Starting phenix.real_space_refine on Wed Mar 4 05:57:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dgt_27429/03_2026/8dgt_27429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dgt_27429/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dgt_27429/03_2026/8dgt_27429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dgt_27429/03_2026/8dgt_27429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dgt_27429/03_2026/8dgt_27429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dgt_27429/03_2026/8dgt_27429.map" } 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-5986/lib/python3.9/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: 2.74, per 1000 atoms: 0.25 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: 0.95 Conformation dependent library (CDL) restraints added in 757.6 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: 0.26 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: 1.83 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 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: 6617 21.56 - 43.13: 260 43.13 - 64.69: 84 64.69 - 86.25: 10 86.25 - 107.81: 4 Dihedral angle restraints: 6975 sinusoidal: 2927 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 6972 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: 1.140 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.600 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5263 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 : 13.248 107.814 4363 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 covalent geometry : bond 0.00587 (11315) covalent geometry : angle 0.86449 (15308) hydrogen bonds : bond 0.14121 ( 596) hydrogen bonds : angle 6.16729 ( 1726) metal coordination : bond 0.13815 ( 8) metal coordination : angle 18.18594 ( 6) Misc. bond : bond 0.00673 ( 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 : 0.439 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: 0.1284 time to fit residues: 83.1709 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 : 0.402 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4443 r_free = 0.4443 target = 0.217416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.181568 restraints weight = 60333.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.179517 restraints weight = 33160.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.175024 restraints weight = 18245.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.176579 restraints weight = 18293.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.180168 restraints weight = 12190.762| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- 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 = 0.16 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 = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 11324 Z= 0.265 Angle : 0.773 9.283 15314 Z= 0.400 Chirality : 0.046 0.238 1695 Planarity : 0.006 0.080 1954 Dihedral : 8.523 109.606 1617 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.89 % Allowed : 17.40 % Favored : 78.71 % 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: 0.19 (0.22), residues: 1359 helix: 0.97 (0.18), residues: 710 sheet: 0.08 (0.44), residues: 132 loop : -0.98 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 575 TYR 0.024 0.003 TYR B 229 PHE 0.026 0.003 PHE B 371 TRP 0.014 0.002 TRP A 476 HIS 0.015 0.002 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00602 (11315) covalent geometry : angle 0.76916 (15308) hydrogen bonds : bond 0.04664 ( 596) hydrogen bonds : angle 5.10229 ( 1726) metal coordination : bond 0.04270 ( 8) metal coordination : angle 3.83444 ( 6) Misc. bond : bond 0.00032 ( 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 336 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 291 time to evaluate : 0.366 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: 0.6898 (m-30) cc_final: 0.6510 (m-30) REVERT: A 624 VAL cc_start: 0.7576 (t) cc_final: 0.7276 (p) REVERT: A 715 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6986 (tt0) REVERT: A 725 HIS cc_start: 0.5846 (m170) cc_final: 0.5576 (m170) REVERT: B 122 ASN cc_start: 0.7245 (m-40) cc_final: 0.5886 (p0) REVERT: B 260 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7059 (ttp80) REVERT: B 319 ASN cc_start: 0.8110 (p0) cc_final: 0.7859 (p0) REVERT: C 77 GLN cc_start: 0.7715 (mp10) cc_final: 0.7406 (mp10) REVERT: D 160 MET cc_start: 0.6463 (ptp) cc_final: 0.6050 (ptt) REVERT: F 55 ILE cc_start: 0.3778 (mm) cc_final: 0.3438 (mm) REVERT: F 142 ILE cc_start: 0.4766 (mt) cc_final: 0.4532 (mp) outliers start: 45 outliers final: 30 residues processed: 317 average time/residue: 0.1076 time to fit residues: 48.1907 Evaluate side-chains 248 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 A residue 715 GLU Chi-restraints excluded: chain B residue 82 VAL 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: 4.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.216029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.180965 restraints weight = 52577.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.181809 restraints weight = 32698.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.176959 restraints weight = 17448.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.179110 restraints weight = 16306.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.181806 restraints weight = 11053.111| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4043 r_free = 0.4043 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 11324 Z= 0.197 Angle : 0.673 8.057 15314 Z= 0.348 Chirality : 0.044 0.176 1695 Planarity : 0.005 0.089 1954 Dihedral : 8.314 109.983 1614 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 4.47 % Allowed : 20.63 % Favored : 74.90 % 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: 0.35 (0.23), residues: 1359 helix: 1.07 (0.19), residues: 716 sheet: 0.11 (0.43), residues: 141 loop : -0.88 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 701 TYR 0.020 0.002 TYR D 118 PHE 0.019 0.002 PHE B 371 TRP 0.024 0.002 TRP A 476 HIS 0.006 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00449 (11315) covalent geometry : angle 0.66977 (15308) hydrogen bonds : bond 0.04209 ( 596) hydrogen bonds : angle 4.83431 ( 1726) metal coordination : bond 0.03238 ( 8) metal coordination : angle 3.57312 ( 6) Misc. bond : bond 0.00755 ( 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 306 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 0.274 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 249 ASP cc_start: 0.8033 (m-30) cc_final: 0.7524 (t0) REVERT: A 564 MET cc_start: 0.7355 (mmm) cc_final: 0.6533 (tpp) REVERT: A 594 ASP cc_start: 0.6933 (m-30) cc_final: 0.6651 (m-30) REVERT: A 650 MET cc_start: 0.8214 (tpp) cc_final: 0.7516 (mmt) REVERT: A 703 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7078 (tt0) REVERT: B 111 ILE cc_start: 0.9488 (mt) cc_final: 0.9241 (mm) REVERT: B 122 ASN cc_start: 0.7194 (m-40) cc_final: 0.5893 (p0) REVERT: B 175 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8469 (mtmm) REVERT: B 219 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7368 (tmm) REVERT: B 260 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6946 (ttp80) REVERT: D 88 LYS cc_start: 0.8298 (tppt) cc_final: 0.7778 (tptp) REVERT: F 55 ILE cc_start: 0.3921 (mm) cc_final: 0.3503 (mm) REVERT: F 150 GLN cc_start: 0.0947 (OUTLIER) cc_final: 0.0613 (pt0) outliers start: 52 outliers final: 30 residues processed: 285 average time/residue: 0.0925 time to fit residues: 38.2324 Evaluate side-chains 259 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 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 669 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU 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 29 VAL 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: 3.9990 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN C 42 ASN C 67 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 194 GLN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.203733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.165034 restraints weight = 49374.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.165204 restraints weight = 33930.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.163515 restraints weight = 16122.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.164746 restraints weight = 14293.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.165108 restraints weight = 11256.887| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 11324 Z= 0.358 Angle : 0.881 12.623 15314 Z= 0.447 Chirality : 0.051 0.266 1695 Planarity : 0.006 0.105 1954 Dihedral : 8.976 113.658 1612 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.88 % Allowed : 20.05 % Favored : 73.07 % 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: -0.22 (0.22), residues: 1359 helix: 0.56 (0.18), residues: 716 sheet: 0.20 (0.47), residues: 122 loop : -1.16 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 671 TYR 0.027 0.003 TYR C 125 PHE 0.030 0.003 PHE C 177 TRP 0.021 0.002 TRP A 476 HIS 0.011 0.002 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00825 (11315) covalent geometry : angle 0.87107 (15308) hydrogen bonds : bond 0.04858 ( 596) hydrogen bonds : angle 5.30672 ( 1726) metal coordination : bond 0.02918 ( 8) metal coordination : angle 6.76692 ( 6) Misc. bond : bond 0.00180 ( 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 334 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 255 time to evaluate : 0.408 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: 0.7243 (ttm) cc_final: 0.6824 (tpp) REVERT: A 735 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6670 (ttm-80) REVERT: B 171 ILE cc_start: 0.7650 (mt) cc_final: 0.6578 (tp) REVERT: B 175 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8379 (mtmm) REVERT: B 195 ASN cc_start: 0.9055 (m-40) cc_final: 0.8376 (m-40) REVERT: B 199 ASN cc_start: 0.6820 (p0) cc_final: 0.5580 (p0) REVERT: B 207 CYS cc_start: 0.6924 (p) cc_final: 0.6693 (t) REVERT: B 219 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7641 (tmm) REVERT: C 101 LEU cc_start: 0.7897 (tp) cc_final: 0.7681 (tp) REVERT: D 50 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8762 (t0) REVERT: D 88 LYS cc_start: 0.8365 (tppt) cc_final: 0.7905 (tptp) REVERT: D 160 MET cc_start: 0.6918 (ptp) cc_final: 0.6537 (ptp) REVERT: F 55 ILE cc_start: 0.4204 (mm) cc_final: 0.3630 (mt) REVERT: F 150 GLN cc_start: 0.1285 (OUTLIER) cc_final: 0.1041 (pt0) outliers start: 79 outliers final: 44 residues processed: 304 average time/residue: 0.0977 time to fit residues: 42.9287 Evaluate side-chains 269 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 244 THR Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 276 VAL 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 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 A residue 719 ARG Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 LYS 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 224 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS 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 69 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 214 SER 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 64 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 153 PHE 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: 3.9990 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN C 146 GLN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.207586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.172101 restraints weight = 54337.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.173526 restraints weight = 31243.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171721 restraints weight = 15215.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.172851 restraints weight = 14806.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173040 restraints weight = 10620.203| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3939 r_free = 0.3939 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.296 11324 Z= 0.191 Angle : 0.711 15.384 15314 Z= 0.358 Chirality : 0.044 0.184 1695 Planarity : 0.005 0.052 1954 Dihedral : 8.598 113.363 1608 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.89 % Allowed : 22.95 % Favored : 72.16 % 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: 0.05 (0.23), residues: 1359 helix: 0.85 (0.19), residues: 717 sheet: 0.12 (0.50), residues: 110 loop : -1.05 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 626 TYR 0.028 0.002 TYR D 118 PHE 0.023 0.002 PHE A 250 TRP 0.030 0.002 TRP A 476 HIS 0.026 0.002 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00425 (11315) covalent geometry : angle 0.68658 (15308) hydrogen bonds : bond 0.04074 ( 596) hydrogen bonds : angle 4.85257 ( 1726) metal coordination : bond 0.10636 ( 8) metal coordination : angle 9.42677 ( 6) Misc. bond : bond 0.00067 ( 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 308 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 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: 0.7346 (ttm) cc_final: 0.6902 (tpp) REVERT: A 234 THR cc_start: 0.7634 (m) cc_final: 0.7296 (p) REVERT: A 564 MET cc_start: 0.7292 (mmm) cc_final: 0.6951 (mmm) REVERT: A 650 MET cc_start: 0.8141 (tpp) cc_final: 0.7685 (mmt) REVERT: A 735 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7000 (ttm-80) REVERT: B 111 ILE cc_start: 0.9415 (mt) cc_final: 0.9193 (mm) REVERT: B 219 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7639 (tmm) REVERT: B 253 LEU cc_start: 0.7683 (mm) cc_final: 0.7406 (mm) REVERT: B 274 MET cc_start: 0.7094 (mtp) cc_final: 0.6885 (mtp) REVERT: D 88 LYS cc_start: 0.8161 (tppt) cc_final: 0.7600 (tptp) REVERT: D 98 LEU cc_start: 0.8322 (mt) cc_final: 0.7926 (mt) REVERT: F 55 ILE cc_start: 0.4104 (mm) cc_final: 0.3460 (mt) REVERT: F 150 GLN cc_start: 0.0797 (OUTLIER) cc_final: 0.0463 (pt0) REVERT: F 159 LEU cc_start: 0.5860 (tp) cc_final: 0.5435 (tp) outliers start: 55 outliers final: 36 residues processed: 289 average time/residue: 0.0914 time to fit residues: 38.8747 Evaluate side-chains 259 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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 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 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 A residue 735 ARG Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 191 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 224 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS 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 43 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 153 PHE 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: 1.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 90 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN C 146 GLN ** F 22 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 = 0.4372 r_free = 0.4372 target = 0.210150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.175302 restraints weight = 62855.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.174245 restraints weight = 30457.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.172032 restraints weight = 14915.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.173725 restraints weight = 12687.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.174220 restraints weight = 9895.938| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3939 r_free = 0.3939 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.207 11324 Z= 0.169 Angle : 0.703 12.246 15314 Z= 0.350 Chirality : 0.045 0.270 1695 Planarity : 0.005 0.049 1954 Dihedral : 8.485 110.311 1608 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.89 % Allowed : 24.69 % Favored : 71.42 % 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: 0.24 (0.23), residues: 1359 helix: 0.99 (0.19), residues: 716 sheet: -0.09 (0.49), residues: 115 loop : -0.87 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 506 TYR 0.033 0.002 TYR D 118 PHE 0.022 0.002 PHE A 250 TRP 0.029 0.002 TRP A 450 HIS 0.016 0.002 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00382 (11315) covalent geometry : angle 0.68883 (15308) hydrogen bonds : bond 0.03912 ( 596) hydrogen bonds : angle 4.77676 ( 1726) metal coordination : bond 0.07462 ( 8) metal coordination : angle 7.06542 ( 6) Misc. bond : bond 0.00382 ( 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 278 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.429 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 186 MET cc_start: 0.7357 (ttm) cc_final: 0.6881 (tpp) REVERT: A 234 THR cc_start: 0.7761 (m) cc_final: 0.7276 (p) REVERT: A 519 TYR cc_start: 0.8019 (p90) cc_final: 0.7621 (p90) REVERT: A 564 MET cc_start: 0.7397 (mmm) cc_final: 0.7023 (mmm) REVERT: B 219 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7611 (tmm) REVERT: B 221 ASN cc_start: 0.8995 (t0) cc_final: 0.8753 (t0) REVERT: D 88 LYS cc_start: 0.8201 (tppt) cc_final: 0.7687 (tptp) REVERT: D 217 ILE cc_start: 0.8694 (mm) cc_final: 0.8425 (mm) REVERT: F 55 ILE cc_start: 0.3956 (mm) cc_final: 0.3342 (mt) REVERT: F 150 GLN cc_start: 0.1422 (OUTLIER) cc_final: 0.1034 (pt0) REVERT: F 159 LEU cc_start: 0.5927 (tp) cc_final: 0.5574 (tp) outliers start: 43 outliers final: 32 residues processed: 264 average time/residue: 0.0892 time to fit residues: 35.2608 Evaluate side-chains 253 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 255 LEU 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 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 100 HIS 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 224 VAL 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 352 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 D residue 63 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain F residue 150 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS B 46 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 243 GLN C 67 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.208821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.169321 restraints weight = 48080.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.170560 restraints weight = 34161.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168641 restraints weight = 15952.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.169933 restraints weight = 17434.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.171122 restraints weight = 11478.525| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3934 r_free = 0.3934 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 11324 Z= 0.183 Angle : 0.705 14.590 15314 Z= 0.353 Chirality : 0.046 0.345 1695 Planarity : 0.005 0.110 1954 Dihedral : 8.434 110.659 1608 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.31 % Allowed : 25.52 % Favored : 70.17 % 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: 0.30 (0.23), residues: 1359 helix: 0.98 (0.19), residues: 719 sheet: -0.06 (0.49), residues: 114 loop : -0.76 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG F 97 TYR 0.030 0.002 TYR D 118 PHE 0.024 0.002 PHE A 250 TRP 0.025 0.002 TRP A 476 HIS 0.012 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00421 (11315) covalent geometry : angle 0.69730 (15308) hydrogen bonds : bond 0.03984 ( 596) hydrogen bonds : angle 4.82004 ( 1726) metal coordination : bond 0.05955 ( 8) metal coordination : angle 5.36905 ( 6) Misc. bond : bond 0.00071 ( 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 275 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 0.305 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: 0.7327 (ttm) cc_final: 0.6847 (tpp) REVERT: A 234 THR cc_start: 0.7824 (m) cc_final: 0.7245 (p) REVERT: A 519 TYR cc_start: 0.8102 (p90) cc_final: 0.7752 (p90) REVERT: A 564 MET cc_start: 0.7515 (mmm) cc_final: 0.7186 (mmm) REVERT: A 650 MET cc_start: 0.8221 (tpp) cc_final: 0.7912 (mmt) REVERT: A 701 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.7029 (ptp-170) REVERT: A 735 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6942 (ttm-80) REVERT: B 103 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8469 (tp) REVERT: B 219 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7652 (tmm) REVERT: B 239 HIS cc_start: 0.7162 (OUTLIER) cc_final: 0.6730 (p90) REVERT: B 339 ASN cc_start: 0.8161 (m-40) cc_final: 0.7875 (m110) REVERT: C 111 ASN cc_start: 0.8237 (t0) cc_final: 0.8034 (t0) REVERT: D 88 LYS cc_start: 0.8256 (tppt) cc_final: 0.7712 (tptp) REVERT: D 113 GLU cc_start: 0.6103 (tp30) cc_final: 0.5241 (mm-30) REVERT: D 217 ILE cc_start: 0.8691 (mm) cc_final: 0.8441 (mm) REVERT: F 55 ILE cc_start: 0.3813 (mm) cc_final: 0.3267 (mm) REVERT: F 150 GLN cc_start: 0.1454 (OUTLIER) cc_final: 0.1084 (pt0) REVERT: F 159 LEU cc_start: 0.6069 (tp) cc_final: 0.5804 (tp) outliers start: 47 outliers final: 33 residues processed: 259 average time/residue: 0.0942 time to fit residues: 36.0073 Evaluate side-chains 253 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 255 LEU 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 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 701 ARG 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 46 GLN Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 103 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 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 220 LEU 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 97 ARG Chi-restraints excluded: chain F residue 150 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.0030 chunk 122 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN B 45 GLN B 46 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 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 = 0.4372 r_free = 0.4372 target = 0.210702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.178008 restraints weight = 52880.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.182549 restraints weight = 50223.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.187900 restraints weight = 15846.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.191134 restraints weight = 6630.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.191190 restraints weight = 3653.310| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4126 r_free = 0.4126 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.6882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 11324 Z= 0.142 Angle : 0.680 13.764 15314 Z= 0.342 Chirality : 0.045 0.262 1695 Planarity : 0.005 0.091 1954 Dihedral : 8.335 109.309 1607 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.89 % Allowed : 25.68 % 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: 0.34 (0.23), residues: 1359 helix: 1.03 (0.19), residues: 724 sheet: -0.10 (0.47), residues: 126 loop : -0.77 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 97 TYR 0.033 0.002 TYR C 48 PHE 0.021 0.002 PHE B 337 TRP 0.034 0.002 TRP B 374 HIS 0.010 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00320 (11315) covalent geometry : angle 0.67331 (15308) hydrogen bonds : bond 0.03822 ( 596) hydrogen bonds : angle 4.68586 ( 1726) metal coordination : bond 0.04698 ( 8) metal coordination : angle 4.77052 ( 6) Misc. bond : bond 0.00033 ( 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 270 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 0.298 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: 0.7295 (ttm) cc_final: 0.6805 (tpp) REVERT: A 234 THR cc_start: 0.7824 (m) cc_final: 0.7165 (p) REVERT: A 519 TYR cc_start: 0.7988 (p90) cc_final: 0.7741 (p90) REVERT: A 551 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.7912 (mt) REVERT: A 564 MET cc_start: 0.7372 (mmm) cc_final: 0.6978 (mmm) REVERT: A 735 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6857 (ttm-80) REVERT: B 103 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8435 (tp) REVERT: B 170 SER cc_start: 0.8523 (m) cc_final: 0.7996 (p) REVERT: B 174 ILE cc_start: 0.8705 (mm) cc_final: 0.8344 (mm) REVERT: B 219 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7683 (tmm) REVERT: B 239 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.6075 (p90) REVERT: B 356 MET cc_start: 0.7291 (mtt) cc_final: 0.7091 (mmt) REVERT: C 111 ASN cc_start: 0.8192 (t0) cc_final: 0.7956 (t0) REVERT: D 88 LYS cc_start: 0.8194 (tppt) cc_final: 0.7565 (tptp) REVERT: D 166 ILE cc_start: 0.9404 (mm) cc_final: 0.9196 (mt) REVERT: D 217 ILE cc_start: 0.8710 (mm) cc_final: 0.8435 (mm) REVERT: F 55 ILE cc_start: 0.3693 (mm) cc_final: 0.3134 (mm) outliers start: 42 outliers final: 28 residues processed: 254 average time/residue: 0.0932 time to fit residues: 35.0041 Evaluate side-chains 244 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 255 LEU 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 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 656 TYR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 103 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 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL 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 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: 0.9990 chunk 104 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 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 = 0.4349 r_free = 0.4349 target = 0.207931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.175567 restraints weight = 51691.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.180991 restraints weight = 49568.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.186809 restraints weight = 13997.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.186432 restraints weight = 7246.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.187107 restraints weight = 5128.258| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 11324 Z= 0.202 Angle : 0.725 13.222 15314 Z= 0.366 Chirality : 0.047 0.271 1695 Planarity : 0.005 0.081 1954 Dihedral : 8.387 106.880 1607 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.65 % Allowed : 26.59 % 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: 0.21 (0.23), residues: 1359 helix: 0.89 (0.19), residues: 723 sheet: 0.03 (0.49), residues: 115 loop : -0.83 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 97 TYR 0.027 0.002 TYR D 118 PHE 0.017 0.002 PHE A 250 TRP 0.050 0.003 TRP B 374 HIS 0.010 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00469 (11315) covalent geometry : angle 0.71994 (15308) hydrogen bonds : bond 0.04063 ( 596) hydrogen bonds : angle 4.89580 ( 1726) metal coordination : bond 0.05114 ( 8) metal coordination : angle 4.44878 ( 6) Misc. bond : bond 0.00069 ( 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 263 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 0.406 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: 0.7296 (ttm) cc_final: 0.6737 (tpp) REVERT: A 519 TYR cc_start: 0.8055 (p90) cc_final: 0.7763 (p90) REVERT: A 564 MET cc_start: 0.7493 (mmm) cc_final: 0.7092 (mmm) REVERT: A 576 ASP cc_start: 0.7961 (m-30) cc_final: 0.7750 (m-30) REVERT: A 650 MET cc_start: 0.7933 (tpp) cc_final: 0.7558 (mmt) REVERT: A 735 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6969 (ttm-80) REVERT: B 174 ILE cc_start: 0.8689 (mm) cc_final: 0.8359 (mm) REVERT: B 219 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7689 (tmm) REVERT: B 356 MET cc_start: 0.7278 (mtt) cc_final: 0.7072 (mmt) REVERT: C 160 MET cc_start: 0.6669 (tpp) cc_final: 0.6361 (tpp) REVERT: D 88 LYS cc_start: 0.8259 (tppt) cc_final: 0.7724 (tptp) REVERT: F 55 ILE cc_start: 0.3743 (mm) cc_final: 0.3249 (mm) outliers start: 39 outliers final: 33 residues processed: 252 average time/residue: 0.0944 time to fit residues: 34.9434 Evaluate side-chains 243 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 255 LEU 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 485 LEU 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 717 LEU Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 100 HIS 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 243 GLN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 81 GLU 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 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: 8.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 118 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 130 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 chunk 115 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 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** B 195 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 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 = 0.4387 r_free = 0.4387 target = 0.212172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.179477 restraints weight = 50262.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.184243 restraints weight = 46608.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189429 restraints weight = 14712.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.192290 restraints weight = 6342.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.192183 restraints weight = 3941.724| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4130 r_free = 0.4130 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4130 r_free = 0.4130 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 11324 Z= 0.146 Angle : 0.704 14.700 15314 Z= 0.354 Chirality : 0.046 0.285 1695 Planarity : 0.005 0.073 1954 Dihedral : 8.273 105.775 1607 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.15 % Allowed : 27.26 % Favored : 69.59 % 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: 0.20 (0.23), residues: 1359 helix: 0.85 (0.19), residues: 735 sheet: 0.07 (0.47), residues: 121 loop : -0.83 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 97 TYR 0.024 0.002 TYR C 48 PHE 0.033 0.002 PHE B 337 TRP 0.059 0.003 TRP B 374 HIS 0.008 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00335 (11315) covalent geometry : angle 0.69916 (15308) hydrogen bonds : bond 0.03911 ( 596) hydrogen bonds : angle 4.78572 ( 1726) metal coordination : bond 0.03980 ( 8) metal coordination : angle 4.06912 ( 6) Misc. bond : bond 0.00036 ( 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 262 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.408 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: 0.7205 (ttm) cc_final: 0.6723 (tpp) REVERT: A 234 THR cc_start: 0.7934 (m) cc_final: 0.7244 (p) REVERT: A 519 TYR cc_start: 0.7995 (p90) cc_final: 0.7699 (p90) REVERT: A 551 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7888 (mt) REVERT: A 564 MET cc_start: 0.7308 (mmm) cc_final: 0.6894 (mmm) REVERT: A 576 ASP cc_start: 0.7862 (m-30) cc_final: 0.7610 (m-30) REVERT: A 627 MET cc_start: 0.8285 (tpp) cc_final: 0.8007 (tpp) REVERT: A 650 MET cc_start: 0.7848 (tpp) cc_final: 0.7456 (mmt) REVERT: A 735 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6879 (ttm-80) REVERT: B 170 SER cc_start: 0.8626 (m) cc_final: 0.8060 (p) REVERT: B 174 ILE cc_start: 0.8729 (mm) cc_final: 0.8395 (mm) REVERT: B 214 GLN cc_start: 0.7971 (tp40) cc_final: 0.7558 (tm-30) REVERT: B 219 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7637 (tmm) REVERT: C 14 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8381 (tp30) REVERT: C 111 ASN cc_start: 0.8191 (t0) cc_final: 0.7863 (t0) REVERT: C 160 MET cc_start: 0.6738 (tpp) cc_final: 0.6391 (tpp) REVERT: D 88 LYS cc_start: 0.8160 (tppt) cc_final: 0.7651 (tptp) REVERT: D 217 ILE cc_start: 0.8786 (mm) cc_final: 0.8549 (mm) REVERT: F 55 ILE cc_start: 0.3646 (mm) cc_final: 0.3125 (mm) outliers start: 33 outliers final: 25 residues processed: 252 average time/residue: 0.0933 time to fit residues: 34.7455 Evaluate side-chains 245 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 255 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 450 TRP 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 669 VAL Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 100 HIS 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 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 153 PHE 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: 2.9990 chunk 18 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 89 optimal weight: 0.5980 chunk 132 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 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** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.212361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174854 restraints weight = 67355.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175841 restraints weight = 34892.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.174431 restraints weight = 15219.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.176316 restraints weight = 12335.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.176736 restraints weight = 9601.030| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.7257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 11324 Z= 0.153 Angle : 0.716 14.216 15314 Z= 0.362 Chirality : 0.046 0.250 1695 Planarity : 0.005 0.067 1954 Dihedral : 8.268 103.272 1607 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.15 % Allowed : 27.34 % Favored : 69.51 % 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: 0.22 (0.23), residues: 1359 helix: 0.86 (0.19), residues: 734 sheet: 0.20 (0.47), residues: 121 loop : -0.84 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 97 TYR 0.025 0.002 TYR D 118 PHE 0.042 0.002 PHE B 337 TRP 0.055 0.003 TRP B 374 HIS 0.009 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00354 (11315) covalent geometry : angle 0.71146 (15308) hydrogen bonds : bond 0.03903 ( 596) hydrogen bonds : angle 4.84710 ( 1726) metal coordination : bond 0.03923 ( 8) metal coordination : angle 4.14212 ( 6) Misc. bond : bond 0.00040 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1807.78 seconds wall clock time: 32 minutes 6.12 seconds (1926.12 seconds total)