Starting phenix.real_space_refine on Fri Jul 3 01:17:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dgt_27429/07_2026/8dgt_27429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dgt_27429/07_2026/8dgt_27429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dgt_27429/07_2026/8dgt_27429.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dgt_27429/07_2026/8dgt_27429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dgt_27429/07_2026/8dgt_27429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dgt_27429/07_2026/8dgt_27429.map" model { file = "/net/cci-nas-00/data/ceres_data/8dgt_27429/07_2026/8dgt_27429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dgt_27429/07_2026/8dgt_27429.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.066 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: 9 Type Number sf(0) Gaussians I 1 10.91 5 Zn 2 6.06 5 P 11 5.49 5 Mg 2 5.21 5 S 65 5.16 5 C 6997 2.51 5 N 1910 2.21 5 O 2107 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11096 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3455 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2441 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 293} Chain breaks: 1 Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1846 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Chain: "D" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1833 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 223} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 1398 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1324 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 167, 1324 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1257 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'AGS': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 764 SG CYS A 248 44.579 48.524 42.978 1.00 92.22 S ATOM 789 SG CYS A 251 42.579 46.312 43.172 1.00 91.18 S ATOM 971 SG CYS A 272 40.590 49.856 42.034 1.00 91.05 S ATOM 877 SG CYS A 261 53.877 58.376 41.455 1.00 90.50 S ATOM 899 SG CYS A 264 53.885 56.709 44.564 1.00 82.84 S ATOM 1029 SG CYS A 280 54.516 60.397 43.977 1.00 77.32 S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N MET F 1 " occ=0.76 ... (3 atoms not shown) pdb=" CB MET F 1 " occ=0.76 residue: pdb=" N MET F 67 " occ=0.94 ... (6 atoms not shown) pdb=" CE MET F 67 " occ=0.94 residue: pdb=" N GLN F 70 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN F 70 " occ=0.97 residue: pdb=" N TYR F 71 " occ=0.84 ... (10 atoms not shown) pdb=" OH TYR F 71 " occ=0.84 residue: pdb=" N AGLN F 99 " occ=0.58 ... (16 atoms not shown) pdb=" NE2BGLN F 99 " occ=0.42 residue: pdb=" N GLU F 107 " occ=0.82 ... (7 atoms not shown) pdb=" OE2 GLU F 107 " occ=0.82 residue: pdb=" N GLN F 150 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN F 150 " occ=0.97 Time building chain proxies: 2.11, per 1000 atoms: 0.19 Number of scatterers: 11096 At special positions: 0 Unit cell: (98.88, 94.76, 127.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) I 1 52.95 Zn 2 29.99 S 65 16.00 P 11 15.00 Mg 2 11.99 F 1 9.00 O 2107 8.00 N 1910 7.00 C 6997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 374.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS A 269 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 272 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 248 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 251 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 280 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 261 " pdb="ZN ZN A 803 " - pdb=" ND1 HIS A 235 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 264 " Number of angles added : 6 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 57.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 176 through 187 removed outlier: 4.895A pdb=" N LYS A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.573A pdb=" N THR A 218 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 removed outlier: 3.711A pdb=" N SER A 273 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'A' and resid 536 through 543 Processing helix chain 'A' and resid 549 through 570 removed outlier: 3.556A pdb=" N LYS A 570 " --> pdb=" O TYR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 634 through 652 Processing helix chain 'A' and resid 661 through 671 removed outlier: 3.899A pdb=" N ILE A 665 " --> pdb=" O ASN A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 706 through 720 removed outlier: 3.810A pdb=" N SER A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.696A pdb=" N LYS B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 151 through 159 Processing helix chain 'B' and resid 162 through 183 removed outlier: 3.645A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 242 through 259 removed outlier: 4.266A pdb=" N SER B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 273 removed outlier: 3.825A pdb=" N GLU B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.577A pdb=" N VAL B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.566A pdb=" N THR C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 70 removed outlier: 3.596A pdb=" N ARG C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL C 52 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 102 removed outlier: 4.119A pdb=" N GLN C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 131 Processing helix chain 'C' and resid 137 through 160 removed outlier: 3.507A pdb=" N ILE C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 181 Processing helix chain 'C' and resid 184 through 202 removed outlier: 3.863A pdb=" N GLU C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 210 removed outlier: 3.607A pdb=" N SER C 210 " --> pdb=" O ASN C 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 210' Processing helix chain 'C' and resid 211 through 229 Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.543A pdb=" N VAL D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY D 33 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 67 removed outlier: 3.521A pdb=" N LEU D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 89 removed outlier: 3.594A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 104 removed outlier: 3.549A pdb=" N CYS D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 133 removed outlier: 3.540A pdb=" N GLU D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 160 removed outlier: 3.930A pdb=" N ASN D 139 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 181 Processing helix chain 'D' and resid 184 through 202 Processing helix chain 'D' and resid 212 through 230 removed outlier: 3.824A pdb=" N SER D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 61 through 63 No H-bonds generated for 'chain 'F' and resid 61 through 63' Processing helix chain 'F' and resid 64 through 75 removed outlier: 3.626A pdb=" N THR F 74 " --> pdb=" O GLN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 151 through 167 Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 208 removed outlier: 4.484A pdb=" N VAL A 197 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU F 37 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR F 2 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASP F 54 " --> pdb=" O THR F 2 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR F 4 " --> pdb=" O ASP F 54 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU F 56 " --> pdb=" O TYR F 4 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU F 6 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR F 58 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL F 8 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE F 78 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL F 114 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYS F 80 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASN F 116 " --> pdb=" O CYS F 80 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE F 82 " --> pdb=" O ASN F 116 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ILE F 142 " --> pdb=" O MET F 111 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU F 113 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 241 Processing sheet with id=AA3, first strand: chain 'A' and resid 458 through 465 removed outlier: 7.440A pdb=" N GLY A 460 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LYS A 475 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG A 462 " --> pdb=" O LYS A 473 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS A 473 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 582 through 585 Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 76 removed outlier: 7.049A pdb=" N ILE B 71 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N SER B 86 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU B 73 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS B 84 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 75 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 131 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU B 144 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE B 129 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 150 596 hydrogen bonds defined for protein. 1726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 3707 1.37 - 1.55: 7452 1.55 - 1.74: 51 1.74 - 1.92: 102 1.92 - 2.11: 3 Bond restraints: 11315 Sorted by residual: bond pdb=" C GLU A 225 " pdb=" N VAL A 226 " ideal model delta sigma weight residual 1.332 1.475 -0.143 1.36e-02 5.41e+03 1.10e+02 bond pdb=" C18 LCJ B 403 " pdb=" N09 LCJ B 403 " ideal model delta sigma weight residual 1.349 1.450 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C11 LCJ B 403 " pdb=" N06 LCJ B 403 " ideal model delta sigma weight residual 1.395 1.303 0.092 2.00e-02 2.50e+03 2.09e+01 bond pdb=" N3B GNP F 202 " pdb=" PG GNP F 202 " ideal model delta sigma weight residual 1.801 1.711 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C10 LCJ B 403 " pdb=" N07 LCJ B 403 " ideal model delta sigma weight residual 1.371 1.455 -0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 11310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.67: 15298 7.67 - 15.34: 7 15.34 - 23.01: 0 23.01 - 30.68: 1 30.68 - 38.35: 2 Bond angle restraints: 15308 Sorted by residual: angle pdb=" O GLU A 225 " pdb=" C GLU A 225 " pdb=" N VAL A 226 " ideal model delta sigma weight residual 121.70 83.35 38.35 1.84e+00 2.95e-01 4.34e+02 angle pdb=" C MET F 1 " pdb=" N THR F 2 " pdb=" CA THR F 2 " ideal model delta sigma weight residual 122.74 91.23 31.51 1.54e+00 4.22e-01 4.19e+02 angle pdb=" CA MET F 1 " pdb=" C MET F 1 " pdb=" N THR F 2 " ideal model delta sigma weight residual 116.20 89.74 26.46 2.00e+00 2.50e-01 1.75e+02 angle pdb=" CA PRO A 152 " pdb=" N PRO A 152 " pdb=" CD PRO A 152 " ideal model delta sigma weight residual 112.00 98.94 13.06 1.40e+00 5.10e-01 8.70e+01 angle pdb=" CA GLU A 225 " pdb=" C GLU A 225 " pdb=" N VAL A 226 " ideal model delta sigma weight residual 116.18 125.88 -9.70 1.15e+00 7.56e-01 7.12e+01 ... (remaining 15303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.56: 6581 21.56 - 43.13: 251 43.13 - 64.69: 79 64.69 - 86.25: 10 86.25 - 107.81: 4 Dihedral angle restraints: 6925 sinusoidal: 2877 harmonic: 4048 Sorted by residual: dihedral pdb=" O1B AGS B 402 " pdb=" O3B AGS B 402 " pdb=" PB AGS B 402 " pdb=" PG AGS B 402 " ideal model delta sinusoidal sigma weight residual 68.91 176.72 -107.81 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" CA THR F 35 " pdb=" C THR F 35 " pdb=" N ILE F 36 " pdb=" CA ILE F 36 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA THR F 144 " pdb=" C THR F 144 " pdb=" N SER F 145 " pdb=" CA SER F 145 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1501 0.082 - 0.163: 160 0.163 - 0.245: 29 0.245 - 0.327: 3 0.327 - 0.409: 2 Chirality restraints: 1695 Sorted by residual: chirality pdb=" CA VAL A 157 " pdb=" N VAL A 157 " pdb=" C VAL A 157 " pdb=" CB VAL A 157 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA VAL A 224 " pdb=" N VAL A 224 " pdb=" C VAL A 224 " pdb=" CB VAL A 224 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB ILE A 214 " pdb=" CA ILE A 214 " pdb=" CG1 ILE A 214 " pdb=" CG2 ILE A 214 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1692 not shown) Planarity restraints: 1954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 225 " 0.133 2.00e-02 2.50e+03 2.00e-01 3.98e+02 pdb=" C GLU A 225 " -0.345 2.00e-02 2.50e+03 pdb=" O GLU A 225 " 0.110 2.00e-02 2.50e+03 pdb=" N VAL A 226 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 1 " 0.049 2.00e-02 2.50e+03 1.30e-01 1.68e+02 pdb=" C MET F 1 " -0.223 2.00e-02 2.50e+03 pdb=" O MET F 1 " 0.100 2.00e-02 2.50e+03 pdb=" N THR F 2 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 151 " -0.124 5.00e-02 4.00e+02 1.74e-01 4.85e+01 pdb=" N PRO A 152 " 0.301 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " -0.083 5.00e-02 4.00e+02 ... (remaining 1951 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.36: 32 2.36 - 3.01: 6289 3.01 - 3.66: 17197 3.66 - 4.31: 26777 4.31 - 4.96: 44600 Nonbonded interactions: 94895 Sorted by model distance: nonbonded pdb=" NH2 ARG A 671 " pdb=" OD1BASP F 33 " model vdw 1.712 3.120 nonbonded pdb=" OG SER A 151 " pdb=" CD PRO A 152 " model vdw 1.908 3.440 nonbonded pdb="MG MG F 201 " pdb=" O2G GNP F 202 " model vdw 2.027 2.170 nonbonded pdb="MG MG F 201 " pdb=" O2B GNP F 202 " model vdw 2.031 2.170 nonbonded pdb=" OH TYR A 673 " pdb=" OD1BASP F 33 " model vdw 2.062 3.040 ... (remaining 94890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 through 201 or (resid \ 202 and (name N or name CA or name C or name O or name CB )) or resid 203 throug \ h 230)) 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=0.16 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.130 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5286 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 0.209 11324 Z= 0.347 Angle : 0.936 38.349 15314 Z= 0.509 Chirality : 0.055 0.409 1695 Planarity : 0.008 0.200 1954 Dihedral : 13.068 107.814 4313 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.76 % Favored : 97.02 % Rotamer: Outliers : 2.90 % Allowed : 6.21 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1359 helix: 0.60 (0.19), residues: 710 sheet: -0.53 (0.42), residues: 137 loop : -1.18 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 161 TYR 0.023 0.002 TYR F 96 PHE 0.033 0.002 PHE A 160 TRP 0.024 0.002 TRP A 216 HIS 0.008 0.001 HIS F 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.32 (11315) covalent geometry : angle 0.86449 / 0.50 (15308) hydrogen bonds : bond 0.14121 / 9.63 ( 596) hydrogen bonds : angle 6.16729 / 4.32 ( 1726) metal coordination : bond 0.13815 / 8.69 ( 8) metal coordination : angle 18.18594 / 9.26 ( 6) Misc. bond : bond 0.00673 / 0.35 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 461 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 PRO cc_start: 0.7225 (OUTLIER) cc_final: 0.6920 (Cg_exo) REVERT: A 463 ILE cc_start: 0.8379 (mm) cc_final: 0.8008 (mm) REVERT: A 475 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7709 (tptp) REVERT: A 517 MET cc_start: 0.8055 (mmm) cc_final: 0.7784 (mtt) REVERT: A 565 ASP cc_start: 0.7920 (t0) cc_final: 0.7663 (t70) REVERT: A 580 ASN cc_start: 0.8153 (m110) cc_final: 0.7873 (m-40) REVERT: A 721 LEU cc_start: 0.4799 (tp) cc_final: 0.4239 (tp) REVERT: B 146 MET cc_start: 0.4725 (mmm) cc_final: 0.4254 (mmm) REVERT: B 171 ILE cc_start: 0.8110 (mt) cc_final: 0.7830 (mt) REVERT: B 188 HIS cc_start: 0.7378 (t-90) cc_final: 0.6969 (t-90) REVERT: B 236 GLN cc_start: 0.7821 (mt0) cc_final: 0.7482 (tm-30) REVERT: B 253 LEU cc_start: 0.8275 (mt) cc_final: 0.7364 (mt) REVERT: B 329 VAL cc_start: 0.7523 (t) cc_final: 0.7226 (t) REVERT: C 14 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8464 (tm-30) REVERT: C 26 MET cc_start: 0.7632 (tpp) cc_final: 0.7349 (tpp) REVERT: C 83 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.7637 (tmm-80) REVERT: C 96 ASP cc_start: 0.7774 (t70) cc_final: 0.6687 (t0) REVERT: C 98 LEU cc_start: 0.8376 (mt) cc_final: 0.8089 (mm) REVERT: C 118 TYR cc_start: 0.8431 (m-10) cc_final: 0.8172 (m-80) REVERT: C 129 LEU cc_start: 0.9019 (mt) cc_final: 0.8383 (mp) REVERT: C 146 GLN cc_start: 0.9118 (tp40) cc_final: 0.8914 (mm-40) REVERT: C 167 ARG cc_start: 0.7786 (ttt180) cc_final: 0.7265 (ttm170) REVERT: C 177 PHE cc_start: 0.8573 (t80) cc_final: 0.8179 (t80) REVERT: C 218 MET cc_start: 0.8164 (tpp) cc_final: 0.7542 (mmm) REVERT: D 27 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7778 (ttpp) REVERT: D 49 LYS cc_start: 0.7583 (tptm) cc_final: 0.7272 (ttmm) REVERT: D 214 SER cc_start: 0.8010 (p) cc_final: 0.7451 (t) REVERT: F 55 ILE cc_start: 0.3273 (mm) cc_final: 0.3050 (mt) outliers start: 32 outliers final: 6 residues processed: 485 average time/residue: 0.1200 time to fit residues: 78.1040 Evaluate side-chains 266 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 259 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PRO Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A 585 HIS A 628 GLN A 661 ASN B 56 GLN B 87 HIS ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN D 207 ASN F 27 HIS F 70 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.217280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.181650 restraints weight = 60358.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.179504 restraints weight = 32754.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174799 restraints weight = 18271.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.176341 restraints weight = 18432.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.179781 restraints weight = 12307.507| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4009 r_free = 0.4009 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.4009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 11324 Z= 0.269 Angle : 0.783 10.398 15314 Z= 0.405 Chirality : 0.047 0.244 1695 Planarity : 0.006 0.081 1954 Dihedral : 7.417 106.477 1567 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.89 % Allowed : 17.48 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.22), residues: 1359 helix: 0.95 (0.18), residues: 710 sheet: 0.07 (0.44), residues: 132 loop : -0.99 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 575 TYR 0.024 0.003 TYR B 229 PHE 0.024 0.003 PHE B 371 TRP 0.014 0.002 TRP A 476 HIS 0.019 0.002 HIS A 725 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.27 (11315) covalent geometry : angle 0.77939 / 0.40 (15308) hydrogen bonds : bond 0.04672 / 3.07 ( 596) hydrogen bonds : angle 5.10381 / 3.59 ( 1726) metal coordination : bond 0.04356 / 2.39 ( 8) metal coordination : angle 3.75970 / 2.03 ( 6) Misc. bond : bond 0.00677 / 0.36 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 290 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASP cc_start: 0.6939 (m-30) cc_final: 0.6540 (m-30) REVERT: A 703 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7092 (tt0) REVERT: A 725 HIS cc_start: 0.5832 (m170) cc_final: 0.5544 (m170) REVERT: B 107 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8249 (mt) REVERT: B 122 ASN cc_start: 0.7263 (m-40) cc_final: 0.5916 (p0) REVERT: B 260 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7060 (ttp80) REVERT: B 319 ASN cc_start: 0.8124 (p0) cc_final: 0.7893 (p0) REVERT: C 77 GLN cc_start: 0.7748 (mp10) cc_final: 0.7422 (mp10) REVERT: D 160 MET cc_start: 0.6554 (ptp) cc_final: 0.6128 (ptt) REVERT: F 55 ILE cc_start: 0.3757 (mm) cc_final: 0.3432 (mm) REVERT: F 142 ILE cc_start: 0.4787 (mt) cc_final: 0.4554 (mp) outliers start: 45 outliers final: 30 residues processed: 316 average time/residue: 0.0999 time to fit residues: 45.0575 Evaluate side-chains 250 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain F residue 150 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 117 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 3 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 98 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 HIS A 585 HIS B 153 GLN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN B 339 ASN C 67 GLN C 146 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.217615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.186723 restraints weight = 52078.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.192041 restraints weight = 48486.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.196962 restraints weight = 14082.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.199271 restraints weight = 6207.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.199272 restraints weight = 3799.363| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4186 r_free = 0.4186 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4184 r_free = 0.4184 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11324 Z= 0.158 Angle : 0.646 8.572 15314 Z= 0.334 Chirality : 0.043 0.200 1695 Planarity : 0.005 0.087 1954 Dihedral : 7.098 104.671 1564 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 4.23 % Allowed : 20.30 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.23), residues: 1359 helix: 1.09 (0.19), residues: 719 sheet: 0.15 (0.44), residues: 141 loop : -0.80 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 671 TYR 0.022 0.002 TYR D 118 PHE 0.019 0.002 PHE B 371 TRP 0.022 0.001 TRP A 476 HIS 0.005 0.001 HIS A 725 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (11315) covalent geometry : angle 0.64396 / 0.33 (15308) hydrogen bonds : bond 0.04104 / 2.67 ( 596) hydrogen bonds : angle 4.75030 / 3.34 ( 1726) metal coordination : bond 0.02336 / 1.25 ( 8) metal coordination : angle 2.89467 / 1.58 ( 6) Misc. bond : bond 0.00709 / 0.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 249 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 LYS cc_start: 0.7934 (tptt) cc_final: 0.7176 (tptt) REVERT: A 564 MET cc_start: 0.7503 (mmm) cc_final: 0.6633 (tpp) REVERT: A 650 MET cc_start: 0.7982 (tpp) cc_final: 0.7372 (mmt) REVERT: B 107 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8179 (mt) REVERT: B 122 ASN cc_start: 0.7085 (m-40) cc_final: 0.5784 (p0) REVERT: B 175 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8507 (mtmm) REVERT: B 214 GLN cc_start: 0.7846 (mp10) cc_final: 0.7618 (mp10) REVERT: B 219 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7349 (tmm) REVERT: B 260 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6854 (ttp80) REVERT: C 92 GLU cc_start: 0.7480 (tp30) cc_final: 0.7163 (tp30) REVERT: D 88 LYS cc_start: 0.8244 (tppt) cc_final: 0.7701 (tptp) REVERT: F 55 ILE cc_start: 0.3858 (mm) cc_final: 0.3460 (mm) REVERT: F 129 GLN cc_start: 0.6795 (mm-40) cc_final: 0.6574 (pt0) REVERT: F 150 GLN cc_start: 0.1104 (OUTLIER) cc_final: 0.0769 (pt0) outliers start: 49 outliers final: 23 residues processed: 278 average time/residue: 0.0884 time to fit residues: 35.8677 Evaluate side-chains 255 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain F residue 150 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.209327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.177179 restraints weight = 49328.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.181673 restraints weight = 49600.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.188339 restraints weight = 15758.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.188742 restraints weight = 6558.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.188829 restraints weight = 4490.356| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4066 r_free = 0.4066 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4066 r_free = 0.4066 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11324 Z= 0.251 Angle : 0.741 9.613 15314 Z= 0.375 Chirality : 0.046 0.230 1695 Planarity : 0.005 0.092 1954 Dihedral : 7.387 106.796 1562 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.88 % Allowed : 18.97 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1359 helix: 1.05 (0.19), residues: 718 sheet: 0.29 (0.46), residues: 128 loop : -0.97 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 671 TYR 0.022 0.002 TYR C 125 PHE 0.020 0.002 PHE A 707 TRP 0.011 0.002 TRP A 476 HIS 0.013 0.002 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 (11315) covalent geometry : angle 0.73285 / 0.37 (15308) hydrogen bonds : bond 0.04205 / 2.74 ( 596) hydrogen bonds : angle 4.88143 / 3.42 ( 1726) metal coordination : bond 0.03175 / 1.74 ( 8) metal coordination : angle 5.51076 / 2.72 ( 6) Misc. bond : bond 0.00472 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 250 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7180 (ttm) cc_final: 0.6661 (tpp) REVERT: A 553 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8107 (tt) REVERT: A 564 MET cc_start: 0.7597 (mmm) cc_final: 0.7233 (mmm) REVERT: A 703 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7252 (tt0) REVERT: A 734 ASN cc_start: 0.7872 (t0) cc_final: 0.7520 (t0) REVERT: B 103 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8488 (tp) REVERT: B 122 ASN cc_start: 0.7306 (m-40) cc_final: 0.5952 (p0) REVERT: B 219 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7388 (tmm) REVERT: B 235 LEU cc_start: 0.8452 (mt) cc_final: 0.8213 (mt) REVERT: B 260 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6971 (ttp80) REVERT: B 345 ASN cc_start: 0.7518 (t0) cc_final: 0.5827 (t0) REVERT: C 92 GLU cc_start: 0.7511 (tp30) cc_final: 0.7176 (tp30) REVERT: D 50 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8628 (t0) REVERT: D 88 LYS cc_start: 0.8336 (tppt) cc_final: 0.7787 (tptp) REVERT: D 98 LEU cc_start: 0.8477 (mt) cc_final: 0.8156 (mt) REVERT: D 118 TYR cc_start: 0.8085 (m-80) cc_final: 0.7730 (m-80) REVERT: F 55 ILE cc_start: 0.4005 (mm) cc_final: 0.3349 (mt) REVERT: F 150 GLN cc_start: 0.1590 (OUTLIER) cc_final: 0.1224 (pt0) outliers start: 67 outliers final: 35 residues processed: 292 average time/residue: 0.0921 time to fit residues: 38.9330 Evaluate side-chains 261 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 150 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 126 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 ASN A 542 HIS ** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN C 67 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.208254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.172497 restraints weight = 55481.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.171961 restraints weight = 31191.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.165311 restraints weight = 19168.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.167535 restraints weight = 17400.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.168026 restraints weight = 11238.495| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 11324 Z= 0.223 Angle : 0.700 9.444 15314 Z= 0.354 Chirality : 0.045 0.204 1695 Planarity : 0.005 0.056 1954 Dihedral : 7.314 107.061 1558 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.81 % Allowed : 21.96 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.23), residues: 1359 helix: 1.12 (0.19), residues: 722 sheet: 0.10 (0.48), residues: 122 loop : -0.93 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 149 TYR 0.022 0.002 TYR C 125 PHE 0.023 0.002 PHE F 28 TRP 0.018 0.002 TRP A 476 HIS 0.012 0.002 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (11315) covalent geometry : angle 0.69404 / 0.35 (15308) hydrogen bonds : bond 0.04073 / 2.69 ( 596) hydrogen bonds : angle 4.81163 / 3.37 ( 1726) metal coordination : bond 0.04373 / 2.36 ( 8) metal coordination : angle 4.64709 / 2.35 ( 6) Misc. bond : bond 0.00086 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7276 (ttm) cc_final: 0.6749 (tpp) REVERT: A 553 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8420 (tt) REVERT: A 564 MET cc_start: 0.7411 (mmm) cc_final: 0.7036 (mmm) REVERT: A 650 MET cc_start: 0.8322 (tpp) cc_final: 0.7890 (mmt) REVERT: A 734 ASN cc_start: 0.7966 (t0) cc_final: 0.7648 (t0) REVERT: B 187 MET cc_start: 0.6512 (pmm) cc_final: 0.6087 (ptm) REVERT: B 204 ILE cc_start: 0.7828 (mp) cc_final: 0.7602 (mp) REVERT: B 219 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7448 (tmm) REVERT: B 260 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7002 (ttp80) REVERT: B 274 MET cc_start: 0.7466 (mtp) cc_final: 0.7165 (mtp) REVERT: C 92 GLU cc_start: 0.7342 (tp30) cc_final: 0.7016 (tp30) REVERT: D 88 LYS cc_start: 0.8170 (tppt) cc_final: 0.7701 (tptp) REVERT: D 98 LEU cc_start: 0.8406 (mt) cc_final: 0.8176 (mt) REVERT: D 150 GLN cc_start: 0.7861 (tp40) cc_final: 0.7526 (tp40) REVERT: F 55 ILE cc_start: 0.4005 (mm) cc_final: 0.3359 (mt) REVERT: F 150 GLN cc_start: 0.1249 (OUTLIER) cc_final: 0.0951 (pt0) outliers start: 54 outliers final: 40 residues processed: 278 average time/residue: 0.0894 time to fit residues: 36.6134 Evaluate side-chains 259 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 150 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 44 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN C 67 GLN C 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.211669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.177985 restraints weight = 62830.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175302 restraints weight = 29726.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.172027 restraints weight = 16942.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.173890 restraints weight = 15864.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174268 restraints weight = 10411.306| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3974 r_free = 0.3974 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3973 r_free = 0.3973 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.6244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.285 11324 Z= 0.161 Angle : 0.677 14.582 15314 Z= 0.341 Chirality : 0.044 0.226 1695 Planarity : 0.004 0.049 1954 Dihedral : 7.217 106.106 1558 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.56 % Allowed : 22.87 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.23), residues: 1359 helix: 1.17 (0.19), residues: 723 sheet: 0.03 (0.44), residues: 141 loop : -0.98 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 166 TYR 0.018 0.002 TYR C 125 PHE 0.015 0.002 PHE A 707 TRP 0.022 0.001 TRP A 476 HIS 0.034 0.002 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11315) covalent geometry : angle 0.65944 / 0.34 (15308) hydrogen bonds : bond 0.03857 / 2.58 ( 596) hydrogen bonds : angle 4.66585 / 3.26 ( 1726) metal coordination : bond 0.10496 / 5.31 ( 8) metal coordination : angle 7.69002 / 3.94 ( 6) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7301 (ttm) cc_final: 0.6765 (tpp) REVERT: A 450 TRP cc_start: 0.6116 (m100) cc_final: 0.5636 (m100) REVERT: A 519 TYR cc_start: 0.7924 (p90) cc_final: 0.7603 (p90) REVERT: A 564 MET cc_start: 0.7309 (mmm) cc_final: 0.6934 (mmm) REVERT: A 693 MET cc_start: 0.8394 (ttp) cc_final: 0.8191 (ttt) REVERT: B 81 VAL cc_start: 0.8364 (t) cc_final: 0.8144 (t) REVERT: B 110 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8118 (tm-30) REVERT: B 111 ILE cc_start: 0.9430 (mt) cc_final: 0.9180 (mt) REVERT: B 174 ILE cc_start: 0.8559 (mm) cc_final: 0.8226 (mm) REVERT: B 187 MET cc_start: 0.6433 (pmm) cc_final: 0.6157 (ptm) REVERT: B 219 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7438 (tmm) REVERT: B 260 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7033 (ttp80) REVERT: C 92 GLU cc_start: 0.7296 (tp30) cc_final: 0.7000 (tp30) REVERT: D 88 LYS cc_start: 0.8170 (tppt) cc_final: 0.7712 (tptp) REVERT: D 92 GLU cc_start: 0.6746 (pm20) cc_final: 0.6144 (pm20) REVERT: D 113 GLU cc_start: 0.6292 (mm-30) cc_final: 0.5375 (mm-30) REVERT: F 55 ILE cc_start: 0.4019 (mm) cc_final: 0.3597 (mm) REVERT: F 159 LEU cc_start: 0.6314 (tp) cc_final: 0.5834 (tp) outliers start: 50 outliers final: 37 residues processed: 275 average time/residue: 0.0897 time to fit residues: 36.3907 Evaluate side-chains 260 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain F residue 43 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 109 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 118 optimal weight: 30.0000 chunk 86 optimal weight: 0.6980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN C 67 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.205420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.173483 restraints weight = 50427.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.178165 restraints weight = 46888.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.182220 restraints weight = 14220.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.184843 restraints weight = 6618.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.184747 restraints weight = 3887.952| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4064 r_free = 0.4064 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4063 r_free = 0.4063 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.271 11324 Z= 0.300 Angle : 0.828 14.694 15314 Z= 0.412 Chirality : 0.049 0.334 1695 Planarity : 0.006 0.100 1954 Dihedral : 7.405 104.168 1558 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.47 % Allowed : 25.19 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.23), residues: 1359 helix: 0.85 (0.18), residues: 724 sheet: 0.12 (0.47), residues: 125 loop : -1.08 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 97 TYR 0.036 0.002 TYR C 48 PHE 0.023 0.003 PHE A 468 TRP 0.025 0.003 TRP A 476 HIS 0.020 0.002 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.30 (11315) covalent geometry : angle 0.81424 / 0.41 (15308) hydrogen bonds : bond 0.04312 / 2.84 ( 596) hydrogen bonds : angle 5.01743 / 3.50 ( 1726) metal coordination : bond 0.11153 / 5.71 ( 8) metal coordination : angle 7.69105 / 4.04 ( 6) Misc. bond : bond 0.00418 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7273 (ttm) cc_final: 0.6814 (tpp) REVERT: A 519 TYR cc_start: 0.8080 (p90) cc_final: 0.7510 (p90) REVERT: A 564 MET cc_start: 0.7519 (mmm) cc_final: 0.7166 (mmm) REVERT: A 627 MET cc_start: 0.8412 (tpp) cc_final: 0.8147 (tpp) REVERT: A 650 MET cc_start: 0.7840 (tpp) cc_final: 0.7456 (mmt) REVERT: A 664 GLN cc_start: 0.7989 (tp40) cc_final: 0.7785 (tp40) REVERT: B 214 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7878 (tm-30) REVERT: B 219 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7488 (tmm) REVERT: B 260 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7136 (ttp80) REVERT: C 92 GLU cc_start: 0.7475 (tp30) cc_final: 0.7135 (tp30) REVERT: C 111 ASN cc_start: 0.8260 (t0) cc_final: 0.7988 (t0) REVERT: D 88 LYS cc_start: 0.8277 (tppt) cc_final: 0.7771 (tptp) REVERT: D 118 TYR cc_start: 0.8154 (m-80) cc_final: 0.7750 (m-80) REVERT: F 37 GLU cc_start: 0.5938 (pt0) cc_final: 0.5702 (pt0) REVERT: F 55 ILE cc_start: 0.4193 (mm) cc_final: 0.3634 (mt) REVERT: F 159 LEU cc_start: 0.6085 (tp) cc_final: 0.5745 (tp) outliers start: 49 outliers final: 36 residues processed: 259 average time/residue: 0.0956 time to fit residues: 36.3329 Evaluate side-chains 248 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 97 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 126 optimal weight: 30.0000 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN B 243 GLN C 67 GLN C 146 GLN F 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.210496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.178223 restraints weight = 53973.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.183381 restraints weight = 47992.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.188462 restraints weight = 15053.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.191792 restraints weight = 6558.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.191661 restraints weight = 3630.730| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4130 r_free = 0.4130 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4130 r_free = 0.4130 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.4130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.6835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 11324 Z= 0.154 Angle : 0.698 10.681 15314 Z= 0.353 Chirality : 0.045 0.243 1695 Planarity : 0.005 0.107 1954 Dihedral : 7.225 102.260 1558 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.56 % Allowed : 26.35 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1359 helix: 1.06 (0.19), residues: 725 sheet: 0.02 (0.47), residues: 126 loop : -0.93 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG F 97 TYR 0.019 0.002 TYR C 48 PHE 0.024 0.002 PHE A 250 TRP 0.035 0.003 TRP B 374 HIS 0.015 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (11315) covalent geometry : angle 0.68911 / 0.35 (15308) hydrogen bonds : bond 0.03817 / 2.55 ( 596) hydrogen bonds : angle 4.70980 / 3.29 ( 1726) metal coordination : bond 0.06741 / 3.43 ( 8) metal coordination : angle 5.60125 / 2.88 ( 6) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7282 (ttm) cc_final: 0.6788 (tpp) REVERT: A 450 TRP cc_start: 0.7320 (OUTLIER) cc_final: 0.6970 (m100) REVERT: A 519 TYR cc_start: 0.7962 (p90) cc_final: 0.7755 (p90) REVERT: A 551 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.7855 (mt) REVERT: A 564 MET cc_start: 0.7323 (mmm) cc_final: 0.6888 (mmm) REVERT: A 650 MET cc_start: 0.7900 (tpp) cc_final: 0.7344 (mmt) REVERT: A 664 GLN cc_start: 0.7659 (tp40) cc_final: 0.7422 (tp40) REVERT: B 143 MET cc_start: 0.6350 (mtp) cc_final: 0.5901 (mtp) REVERT: B 214 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7578 (tm-30) REVERT: B 219 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7594 (tmm) REVERT: B 239 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.6349 (p90) REVERT: B 260 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6957 (ttp80) REVERT: C 92 GLU cc_start: 0.7363 (tp30) cc_final: 0.7037 (tp30) REVERT: C 111 ASN cc_start: 0.8169 (t0) cc_final: 0.7937 (t0) REVERT: D 88 LYS cc_start: 0.8190 (tppt) cc_final: 0.7756 (tptp) REVERT: D 92 GLU cc_start: 0.6675 (pm20) cc_final: 0.6106 (pm20) REVERT: D 98 LEU cc_start: 0.8416 (mt) cc_final: 0.8092 (mt) REVERT: D 166 ILE cc_start: 0.9348 (mm) cc_final: 0.9141 (mt) REVERT: F 55 ILE cc_start: 0.3810 (mm) cc_final: 0.3313 (mm) REVERT: F 93 ILE cc_start: 0.7065 (mm) cc_final: 0.6676 (mm) outliers start: 38 outliers final: 25 residues processed: 259 average time/residue: 0.0907 time to fit residues: 34.7802 Evaluate side-chains 253 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 97 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN C 67 GLN ** C 146 GLN ** 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 = 0.4369 r_free = 0.4369 target = 0.210328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178673 restraints weight = 53353.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.183821 restraints weight = 48583.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.188911 restraints weight = 14589.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.191048 restraints weight = 6204.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.191055 restraints weight = 3958.155| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4090 r_free = 0.4090 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4089 r_free = 0.4089 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.4089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 11324 Z= 0.155 Angle : 0.695 9.626 15314 Z= 0.352 Chirality : 0.045 0.233 1695 Planarity : 0.005 0.079 1954 Dihedral : 7.116 98.746 1557 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.48 % Allowed : 26.76 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1359 helix: 1.06 (0.19), residues: 729 sheet: 0.35 (0.49), residues: 110 loop : -1.00 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 97 TYR 0.022 0.002 TYR C 48 PHE 0.028 0.002 PHE A 250 TRP 0.050 0.002 TRP B 374 HIS 0.015 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (11315) covalent geometry : angle 0.68905 / 0.35 (15308) hydrogen bonds : bond 0.03750 / 2.47 ( 596) hydrogen bonds : angle 4.75526 / 3.31 ( 1726) metal coordination : bond 0.05866 / 2.99 ( 8) metal coordination : angle 4.57094 / 2.34 ( 6) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7256 (ttm) cc_final: 0.6771 (tpp) REVERT: A 519 TYR cc_start: 0.7909 (p90) cc_final: 0.7539 (p90) REVERT: A 551 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.7802 (mt) REVERT: A 564 MET cc_start: 0.7381 (mmm) cc_final: 0.6962 (mmm) REVERT: A 627 MET cc_start: 0.8126 (tpp) cc_final: 0.7923 (tpp) REVERT: A 664 GLN cc_start: 0.7754 (tp40) cc_final: 0.7543 (tp40) REVERT: A 735 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6625 (ttm-80) REVERT: B 49 ARG cc_start: 0.7391 (mmp-170) cc_final: 0.6862 (mtm110) REVERT: B 219 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7625 (tmm) REVERT: B 239 HIS cc_start: 0.6367 (OUTLIER) cc_final: 0.6141 (p90) REVERT: B 260 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6968 (ttp80) REVERT: C 14 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8338 (tp30) REVERT: C 92 GLU cc_start: 0.7424 (tp30) cc_final: 0.7096 (tp30) REVERT: C 111 ASN cc_start: 0.8186 (t0) cc_final: 0.7975 (t0) REVERT: D 88 LYS cc_start: 0.8218 (tppt) cc_final: 0.7784 (tptp) REVERT: D 92 GLU cc_start: 0.6783 (pm20) cc_final: 0.6227 (pm20) REVERT: D 98 LEU cc_start: 0.8499 (mt) cc_final: 0.8212 (mt) REVERT: D 160 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5464 (mtt) REVERT: D 228 TRP cc_start: 0.6508 (m-10) cc_final: 0.6290 (m-10) REVERT: F 55 ILE cc_start: 0.3792 (mm) cc_final: 0.3329 (mm) outliers start: 37 outliers final: 23 residues processed: 259 average time/residue: 0.0964 time to fit residues: 36.9060 Evaluate side-chains 255 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain F residue 97 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 65 optimal weight: 0.0770 chunk 130 optimal weight: 0.0010 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 overall best weight: 0.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.211444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.179488 restraints weight = 50982.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.184183 restraints weight = 49962.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.190034 restraints weight = 15803.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.191737 restraints weight = 6688.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.191950 restraints weight = 4277.206| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.4139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 11324 Z= 0.151 Angle : 0.711 9.857 15314 Z= 0.362 Chirality : 0.045 0.229 1695 Planarity : 0.005 0.062 1954 Dihedral : 7.018 95.329 1557 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.07 % Allowed : 26.51 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1359 helix: 1.03 (0.19), residues: 735 sheet: 0.45 (0.50), residues: 110 loop : -0.98 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 166 TYR 0.019 0.002 TYR C 48 PHE 0.030 0.002 PHE B 337 TRP 0.059 0.003 TRP B 374 HIS 0.015 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (11315) covalent geometry : angle 0.70691 / 0.36 (15308) hydrogen bonds : bond 0.03858 / 2.57 ( 596) hydrogen bonds : angle 4.77396 / 3.33 ( 1726) metal coordination : bond 0.05394 / 2.75 ( 8) metal coordination : angle 4.02470 / 2.05 ( 6) Misc. bond : bond 0.00034 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7241 (ttm) cc_final: 0.6749 (tpp) REVERT: A 519 TYR cc_start: 0.7916 (p90) cc_final: 0.7540 (p90) REVERT: A 551 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.7774 (mt) REVERT: A 564 MET cc_start: 0.7344 (mmm) cc_final: 0.6937 (mmm) REVERT: A 650 MET cc_start: 0.7930 (tpp) cc_final: 0.7542 (mmt) REVERT: A 664 GLN cc_start: 0.7669 (tp40) cc_final: 0.7333 (tp40) REVERT: B 219 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: B 221 ASN cc_start: 0.9042 (t0) cc_final: 0.8834 (t0) REVERT: B 239 HIS cc_start: 0.6454 (OUTLIER) cc_final: 0.6215 (p90) REVERT: B 260 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6724 (ttp80) REVERT: C 14 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8374 (tp30) REVERT: C 160 MET cc_start: 0.6574 (tpp) cc_final: 0.6160 (tpp) REVERT: D 88 LYS cc_start: 0.8245 (tppt) cc_final: 0.7811 (tptp) REVERT: D 92 GLU cc_start: 0.6768 (pm20) cc_final: 0.6267 (pm20) REVERT: F 55 ILE cc_start: 0.3834 (mm) cc_final: 0.3379 (mm) outliers start: 32 outliers final: 26 residues processed: 245 average time/residue: 0.0905 time to fit residues: 33.2744 Evaluate side-chains 245 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 97 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.210882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.173845 restraints weight = 70424.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.175452 restraints weight = 38267.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.173779 restraints weight = 15825.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.175751 restraints weight = 12666.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.177616 restraints weight = 9524.568| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.4011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 11324 Z= 0.154 Angle : 0.711 11.729 15314 Z= 0.361 Chirality : 0.046 0.261 1695 Planarity : 0.005 0.061 1954 Dihedral : 6.955 90.414 1557 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.15 % Allowed : 26.35 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.23), residues: 1359 helix: 0.98 (0.19), residues: 743 sheet: 0.45 (0.48), residues: 121 loop : -0.97 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 222 TYR 0.022 0.002 TYR D 178 PHE 0.027 0.002 PHE A 250 TRP 0.060 0.003 TRP B 374 HIS 0.014 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11315) covalent geometry : angle 0.70678 / 0.36 (15308) hydrogen bonds : bond 0.03878 / 2.57 ( 596) hydrogen bonds : angle 4.79627 / 3.36 ( 1726) metal coordination : bond 0.05334 / 2.73 ( 8) metal coordination : angle 3.88946 / 1.98 ( 6) Misc. bond : bond 0.00049 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1827.21 seconds wall clock time: 32 minutes 32.07 seconds (1952.07 seconds total)