D 75 ASP cc_start: 0.8073 (t0) cc_final: 0.7530 (t0) REVERT: D 90 SER cc_start: 0.8774 (m) cc_final: 0.8561 (t) REVERT: D 129 ASP cc_start: 0.8662 (t0) cc_final: 0.8186 (t0) REVERT: D 141 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8594 (pm20) REVERT: D 146 LYS cc_start: 0.8502 (mttt) cc_final: 0.8192 (mtmp) REVERT: D 201 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7568 (mp0) REVERT: D 206 ASP cc_start: 0.8049 (t0) cc_final: 0.7652 (t0) REVERT: D 259 ILE cc_start: 0.9356 (pt) cc_final: 0.9115 (mm) REVERT: D 272 TYR cc_start: 0.8590 (t80) cc_final: 0.7989 (t80) REVERT: E 75 ASP cc_start: 0.7863 (t0) cc_final: 0.7093 (t0) REVERT: E 78 ARG cc_start: 0.9023 (mtp180) cc_final: 0.8540 (mtp-110) REVERT: E 90 SER cc_start: 0.8635 (m) cc_final: 0.8419 (t) REVERT: E 146 LYS cc_start: 0.8419 (mttt) cc_final: 0.8056 (mttp) REVERT: E 201 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7657 (mp0) REVERT: E 206 ASP cc_start: 0.8114 (t0) cc_final: 0.7698 (t0) outliers start: 30 outliers final: 15 residues processed: 256 average time/residue: 0.9220 time to fit residues: 265.6506 Evaluate side-chains 243 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 235 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 125 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 HIS C 210 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.098889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.080235 restraints weight = 19314.447| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.76 r_work: 0.2821 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13385 Z= 0.426 Angle : 0.606 7.612 18305 Z= 0.302 Chirality : 0.043 0.209 2235 Planarity : 0.004 0.054 2250 Dihedral : 3.989 17.838 2060 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.24 % Allowed : 18.74 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.99 (0.21), residues: 1600 helix: 2.89 (0.20), residues: 530 sheet: 0.38 (0.23), residues: 495 loop : 0.83 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 112 HIS 0.003 0.001 HIS A 168 PHE 0.019 0.002 PHE A 72 TYR 0.040 0.003 TYR B 176 ARG 0.011 0.000 ARG E 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 1.403 Fit side-chains REVERT: A 75 ASP cc_start: 0.8113 (t0) cc_final: 0.7535 (t0) REVERT: A 77 LEU cc_start: 0.9274 (mt) cc_final: 0.9016 (mm) REVERT: A 112 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.7823 (t-100) REVERT: A 146 LYS cc_start: 0.8387 (mttt) cc_final: 0.8091 (mttp) REVERT: A 160 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6824 (tm-30) REVERT: A 201 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7557 (mp0) REVERT: A 206 ASP cc_start: 0.8152 (t0) cc_final: 0.7888 (t0) REVERT: A 260 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: A 272 TYR cc_start: 0.8599 (t80) cc_final: 0.8223 (t80) REVERT: A 364 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8254 (mt-10) REVERT: B 75 ASP cc_start: 0.7944 (t0) cc_final: 0.6955 (t0) REVERT: B 78 ARG cc_start: 0.9011 (mtp180) cc_final: 0.8527 (mtp-110) REVERT: B 129 ASP cc_start: 0.8615 (t0) cc_final: 0.8085 (t0) REVERT: B 146 LYS cc_start: 0.8426 (mttt) cc_final: 0.8043 (mttp) REVERT: B 201 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7576 (mp0) REVERT: B 214 GLN cc_start: 0.8467 (mm-40) cc_final: 0.7960 (pp30) REVERT: B 390 MET cc_start: 0.8506 (mmm) cc_final: 0.7992 (mmt) REVERT: C 75 ASP cc_start: 0.7971 (t0) cc_final: 0.7146 (t0) REVERT: C 77 LEU cc_start: 0.9235 (mt) cc_final: 0.8989 (mm) REVERT: C 112 TRP cc_start: 0.8680 (OUTLIER) cc_final: 0.7940 (t-100) REVERT: C 146 LYS cc_start: 0.8239 (mttt) cc_final: 0.7943 (mttp) REVERT: C 201 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7653 (mp0) REVERT: C 259 ILE cc_start: 0.9456 (pt) cc_final: 0.8941 (mm) REVERT: C 275 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8185 (mp) REVERT: C 306 LEU cc_start: 0.8603 (tp) cc_final: 0.8401 (tp) REVERT: D 75 ASP cc_start: 0.8108 (t0) cc_final: 0.7431 (t0) REVERT: D 129 ASP cc_start: 0.8608 (t0) cc_final: 0.8170 (t0) REVERT: D 141 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8589 (pm20) REVERT: D 146 LYS cc_start: 0.8453 (mttt) cc_final: 0.8070 (mtmp) REVERT: D 201 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7488 (mp0) REVERT: D 206 ASP cc_start: 0.8081 (t0) cc_final: 0.7629 (t0) REVERT: D 259 ILE cc_start: 0.9390 (pt) cc_final: 0.9143 (mp) REVERT: D 272 TYR cc_start: 0.8685 (t80) cc_final: 0.8088 (t80) REVERT: E 75 ASP cc_start: 0.7870 (t0) cc_final: 0.7079 (t0) REVERT: E 78 ARG cc_start: 0.9022 (mtp180) cc_final: 0.8514 (mtp-110) REVERT: E 146 LYS cc_start: 0.8396 (mttt) cc_final: 0.8045 (mttp) REVERT: E 201 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7658 (mp0) REVERT: E 206 ASP cc_start: 0.8142 (t0) cc_final: 0.7702 (t0) REVERT: E 259 ILE cc_start: 0.9470 (pt) cc_final: 0.9008 (mp) outliers start: 32 outliers final: 12 residues processed: 269 average time/residue: 0.9774 time to fit residues: 294.1606 Evaluate side-chains 256 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 112 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.101580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.083063 restraints weight = 18728.654| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.77 r_work: 0.2872 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13385 Z= 0.206 Angle : 0.555 8.403 18305 Z= 0.274 Chirality : 0.040 0.141 2235 Planarity : 0.003 0.050 2250 Dihedral : 3.883 18.997 2060 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.61 % Allowed : 19.65 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.22), residues: 1600 helix: 3.14 (0.20), residues: 500 sheet: 0.46 (0.24), residues: 485 loop : 0.75 (0.28), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 112 HIS 0.004 0.000 HIS C 144 PHE 0.023 0.002 PHE C 305 TYR 0.042 0.002 TYR B 176 ARG 0.011 0.000 ARG E 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 1.386 Fit side-chains REVERT: A 75 ASP cc_start: 0.8071 (t0) cc_final: 0.7506 (t0) REVERT: A 77 LEU cc_start: 0.9245 (mt) cc_final: 0.9007 (mm) REVERT: A 112 TRP cc_start: 0.8228 (OUTLIER) cc_final: 0.7835 (t-100) REVERT: A 146 LYS cc_start: 0.8413 (mttt) cc_final: 0.8093 (mttp) REVERT: A 160 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6798 (tm-30) REVERT: A 201 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7556 (mp0) REVERT: A 259 ILE cc_start: 0.9528 (pt) cc_final: 0.9107 (mm) REVERT: A 260 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: A 272 TYR cc_start: 0.8571 (t80) cc_final: 0.8251 (t80) REVERT: A 364 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8206 (mt-10) REVERT: B 75 ASP cc_start: 0.7846 (t0) cc_final: 0.6886 (t0) REVERT: B 78 ARG cc_start: 0.8970 (mtp180) cc_final: 0.8528 (mtp-110) REVERT: B 129 ASP cc_start: 0.8608 (t0) cc_final: 0.8074 (t0) REVERT: B 146 LYS cc_start: 0.8456 (mttt) cc_final: 0.8065 (mtmp) REVERT: B 201 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7586 (mp0) REVERT: B 272 TYR cc_start: 0.8659 (t80) cc_final: 0.8296 (t80) REVERT: B 390 MET cc_start: 0.8497 (mmm) cc_final: 0.7986 (mmt) REVERT: C 75 ASP cc_start: 0.7933 (t0) cc_final: 0.7138 (t0) REVERT: C 77 LEU cc_start: 0.9194 (mt) cc_final: 0.8970 (mm) REVERT: C 112 TRP cc_start: 0.8506 (OUTLIER) cc_final: 0.7960 (t-100) REVERT: C 146 LYS cc_start: 0.8309 (mttt) cc_final: 0.8018 (mtmm) REVERT: C 201 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7715 (mp0) REVERT: C 259 ILE cc_start: 0.9435 (pt) cc_final: 0.8982 (mm) REVERT: C 260 GLU cc_start: 0.8709 (pt0) cc_final: 0.8499 (mt-10) REVERT: C 280 VAL cc_start: 0.8560 (t) cc_final: 0.8359 (m) REVERT: C 306 LEU cc_start: 0.8547 (tp) cc_final: 0.8316 (tp) REVERT: D 75 ASP cc_start: 0.8075 (t0) cc_final: 0.7458 (t0) REVERT: D 90 SER cc_start: 0.8759 (m) cc_final: 0.8533 (t) REVERT: D 129 ASP cc_start: 0.8603 (t0) cc_final: 0.8147 (t0) REVERT: D 141 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: D 146 LYS cc_start: 0.8477 (mttt) cc_final: 0.8174 (mtmp) REVERT: D 201 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7516 (mp0) REVERT: D 206 ASP cc_start: 0.8121 (t0) cc_final: 0.7630 (t0) REVERT: D 259 ILE cc_start: 0.9365 (pt) cc_final: 0.9147 (mp) REVERT: D 272 TYR cc_start: 0.8597 (t80) cc_final: 0.7992 (t80) REVERT: E 75 ASP cc_start: 0.7829 (t0) cc_final: 0.7080 (t0) REVERT: E 78 ARG cc_start: 0.9022 (mtp180) cc_final: 0.8542 (mtp-110) REVERT: E 146 LYS cc_start: 0.8408 (mttt) cc_final: 0.8067 (mttp) REVERT: E 201 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7626 (mp0) REVERT: E 206 ASP cc_start: 0.8130 (t0) cc_final: 0.7689 (t0) REVERT: E 259 ILE cc_start: 0.9468 (pt) cc_final: 0.8930 (mp) outliers start: 23 outliers final: 15 residues processed: 258 average time/residue: 0.9525 time to fit residues: 275.0014 Evaluate side-chains 250 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 27 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081530 restraints weight = 18844.230| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.81 r_work: 0.2824 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13385 Z= 0.319 Angle : 0.583 7.747 18305 Z= 0.289 Chirality : 0.042 0.146 2235 Planarity : 0.004 0.049 2250 Dihedral : 3.966 18.540 2060 Min Nonbonded Distance : 1.590 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.61 % Allowed : 19.65 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.90 (0.21), residues: 1600 helix: 3.03 (0.20), residues: 500 sheet: 0.33 (0.24), residues: 495 loop : 0.69 (0.27), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 112 HIS 0.006 0.001 HIS C 144 PHE 0.020 0.002 PHE B 305 TYR 0.046 0.003 TYR B 176 ARG 0.011 0.000 ARG E 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7256.06 seconds wall clock time: 129 minutes 30.91 seconds (7770.91 seconds total)