Starting phenix.real_space_refine on Sun Aug 24 17:28:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5a_29737/08_2025/8g5a_29737_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5a_29737/08_2025/8g5a_29737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g5a_29737/08_2025/8g5a_29737_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5a_29737/08_2025/8g5a_29737_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g5a_29737/08_2025/8g5a_29737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5a_29737/08_2025/8g5a_29737.map" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13566 2.51 5 N 3687 2.21 5 O 4317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21666 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3880 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain: "H" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1639 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain: "L" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1647 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: B, C, I, J, M, N Residues with excluded nonbonded symmetry interactions: 51 residue: pdb=" N THR A 24 " occ=0.63 ... (5 atoms not shown) pdb=" CG2 THR A 24 " occ=0.63 residue: pdb=" N THR A 30 " occ=0.83 ... (5 atoms not shown) pdb=" CG2 THR A 30 " occ=0.83 residue: pdb=" N ASP A 32 " occ=0.72 ... (6 atoms not shown) pdb=" OD2 ASP A 32 " occ=0.72 residue: pdb=" N VAL A 78 " occ=0.43 ... (5 atoms not shown) pdb=" CG2 VAL A 78 " occ=0.43 residue: pdb=" N ARG A 207 " occ=0.48 ... (9 atoms not shown) pdb=" NH2 ARG A 207 " occ=0.48 residue: pdb=" N SER A 227 " occ=0.54 ... (4 atoms not shown) pdb=" OG SER A 227 " occ=0.54 residue: pdb=" N SER A 228 " occ=0.54 ... (4 atoms not shown) pdb=" OG SER A 228 " occ=0.54 residue: pdb=" N TRP A 234 " occ=0.52 ... (12 atoms not shown) pdb=" CH2 TRP A 234 " occ=0.52 residue: pdb=" N MET A 260 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET A 260 " occ=0.50 residue: pdb=" N ILE A 274 " occ=0.62 ... (6 atoms not shown) pdb=" CD1 ILE A 274 " occ=0.62 residue: pdb=" N ASP A 275 " occ=0.62 ... (6 atoms not shown) pdb=" OD2 ASP A 275 " occ=0.62 residue: pdb=" N MET A 346 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET A 346 " occ=0.50 ... (remaining 39 not shown) Time building chain proxies: 4.77, per 1000 atoms: 0.22 Number of scatterers: 21666 At special positions: 0 Unit cell: (155.925, 155.925, 193.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4317 8.00 N 3687 7.00 C 13566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 483 " " NAG A 702 " - " ASN A 22 " " NAG A 703 " - " ASN A 38 " " NAG A 704 " - " ASN A 81 " " NAG B 701 " - " ASN B 483 " " NAG B 702 " - " ASN B 22 " " NAG B 703 " - " ASN B 38 " " NAG B 704 " - " ASN B 81 " " NAG C 701 " - " ASN C 483 " " NAG C 702 " - " ASN C 22 " " NAG C 703 " - " ASN C 38 " " NAG C 704 " - " ASN C 81 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 696.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 63 sheets defined 19.0% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.603A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 404 through 455 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 488 through 502 removed outlier: 4.320A pdb=" N ASP A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.603A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL B 78 " --> pdb=" O HIS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 404 through 455 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 488 through 502 removed outlier: 4.319A pdb=" N ASP B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.604A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 366 through 386 Processing helix chain 'C' and resid 404 through 455 Processing helix chain 'C' and resid 474 through 484 Processing helix chain 'C' and resid 488 through 502 removed outlier: 4.320A pdb=" N ASP C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 100 through 104 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 194 through 198 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 100 through 104 Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'I' and resid 194 through 198 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 100 through 104 Processing helix chain 'J' and resid 163 through 165 No H-bonds generated for 'chain 'J' and resid 163 through 165' Processing helix chain 'J' and resid 194 through 198 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.503A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 126 Processing helix chain 'M' and resid 183 through 189 removed outlier: 3.503A pdb=" N LYS M 188 " --> pdb=" O ALA M 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 126 Processing helix chain 'N' and resid 183 through 189 removed outlier: 3.503A pdb=" N LYS N 188 " --> pdb=" O ALA N 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.610A pdb=" N CYS A 277 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.965A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.757A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 removed outlier: 4.934A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AB3, first strand: chain 'B' and resid 360 through 365 Processing sheet with id=AB4, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.610A pdb=" N CYS B 277 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 58 through 61 Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 101 removed outlier: 4.965A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 101 removed outlier: 7.757A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.934A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AC5, first strand: chain 'C' and resid 360 through 365 Processing sheet with id=AC6, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.611A pdb=" N CYS C 277 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 101 removed outlier: 4.965A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.756A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD5, first strand: chain 'C' and resid 164 through 169 removed outlier: 4.935A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.510A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.510A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 127 through 131 removed outlier: 5.305A pdb=" N ALA H 144 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL H 191 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY H 146 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL H 189 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER H 186 " --> pdb=" O PRO H 174 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL H 188 " --> pdb=" O THR H 172 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR H 172 " --> pdb=" O VAL H 188 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.076A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.509A pdb=" N GLU I 10 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE I 34 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.509A pdb=" N GLU I 10 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR I 109 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 127 through 131 removed outlier: 5.305A pdb=" N ALA I 144 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL I 191 " --> pdb=" O ALA I 144 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY I 146 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL I 189 " --> pdb=" O GLY I 146 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU I 148 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER I 187 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS I 150 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU I 185 " --> pdb=" O LYS I 150 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER I 186 " --> pdb=" O PRO I 174 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL I 188 " --> pdb=" O THR I 172 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR I 172 " --> pdb=" O VAL I 188 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 158 through 161 removed outlier: 4.075A pdb=" N TYR I 201 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.509A pdb=" N GLU J 10 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE J 34 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.509A pdb=" N GLU J 10 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR J 109 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 127 through 131 removed outlier: 5.305A pdb=" N ALA J 144 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL J 191 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY J 146 " --> pdb=" O VAL J 189 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL J 189 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU J 148 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER J 187 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS J 150 " --> pdb=" O LEU J 185 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU J 185 " --> pdb=" O LYS J 150 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER J 186 " --> pdb=" O PRO J 174 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL J 188 " --> pdb=" O THR J 172 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR J 172 " --> pdb=" O VAL J 188 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 158 through 161 removed outlier: 4.075A pdb=" N TYR J 201 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.176A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.988A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.539A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.690A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.176A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.989A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 114 through 118 removed outlier: 3.539A pdb=" N VAL M 133 " --> pdb=" O PHE M 118 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER M 131 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU M 181 " --> pdb=" O SER M 131 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL M 133 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU M 179 " --> pdb=" O VAL M 133 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU M 135 " --> pdb=" O SER M 177 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER M 177 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN M 137 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU M 175 " --> pdb=" O ASN M 137 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 153 through 155 removed outlier: 4.690A pdb=" N TRP M 148 " --> pdb=" O GLN M 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.175A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.989A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 114 through 118 removed outlier: 3.540A pdb=" N VAL N 133 " --> pdb=" O PHE N 118 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER N 131 " --> pdb=" O LEU N 181 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU N 181 " --> pdb=" O SER N 131 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL N 133 " --> pdb=" O LEU N 179 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU N 179 " --> pdb=" O VAL N 133 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU N 135 " --> pdb=" O SER N 177 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER N 177 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASN N 137 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU N 175 " --> pdb=" O ASN N 137 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 153 through 155 removed outlier: 4.690A pdb=" N TRP N 148 " --> pdb=" O GLN N 155 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7071 1.34 - 1.46: 5311 1.46 - 1.58: 9629 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 22143 Sorted by residual: bond pdb=" C ARG A 456 " pdb=" O ARG A 456 " ideal model delta sigma weight residual 1.236 1.299 -0.062 1.15e-02 7.56e+03 2.95e+01 bond pdb=" C ARG C 456 " pdb=" O ARG C 456 " ideal model delta sigma weight residual 1.236 1.299 -0.062 1.15e-02 7.56e+03 2.94e+01 bond pdb=" C ARG B 456 " pdb=" O ARG B 456 " ideal model delta sigma weight residual 1.236 1.298 -0.062 1.15e-02 7.56e+03 2.93e+01 bond pdb=" C ALA C 334 " pdb=" O ALA C 334 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.21e-02 6.83e+03 2.48e+01 bond pdb=" C ALA A 334 " pdb=" O ALA A 334 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.21e-02 6.83e+03 2.48e+01 ... (remaining 22138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 29635 2.39 - 4.78: 359 4.78 - 7.17: 48 7.17 - 9.56: 6 9.56 - 11.94: 6 Bond angle restraints: 30054 Sorted by residual: angle pdb=" OG1 THR C 328 " pdb=" CB THR C 328 " pdb=" CG2 THR C 328 " ideal model delta sigma weight residual 109.30 120.82 -11.52 2.00e+00 2.50e-01 3.32e+01 angle pdb=" OG1 THR B 328 " pdb=" CB THR B 328 " pdb=" CG2 THR B 328 " ideal model delta sigma weight residual 109.30 120.81 -11.51 2.00e+00 2.50e-01 3.31e+01 angle pdb=" OG1 THR A 328 " pdb=" CB THR A 328 " pdb=" CG2 THR A 328 " ideal model delta sigma weight residual 109.30 120.79 -11.49 2.00e+00 2.50e-01 3.30e+01 angle pdb=" CA ILE C 335 " pdb=" C ILE C 335 " pdb=" O ILE C 335 " ideal model delta sigma weight residual 120.48 114.68 5.80 1.10e+00 8.26e-01 2.78e+01 angle pdb=" CA ILE B 335 " pdb=" C ILE B 335 " pdb=" O ILE B 335 " ideal model delta sigma weight residual 120.48 114.70 5.78 1.10e+00 8.26e-01 2.76e+01 ... (remaining 30049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 12159 16.07 - 32.14: 896 32.14 - 48.21: 232 48.21 - 64.28: 69 64.28 - 80.35: 36 Dihedral angle restraints: 13392 sinusoidal: 5397 harmonic: 7995 Sorted by residual: dihedral pdb=" CA GLU N 93 " pdb=" C GLU N 93 " pdb=" N TYR N 94 " pdb=" CA TYR N 94 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLU M 93 " pdb=" C GLU M 93 " pdb=" N TYR M 94 " pdb=" CA TYR M 94 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLU L 93 " pdb=" C GLU L 93 " pdb=" N TYR L 94 " pdb=" CA TYR L 94 " ideal model delta harmonic sigma weight residual -180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 13389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 3339 0.304 - 0.607: 12 0.607 - 0.911: 0 0.911 - 1.214: 0 1.214 - 1.518: 6 Chirality restraints: 3357 Sorted by residual: chirality pdb=" C4 NAG B 702 " pdb=" C3 NAG B 702 " pdb=" C5 NAG B 702 " pdb=" O4 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.53 -1.01 -1.52 2.00e-01 2.50e+01 5.76e+01 chirality pdb=" C4 NAG A 702 " pdb=" C3 NAG A 702 " pdb=" C5 NAG A 702 " pdb=" O4 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.53 -1.02 -1.52 2.00e-01 2.50e+01 5.74e+01 chirality pdb=" C4 NAG C 702 " pdb=" C3 NAG C 702 " pdb=" C5 NAG C 702 " pdb=" O4 NAG C 702 " both_signs ideal model delta sigma weight residual False -2.53 -1.02 -1.51 2.00e-01 2.50e+01 5.74e+01 ... (remaining 3354 not shown) Planarity restraints: 3894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 331 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU A 331 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU A 331 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 332 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 331 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU C 331 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU C 331 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE C 332 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 331 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LEU B 331 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU B 331 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE B 332 " 0.020 2.00e-02 2.50e+03 ... (remaining 3891 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 199 2.60 - 3.18: 19120 3.18 - 3.75: 33240 3.75 - 4.33: 48434 4.33 - 4.90: 81521 Nonbonded interactions: 182514 Sorted by model distance: nonbonded pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS N 134 " pdb=" SG CYS N 194 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " model vdw 2.033 3.760 ... (remaining 182509 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.43 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 20.670 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22173 Z= 0.298 Angle : 0.696 11.945 30126 Z= 0.403 Chirality : 0.081 1.518 3357 Planarity : 0.005 0.093 3882 Dihedral : 13.255 80.348 8226 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.88 % Allowed : 0.75 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.16), residues: 2763 helix: 1.84 (0.25), residues: 429 sheet: -0.21 (0.16), residues: 1017 loop : -0.71 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 211 TYR 0.030 0.002 TYR N 192 PHE 0.015 0.001 PHE N 116 TRP 0.011 0.001 TRP J 47 HIS 0.004 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00499 (22143) covalent geometry : angle 0.69310 (30054) SS BOND : bond 0.00278 ( 18) SS BOND : angle 1.20516 ( 36) hydrogen bonds : bond 0.12086 ( 891) hydrogen bonds : angle 6.64901 ( 2412) link_NAG-ASN : bond 0.00325 ( 12) link_NAG-ASN : angle 1.72431 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 280 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 338 PHE cc_start: 0.5781 (OUTLIER) cc_final: 0.4566 (m-80) REVERT: A 444 MET cc_start: 0.8771 (tpt) cc_final: 0.8529 (tpt) REVERT: A 470 TYR cc_start: 0.8260 (m-80) cc_final: 0.8036 (m-80) REVERT: B 338 PHE cc_start: 0.5729 (OUTLIER) cc_final: 0.4506 (m-80) REVERT: B 444 MET cc_start: 0.8772 (tpt) cc_final: 0.8434 (tpt) REVERT: B 470 TYR cc_start: 0.8247 (m-80) cc_final: 0.8002 (m-80) REVERT: C 338 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.4760 (m-80) REVERT: H 112 GLN cc_start: 0.7800 (pm20) cc_final: 0.7464 (pm20) REVERT: H 216 LYS cc_start: 0.5340 (mmmm) cc_final: 0.5087 (tppt) REVERT: J 35 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7835 (mt-10) REVERT: L 24 ARG cc_start: 0.6211 (ttm-80) cc_final: 0.5822 (tmm-80) REVERT: L 79 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6400 (mm-30) REVERT: L 106 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.4828 (mt) REVERT: L 123 GLU cc_start: 0.6699 (pm20) cc_final: 0.6400 (mp0) REVERT: M 24 ARG cc_start: 0.6079 (ttm-80) cc_final: 0.5545 (ttm-80) REVERT: M 79 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6404 (mm-30) REVERT: M 81 GLU cc_start: 0.6938 (pt0) cc_final: 0.5737 (mp0) REVERT: M 106 LEU cc_start: 0.5672 (OUTLIER) cc_final: 0.4975 (mt) REVERT: M 175 LEU cc_start: 0.7803 (tt) cc_final: 0.7599 (tt) REVERT: N 24 ARG cc_start: 0.6031 (ttm-80) cc_final: 0.5684 (tmm-80) REVERT: N 79 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6400 (mm-30) REVERT: N 81 GLU cc_start: 0.6951 (pt0) cc_final: 0.5790 (mp0) REVERT: N 106 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.4882 (mt) REVERT: N 123 GLU cc_start: 0.6786 (pm20) cc_final: 0.6403 (mp0) outliers start: 21 outliers final: 9 residues processed: 298 average time/residue: 0.1454 time to fit residues: 66.5278 Evaluate side-chains 214 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 0.5980 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN C 216 ASN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 178 GLN I 207 HIS J 178 GLN L 152 ASN M 152 ASN N 152 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.135083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.088480 restraints weight = 36969.772| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.95 r_work: 0.3002 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 22173 Z= 0.381 Angle : 0.730 8.262 30126 Z= 0.388 Chirality : 0.051 0.214 3357 Planarity : 0.005 0.047 3882 Dihedral : 6.061 55.965 3264 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.88 % Allowed : 6.57 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.15), residues: 2763 helix: 1.52 (0.24), residues: 414 sheet: -0.19 (0.16), residues: 978 loop : -0.87 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 98 TYR 0.036 0.002 TYR M 94 PHE 0.025 0.003 PHE C 338 TRP 0.020 0.003 TRP C 222 HIS 0.011 0.002 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00890 (22143) covalent geometry : angle 0.72528 (30054) SS BOND : bond 0.00706 ( 18) SS BOND : angle 1.33038 ( 36) hydrogen bonds : bond 0.04371 ( 891) hydrogen bonds : angle 5.75975 ( 2412) link_NAG-ASN : bond 0.00434 ( 12) link_NAG-ASN : angle 2.15246 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 401 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8074 (mm-30) REVERT: A 444 MET cc_start: 0.9070 (tpt) cc_final: 0.8781 (tpt) REVERT: A 470 TYR cc_start: 0.8641 (m-80) cc_final: 0.8321 (m-80) REVERT: B 338 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.5313 (m-80) REVERT: B 401 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8091 (mm-30) REVERT: B 444 MET cc_start: 0.9026 (tpt) cc_final: 0.8476 (tpt) REVERT: B 468 LYS cc_start: 0.8402 (ttpt) cc_final: 0.8121 (ttpt) REVERT: B 470 TYR cc_start: 0.8677 (m-80) cc_final: 0.8417 (m-80) REVERT: C 338 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.5290 (m-80) REVERT: I 35 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8330 (mt-10) REVERT: I 39 GLN cc_start: 0.8423 (tt0) cc_final: 0.7956 (tt0) REVERT: J 35 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8305 (mt-10) REVERT: L 24 ARG cc_start: 0.6765 (ttm-80) cc_final: 0.5986 (ttp-110) REVERT: L 106 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.4638 (mt) REVERT: L 152 ASN cc_start: 0.3098 (OUTLIER) cc_final: 0.2883 (p0) REVERT: L 175 LEU cc_start: 0.7870 (tt) cc_final: 0.7579 (tt) REVERT: M 24 ARG cc_start: 0.6746 (ttm-80) cc_final: 0.6089 (ttp-110) REVERT: M 106 LEU cc_start: 0.5683 (OUTLIER) cc_final: 0.4649 (mt) REVERT: M 152 ASN cc_start: 0.3263 (OUTLIER) cc_final: 0.3052 (p0) REVERT: N 24 ARG cc_start: 0.6736 (ttm-80) cc_final: 0.6025 (ttp-110) REVERT: N 106 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.4707 (mt) REVERT: N 148 TRP cc_start: 0.6431 (m100) cc_final: 0.5690 (m-10) REVERT: N 152 ASN cc_start: 0.3408 (OUTLIER) cc_final: 0.3176 (p0) outliers start: 45 outliers final: 29 residues processed: 265 average time/residue: 0.1217 time to fit residues: 51.9862 Evaluate side-chains 244 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 152 ASN Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 147 GLN Chi-restraints excluded: chain M residue 152 ASN Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 152 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 273 optimal weight: 0.6980 chunk 270 optimal weight: 30.0000 chunk 4 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 53 ASN B 216 ASN C 216 ASN H 59 ASN H 178 GLN I 59 ASN I 178 GLN J 59 ASN L 147 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.138679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093737 restraints weight = 36452.656| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.99 r_work: 0.2991 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22173 Z= 0.120 Angle : 0.543 7.779 30126 Z= 0.290 Chirality : 0.043 0.159 3357 Planarity : 0.004 0.047 3882 Dihedral : 5.302 47.327 3264 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.55 % Allowed : 8.53 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.15), residues: 2763 helix: 1.94 (0.24), residues: 432 sheet: -0.00 (0.16), residues: 972 loop : -0.89 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 217 TYR 0.025 0.001 TYR L 94 PHE 0.020 0.002 PHE I 129 TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS J 207 Details of bonding type rmsd covalent geometry : bond 0.00262 (22143) covalent geometry : angle 0.53868 (30054) SS BOND : bond 0.00309 ( 18) SS BOND : angle 0.97031 ( 36) hydrogen bonds : bond 0.03285 ( 891) hydrogen bonds : angle 5.30588 ( 2412) link_NAG-ASN : bond 0.00217 ( 12) link_NAG-ASN : angle 1.77345 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5191 (m-80) REVERT: A 401 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7967 (mm-30) REVERT: A 408 ASP cc_start: 0.8433 (m-30) cc_final: 0.8187 (m-30) REVERT: B 338 PHE cc_start: 0.6196 (OUTLIER) cc_final: 0.5160 (m-80) REVERT: B 401 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 444 MET cc_start: 0.9031 (tpt) cc_final: 0.8614 (tpt) REVERT: B 468 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8168 (ttpt) REVERT: C 338 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.5327 (m-80) REVERT: C 460 GLU cc_start: 0.7669 (tp30) cc_final: 0.7329 (tp30) REVERT: I 39 GLN cc_start: 0.8324 (tt0) cc_final: 0.7836 (tt0) REVERT: J 152 TYR cc_start: 0.7643 (p90) cc_final: 0.7322 (p90) REVERT: L 24 ARG cc_start: 0.6674 (ttm-80) cc_final: 0.6070 (ttm-80) REVERT: L 106 LEU cc_start: 0.5545 (OUTLIER) cc_final: 0.4755 (mt) REVERT: L 148 TRP cc_start: 0.6290 (m100) cc_final: 0.5768 (m-10) REVERT: M 24 ARG cc_start: 0.6825 (ttm-80) cc_final: 0.6121 (ttm-80) REVERT: M 79 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6637 (mm-30) REVERT: M 82 ASP cc_start: 0.7031 (m-30) cc_final: 0.6742 (m-30) REVERT: M 106 LEU cc_start: 0.5501 (OUTLIER) cc_final: 0.4663 (mt) REVERT: N 22 ASN cc_start: 0.6696 (m-40) cc_final: 0.6425 (p0) REVERT: N 24 ARG cc_start: 0.6670 (ttm-80) cc_final: 0.6206 (ttm-80) REVERT: N 106 LEU cc_start: 0.5562 (OUTLIER) cc_final: 0.4693 (mt) REVERT: N 148 TRP cc_start: 0.6419 (m100) cc_final: 0.5689 (m-10) outliers start: 37 outliers final: 22 residues processed: 267 average time/residue: 0.1319 time to fit residues: 56.2978 Evaluate side-chains 239 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 46 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 274 optimal weight: 30.0000 chunk 209 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.135791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089262 restraints weight = 36578.411| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.90 r_work: 0.2969 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22173 Z= 0.239 Angle : 0.596 8.075 30126 Z= 0.316 Chirality : 0.045 0.173 3357 Planarity : 0.005 0.047 3882 Dihedral : 5.476 48.216 3264 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.47 % Allowed : 9.33 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.15), residues: 2763 helix: 1.80 (0.24), residues: 432 sheet: -0.14 (0.16), residues: 1005 loop : -0.86 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.034 0.002 TYR N 94 PHE 0.019 0.002 PHE J 105 TRP 0.014 0.002 TRP C 222 HIS 0.006 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00560 (22143) covalent geometry : angle 0.59195 (30054) SS BOND : bond 0.00491 ( 18) SS BOND : angle 1.08869 ( 36) hydrogen bonds : bond 0.03630 ( 891) hydrogen bonds : angle 5.32309 ( 2412) link_NAG-ASN : bond 0.00277 ( 12) link_NAG-ASN : angle 1.97936 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.6229 (OUTLIER) cc_final: 0.5197 (m-80) REVERT: A 378 ASN cc_start: 0.7701 (m110) cc_final: 0.7354 (m-40) REVERT: A 401 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8008 (mm-30) REVERT: A 408 ASP cc_start: 0.8421 (m-30) cc_final: 0.8161 (m-30) REVERT: B 338 PHE cc_start: 0.6158 (OUTLIER) cc_final: 0.5197 (m-80) REVERT: B 378 ASN cc_start: 0.7364 (m110) cc_final: 0.6947 (m-40) REVERT: B 401 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8017 (mm-30) REVERT: B 444 MET cc_start: 0.9024 (tpt) cc_final: 0.8562 (tpt) REVERT: B 468 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8036 (ttpt) REVERT: B 469 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8248 (mm) REVERT: C 338 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.5187 (m-80) REVERT: C 460 GLU cc_start: 0.7676 (tp30) cc_final: 0.7372 (tp30) REVERT: C 469 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8324 (mm) REVERT: I 39 GLN cc_start: 0.8415 (tt0) cc_final: 0.7901 (tt0) REVERT: J 152 TYR cc_start: 0.7666 (p90) cc_final: 0.7369 (p90) REVERT: L 24 ARG cc_start: 0.6751 (ttm-80) cc_final: 0.6044 (ttm-80) REVERT: L 47 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8254 (mt) REVERT: L 79 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6275 (tm-30) REVERT: L 106 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.4718 (mt) REVERT: L 148 TRP cc_start: 0.6131 (m100) cc_final: 0.5852 (m-10) REVERT: M 22 ASN cc_start: 0.6720 (m-40) cc_final: 0.6411 (p0) REVERT: M 24 ARG cc_start: 0.6866 (ttm-80) cc_final: 0.6120 (ttm-80) REVERT: M 106 LEU cc_start: 0.5464 (OUTLIER) cc_final: 0.4636 (mt) REVERT: M 148 TRP cc_start: 0.6416 (m100) cc_final: 0.6135 (m-10) REVERT: N 22 ASN cc_start: 0.6788 (m-40) cc_final: 0.6489 (p0) REVERT: N 24 ARG cc_start: 0.6705 (ttm-80) cc_final: 0.6022 (ttm-80) REVERT: N 106 LEU cc_start: 0.5574 (OUTLIER) cc_final: 0.4718 (mt) REVERT: N 148 TRP cc_start: 0.6546 (m100) cc_final: 0.5952 (m100) REVERT: N 154 LEU cc_start: 0.4183 (OUTLIER) cc_final: 0.3826 (mt) outliers start: 59 outliers final: 37 residues processed: 270 average time/residue: 0.1220 time to fit residues: 53.7828 Evaluate side-chains 255 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 240 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 268 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 178 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.090130 restraints weight = 36476.778| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.96 r_work: 0.2897 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 22173 Z= 0.313 Angle : 0.645 8.105 30126 Z= 0.341 Chirality : 0.047 0.202 3357 Planarity : 0.005 0.050 3882 Dihedral : 5.773 50.419 3264 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.05 % Allowed : 10.66 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.15), residues: 2763 helix: 1.89 (0.24), residues: 414 sheet: -0.20 (0.16), residues: 960 loop : -0.96 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 150 TYR 0.046 0.002 TYR N 94 PHE 0.023 0.002 PHE J 105 TRP 0.015 0.002 TRP C 222 HIS 0.007 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00738 (22143) covalent geometry : angle 0.63971 (30054) SS BOND : bond 0.00578 ( 18) SS BOND : angle 1.00607 ( 36) hydrogen bonds : bond 0.03901 ( 891) hydrogen bonds : angle 5.49232 ( 2412) link_NAG-ASN : bond 0.00360 ( 12) link_NAG-ASN : angle 2.28562 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 216 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.6303 (OUTLIER) cc_final: 0.5622 (m-80) REVERT: A 378 ASN cc_start: 0.7850 (m110) cc_final: 0.7495 (m-40) REVERT: A 401 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8077 (mm-30) REVERT: A 408 ASP cc_start: 0.8582 (m-30) cc_final: 0.8324 (m-30) REVERT: B 338 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.5872 (m-80) REVERT: B 378 ASN cc_start: 0.7542 (m110) cc_final: 0.7115 (m-40) REVERT: B 444 MET cc_start: 0.9038 (tpt) cc_final: 0.8530 (tpt) REVERT: B 468 LYS cc_start: 0.8538 (ttpt) cc_final: 0.7976 (ttpt) REVERT: B 469 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8303 (mm) REVERT: B 470 TYR cc_start: 0.8518 (m-80) cc_final: 0.8149 (m-10) REVERT: C 338 PHE cc_start: 0.6310 (OUTLIER) cc_final: 0.5464 (m-80) REVERT: C 408 ASP cc_start: 0.8601 (m-30) cc_final: 0.8283 (m-30) REVERT: C 460 GLU cc_start: 0.7807 (tp30) cc_final: 0.7492 (tp30) REVERT: C 468 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8273 (ttpt) REVERT: C 469 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8453 (mm) REVERT: H 90 ASP cc_start: 0.7981 (t0) cc_final: 0.7759 (t0) REVERT: I 39 GLN cc_start: 0.8478 (tt0) cc_final: 0.8021 (tt0) REVERT: J 152 TYR cc_start: 0.7702 (p90) cc_final: 0.7305 (p90) REVERT: L 24 ARG cc_start: 0.6846 (ttm-80) cc_final: 0.6136 (ttm-80) REVERT: L 47 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8319 (mt) REVERT: L 106 LEU cc_start: 0.5520 (OUTLIER) cc_final: 0.4743 (mt) REVERT: L 148 TRP cc_start: 0.6740 (m100) cc_final: 0.6153 (m-10) REVERT: M 22 ASN cc_start: 0.6759 (m-40) cc_final: 0.6310 (p0) REVERT: M 24 ARG cc_start: 0.7094 (ttm-80) cc_final: 0.6171 (ttm-80) REVERT: M 106 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.4757 (mt) REVERT: M 147 GLN cc_start: 0.6152 (tp-100) cc_final: 0.5618 (tm-30) REVERT: M 148 TRP cc_start: 0.6817 (m100) cc_final: 0.5756 (m-10) REVERT: N 22 ASN cc_start: 0.6978 (m-40) cc_final: 0.6569 (p0) REVERT: N 24 ARG cc_start: 0.6895 (ttm-80) cc_final: 0.6101 (ttm-80) REVERT: N 78 LEU cc_start: 0.6900 (mt) cc_final: 0.6672 (tt) REVERT: N 106 LEU cc_start: 0.5659 (OUTLIER) cc_final: 0.4804 (mt) REVERT: N 148 TRP cc_start: 0.6641 (m100) cc_final: 0.6010 (m100) outliers start: 73 outliers final: 47 residues processed: 278 average time/residue: 0.1342 time to fit residues: 60.2807 Evaluate side-chains 263 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 13 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 225 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN C 216 ASN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 162 ASN I 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.138380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094411 restraints weight = 36387.510| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.11 r_work: 0.2975 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22173 Z= 0.105 Angle : 0.523 7.802 30126 Z= 0.275 Chirality : 0.042 0.179 3357 Planarity : 0.004 0.052 3882 Dihedral : 5.006 44.899 3260 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.09 % Allowed : 12.21 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.16), residues: 2763 helix: 2.10 (0.24), residues: 432 sheet: -0.10 (0.16), residues: 990 loop : -0.83 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 452 TYR 0.028 0.001 TYR N 94 PHE 0.021 0.001 PHE H 129 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS J 207 Details of bonding type rmsd covalent geometry : bond 0.00233 (22143) covalent geometry : angle 0.51902 (30054) SS BOND : bond 0.00307 ( 18) SS BOND : angle 0.97976 ( 36) hydrogen bonds : bond 0.02986 ( 891) hydrogen bonds : angle 5.08830 ( 2412) link_NAG-ASN : bond 0.00206 ( 12) link_NAG-ASN : angle 1.82486 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 232 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 408 ASP cc_start: 0.8538 (m-30) cc_final: 0.8299 (m-30) REVERT: A 468 LYS cc_start: 0.8493 (ttpt) cc_final: 0.8253 (ttpt) REVERT: B 378 ASN cc_start: 0.7384 (m110) cc_final: 0.6951 (m-40) REVERT: B 444 MET cc_start: 0.8969 (tpt) cc_final: 0.8553 (tpt) REVERT: B 468 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8025 (ttpt) REVERT: B 469 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8230 (mm) REVERT: B 470 TYR cc_start: 0.8420 (m-80) cc_final: 0.7983 (m-10) REVERT: C 460 GLU cc_start: 0.7719 (tp30) cc_final: 0.7507 (tp30) REVERT: C 468 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8187 (ttpt) REVERT: H 35 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8214 (mp0) REVERT: H 39 GLN cc_start: 0.8424 (tt0) cc_final: 0.8133 (tt0) REVERT: H 90 ASP cc_start: 0.7904 (t0) cc_final: 0.7674 (t0) REVERT: H 131 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6716 (mt) REVERT: I 39 GLN cc_start: 0.8436 (tt0) cc_final: 0.8017 (tt0) REVERT: J 10 GLU cc_start: 0.7711 (mp0) cc_final: 0.7503 (mp0) REVERT: J 35 GLU cc_start: 0.8905 (mp0) cc_final: 0.8667 (mp0) REVERT: J 152 TYR cc_start: 0.7671 (p90) cc_final: 0.7375 (p90) REVERT: L 24 ARG cc_start: 0.6678 (ttm-80) cc_final: 0.5940 (ttm-80) REVERT: L 47 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8162 (mt) REVERT: L 106 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.4735 (mt) REVERT: L 148 TRP cc_start: 0.6643 (m100) cc_final: 0.6076 (m-10) REVERT: L 175 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7704 (tt) REVERT: M 24 ARG cc_start: 0.6922 (ttm-80) cc_final: 0.6181 (ttm-80) REVERT: M 106 LEU cc_start: 0.5469 (OUTLIER) cc_final: 0.4723 (mt) REVERT: M 148 TRP cc_start: 0.6754 (m100) cc_final: 0.6077 (m-10) REVERT: N 24 ARG cc_start: 0.6676 (ttm-80) cc_final: 0.5994 (ttm-80) REVERT: N 106 LEU cc_start: 0.5487 (OUTLIER) cc_final: 0.4781 (mt) REVERT: N 148 TRP cc_start: 0.6608 (m100) cc_final: 0.5788 (m-10) REVERT: N 167 ASP cc_start: 0.4353 (t70) cc_final: 0.4049 (t0) outliers start: 50 outliers final: 25 residues processed: 271 average time/residue: 0.1430 time to fit residues: 63.3494 Evaluate side-chains 245 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 201 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 228 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 112 GLN I 162 ASN I 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.135158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092869 restraints weight = 36290.293| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.00 r_work: 0.2933 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 22173 Z= 0.290 Angle : 0.636 8.740 30126 Z= 0.333 Chirality : 0.047 0.232 3357 Planarity : 0.005 0.046 3882 Dihedral : 5.375 48.936 3252 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.55 % Allowed : 12.97 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.15), residues: 2763 helix: 2.01 (0.25), residues: 414 sheet: -0.13 (0.17), residues: 930 loop : -0.94 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 208 TYR 0.053 0.002 TYR M 94 PHE 0.021 0.002 PHE J 105 TRP 0.015 0.002 TRP C 222 HIS 0.008 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00687 (22143) covalent geometry : angle 0.63113 (30054) SS BOND : bond 0.00543 ( 18) SS BOND : angle 1.11825 ( 36) hydrogen bonds : bond 0.03698 ( 891) hydrogen bonds : angle 5.29346 ( 2412) link_NAG-ASN : bond 0.00342 ( 12) link_NAG-ASN : angle 2.17505 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 212 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 378 ASN cc_start: 0.7687 (m110) cc_final: 0.7366 (m-40) REVERT: A 401 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 408 ASP cc_start: 0.8549 (m-30) cc_final: 0.8286 (m-30) REVERT: A 468 LYS cc_start: 0.8573 (ttpt) cc_final: 0.8340 (ttpt) REVERT: B 378 ASN cc_start: 0.7470 (m110) cc_final: 0.7048 (m-40) REVERT: B 401 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8145 (tp30) REVERT: B 444 MET cc_start: 0.9021 (tpt) cc_final: 0.8463 (tpt) REVERT: B 468 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8257 (ttmt) REVERT: B 469 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8339 (mm) REVERT: B 470 TYR cc_start: 0.8473 (m-80) cc_final: 0.8108 (m-10) REVERT: C 408 ASP cc_start: 0.8523 (m-30) cc_final: 0.8192 (m-30) REVERT: C 460 GLU cc_start: 0.7762 (tp30) cc_final: 0.7476 (tp30) REVERT: C 468 LYS cc_start: 0.8512 (ttpt) cc_final: 0.8257 (ttpt) REVERT: H 90 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7695 (t0) REVERT: I 39 GLN cc_start: 0.8499 (tt0) cc_final: 0.8059 (tt0) REVERT: J 3 GLN cc_start: 0.7600 (pt0) cc_final: 0.7303 (tt0) REVERT: J 10 GLU cc_start: 0.7769 (mp0) cc_final: 0.7476 (mp0) REVERT: J 35 GLU cc_start: 0.8923 (mp0) cc_final: 0.8686 (mp0) REVERT: J 152 TYR cc_start: 0.7735 (p90) cc_final: 0.7352 (p90) REVERT: L 24 ARG cc_start: 0.6817 (ttm-80) cc_final: 0.5934 (ttp-110) REVERT: L 47 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8302 (mt) REVERT: L 106 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.4770 (mt) REVERT: L 148 TRP cc_start: 0.6774 (m100) cc_final: 0.6198 (m-10) REVERT: M 24 ARG cc_start: 0.6753 (ttm-80) cc_final: 0.5955 (ttp-110) REVERT: M 106 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.4781 (mt) REVERT: M 148 TRP cc_start: 0.6882 (m100) cc_final: 0.6137 (m-10) REVERT: N 24 ARG cc_start: 0.6615 (ttm-80) cc_final: 0.5958 (ttp-110) REVERT: N 106 LEU cc_start: 0.5533 (OUTLIER) cc_final: 0.4835 (mt) REVERT: N 148 TRP cc_start: 0.6653 (m100) cc_final: 0.5874 (m-10) REVERT: N 154 LEU cc_start: 0.4332 (OUTLIER) cc_final: 0.3964 (mt) REVERT: N 175 LEU cc_start: 0.7716 (tt) cc_final: 0.7491 (tt) outliers start: 61 outliers final: 42 residues processed: 263 average time/residue: 0.1479 time to fit residues: 63.2078 Evaluate side-chains 253 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 193 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 162 ASN I 178 GLN J 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.138869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094189 restraints weight = 36403.030| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.12 r_work: 0.2996 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22173 Z= 0.117 Angle : 0.538 9.422 30126 Z= 0.279 Chirality : 0.043 0.190 3357 Planarity : 0.004 0.051 3882 Dihedral : 4.856 44.644 3252 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.97 % Allowed : 13.47 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2763 helix: 2.35 (0.25), residues: 414 sheet: -0.11 (0.17), residues: 972 loop : -0.79 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 208 TYR 0.031 0.001 TYR L 94 PHE 0.026 0.001 PHE I 129 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00265 (22143) covalent geometry : angle 0.53438 (30054) SS BOND : bond 0.00301 ( 18) SS BOND : angle 1.01211 ( 36) hydrogen bonds : bond 0.03003 ( 891) hydrogen bonds : angle 4.97259 ( 2412) link_NAG-ASN : bond 0.00206 ( 12) link_NAG-ASN : angle 1.78742 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASN cc_start: 0.7540 (m110) cc_final: 0.7243 (m-40) REVERT: A 408 ASP cc_start: 0.8479 (m-30) cc_final: 0.8244 (m-30) REVERT: A 468 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8345 (ttpt) REVERT: B 378 ASN cc_start: 0.7346 (m110) cc_final: 0.6913 (m-40) REVERT: B 444 MET cc_start: 0.8992 (tpt) cc_final: 0.8550 (tpt) REVERT: B 468 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8098 (ttpt) REVERT: B 469 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8166 (mm) REVERT: C 460 GLU cc_start: 0.7626 (tp30) cc_final: 0.7403 (tp30) REVERT: C 468 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8246 (ttpt) REVERT: H 35 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8489 (mp0) REVERT: H 39 GLN cc_start: 0.8472 (tt0) cc_final: 0.8155 (tt0) REVERT: I 39 GLN cc_start: 0.8449 (tt0) cc_final: 0.8072 (tt0) REVERT: J 3 GLN cc_start: 0.7377 (pt0) cc_final: 0.7130 (tt0) REVERT: J 152 TYR cc_start: 0.7689 (p90) cc_final: 0.7278 (p90) REVERT: L 24 ARG cc_start: 0.6780 (ttm-80) cc_final: 0.5927 (ttm-80) REVERT: L 47 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8148 (mt) REVERT: L 79 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6180 (tm-30) REVERT: L 106 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.4733 (mt) REVERT: L 148 TRP cc_start: 0.6670 (m100) cc_final: 0.6126 (m-10) REVERT: L 175 LEU cc_start: 0.7747 (tt) cc_final: 0.7513 (tt) REVERT: M 24 ARG cc_start: 0.6680 (ttm-80) cc_final: 0.5908 (ttp-110) REVERT: M 106 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.4799 (mt) REVERT: M 148 TRP cc_start: 0.6567 (m100) cc_final: 0.6096 (m100) REVERT: N 24 ARG cc_start: 0.6527 (ttm-80) cc_final: 0.5912 (ttp-110) REVERT: N 106 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.4815 (mt) REVERT: N 148 TRP cc_start: 0.6591 (m100) cc_final: 0.5833 (m-10) REVERT: N 154 LEU cc_start: 0.4307 (OUTLIER) cc_final: 0.3888 (mt) REVERT: N 175 LEU cc_start: 0.7701 (tt) cc_final: 0.7499 (tt) outliers start: 47 outliers final: 32 residues processed: 257 average time/residue: 0.1400 time to fit residues: 59.7246 Evaluate side-chains 246 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 256 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 189 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 178 GLN M 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.139724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098981 restraints weight = 36210.486| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.08 r_work: 0.3022 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22173 Z= 0.109 Angle : 0.523 9.304 30126 Z= 0.271 Chirality : 0.042 0.202 3357 Planarity : 0.004 0.049 3882 Dihedral : 4.628 44.040 3252 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.67 % Allowed : 13.38 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.16), residues: 2763 helix: 2.30 (0.25), residues: 432 sheet: -0.06 (0.17), residues: 972 loop : -0.74 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 208 TYR 0.027 0.001 TYR L 94 PHE 0.021 0.001 PHE N 118 TRP 0.009 0.001 TRP I 47 HIS 0.004 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00246 (22143) covalent geometry : angle 0.51935 (30054) SS BOND : bond 0.00309 ( 18) SS BOND : angle 0.96775 ( 36) hydrogen bonds : bond 0.02881 ( 891) hydrogen bonds : angle 4.85541 ( 2412) link_NAG-ASN : bond 0.00203 ( 12) link_NAG-ASN : angle 1.65052 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ASP cc_start: 0.8467 (m-30) cc_final: 0.8232 (m-30) REVERT: A 468 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8315 (ttpt) REVERT: A 470 TYR cc_start: 0.8504 (m-80) cc_final: 0.8117 (m-80) REVERT: B 444 MET cc_start: 0.8990 (tpt) cc_final: 0.8376 (tpt) REVERT: B 468 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8150 (ttpt) REVERT: B 469 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8067 (mm) REVERT: C 460 GLU cc_start: 0.7556 (tp30) cc_final: 0.7338 (tp30) REVERT: C 468 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8254 (ttpt) REVERT: H 35 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8435 (mp0) REVERT: I 39 GLN cc_start: 0.8418 (tt0) cc_final: 0.7975 (tt0) REVERT: J 152 TYR cc_start: 0.7680 (p90) cc_final: 0.7255 (p90) REVERT: L 24 ARG cc_start: 0.6647 (ttm-80) cc_final: 0.5734 (ttp-110) REVERT: L 47 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8113 (mt) REVERT: L 78 LEU cc_start: 0.6826 (mt) cc_final: 0.6536 (tt) REVERT: L 79 GLU cc_start: 0.6702 (mm-30) cc_final: 0.6357 (tm-30) REVERT: L 106 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.4748 (mt) REVERT: L 148 TRP cc_start: 0.6660 (m100) cc_final: 0.6138 (m-10) REVERT: M 24 ARG cc_start: 0.6547 (ttm-80) cc_final: 0.5862 (ttp-110) REVERT: M 78 LEU cc_start: 0.6972 (mt) cc_final: 0.6666 (tt) REVERT: M 82 ASP cc_start: 0.7402 (m-30) cc_final: 0.7156 (m-30) REVERT: M 106 LEU cc_start: 0.5464 (OUTLIER) cc_final: 0.4784 (mt) REVERT: M 148 TRP cc_start: 0.6682 (m100) cc_final: 0.6205 (m100) REVERT: N 24 ARG cc_start: 0.6467 (ttm-80) cc_final: 0.5955 (ttp-110) REVERT: N 106 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.4808 (mt) REVERT: N 148 TRP cc_start: 0.6575 (m100) cc_final: 0.5828 (m-10) REVERT: N 154 LEU cc_start: 0.4242 (OUTLIER) cc_final: 0.3809 (mt) outliers start: 40 outliers final: 29 residues processed: 256 average time/residue: 0.1395 time to fit residues: 59.1943 Evaluate side-chains 251 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 246 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 25 optimal weight: 0.0050 chunk 210 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.0470 chunk 125 optimal weight: 0.8980 overall best weight: 0.5694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 178 GLN L 6 GLN N 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.140920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.098460 restraints weight = 36282.715| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.01 r_work: 0.3046 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22173 Z= 0.098 Angle : 0.512 9.175 30126 Z= 0.263 Chirality : 0.042 0.195 3357 Planarity : 0.004 0.050 3882 Dihedral : 4.428 41.973 3252 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.38 % Allowed : 13.63 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.16), residues: 2763 helix: 2.67 (0.25), residues: 414 sheet: 0.07 (0.17), residues: 975 loop : -0.63 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 208 TYR 0.019 0.001 TYR L 94 PHE 0.014 0.001 PHE I 129 TRP 0.010 0.001 TRP I 47 HIS 0.004 0.001 HIS J 207 Details of bonding type rmsd covalent geometry : bond 0.00221 (22143) covalent geometry : angle 0.50891 (30054) SS BOND : bond 0.00288 ( 18) SS BOND : angle 0.95297 ( 36) hydrogen bonds : bond 0.02734 ( 891) hydrogen bonds : angle 4.73244 ( 2412) link_NAG-ASN : bond 0.00195 ( 12) link_NAG-ASN : angle 1.46980 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ASP cc_start: 0.8427 (m-30) cc_final: 0.8191 (m-30) REVERT: A 446 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8698 (ttmm) REVERT: B 444 MET cc_start: 0.9013 (tpt) cc_final: 0.8394 (tpt) REVERT: B 468 LYS cc_start: 0.8612 (ttpt) cc_final: 0.8115 (ttpt) REVERT: C 436 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9042 (m) REVERT: C 460 GLU cc_start: 0.7519 (tp30) cc_final: 0.7305 (tp30) REVERT: C 468 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8250 (ttpt) REVERT: H 39 GLN cc_start: 0.8518 (tt0) cc_final: 0.8255 (tt0) REVERT: H 90 ASP cc_start: 0.7826 (t0) cc_final: 0.7543 (t0) REVERT: H 202 ILE cc_start: 0.6577 (OUTLIER) cc_final: 0.6167 (pt) REVERT: I 39 GLN cc_start: 0.8392 (tt0) cc_final: 0.8004 (tt0) REVERT: J 73 ASP cc_start: 0.8304 (t0) cc_final: 0.8090 (t0) REVERT: J 152 TYR cc_start: 0.7659 (p90) cc_final: 0.7224 (p90) REVERT: L 24 ARG cc_start: 0.6594 (ttm-80) cc_final: 0.5841 (ttp-110) REVERT: L 47 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8143 (mt) REVERT: L 78 LEU cc_start: 0.6890 (mt) cc_final: 0.6606 (tt) REVERT: L 79 GLU cc_start: 0.6645 (mm-30) cc_final: 0.6152 (tm-30) REVERT: L 106 LEU cc_start: 0.5495 (OUTLIER) cc_final: 0.4804 (mt) REVERT: L 148 TRP cc_start: 0.6718 (m100) cc_final: 0.6194 (m-10) REVERT: M 24 ARG cc_start: 0.6564 (ttm-80) cc_final: 0.5885 (ttp-110) REVERT: M 78 LEU cc_start: 0.6961 (mt) cc_final: 0.6654 (tt) REVERT: M 82 ASP cc_start: 0.7398 (m-30) cc_final: 0.7139 (m-30) REVERT: M 106 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.4865 (mt) REVERT: M 148 TRP cc_start: 0.6644 (m100) cc_final: 0.6181 (m100) REVERT: N 24 ARG cc_start: 0.6344 (ttm-80) cc_final: 0.5860 (ttp-110) REVERT: N 106 LEU cc_start: 0.5421 (OUTLIER) cc_final: 0.4775 (mt) REVERT: N 148 TRP cc_start: 0.6546 (m100) cc_final: 0.5868 (m-10) REVERT: N 167 ASP cc_start: 0.4608 (t70) cc_final: 0.4321 (t0) outliers start: 33 outliers final: 24 residues processed: 254 average time/residue: 0.1448 time to fit residues: 60.4522 Evaluate side-chains 240 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 148 optimal weight: 0.0970 chunk 154 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 chunk 201 optimal weight: 7.9990 chunk 107 optimal weight: 0.0470 chunk 143 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 overall best weight: 1.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 356 GLN B 189 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN B 454 GLN B 471 HIS C 454 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 77 ASN I 178 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.137702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093688 restraints weight = 36297.789| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.02 r_work: 0.2974 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22173 Z= 0.159 Angle : 0.548 8.797 30126 Z= 0.283 Chirality : 0.044 0.243 3357 Planarity : 0.004 0.053 3882 Dihedral : 4.656 43.987 3252 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.63 % Allowed : 13.43 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.16), residues: 2763 helix: 2.47 (0.25), residues: 414 sheet: -0.03 (0.17), residues: 996 loop : -0.63 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 208 TYR 0.035 0.002 TYR N 94 PHE 0.022 0.002 PHE N 118 TRP 0.013 0.001 TRP B 222 HIS 0.005 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00373 (22143) covalent geometry : angle 0.54501 (30054) SS BOND : bond 0.00365 ( 18) SS BOND : angle 0.98483 ( 36) hydrogen bonds : bond 0.03075 ( 891) hydrogen bonds : angle 4.86433 ( 2412) link_NAG-ASN : bond 0.00219 ( 12) link_NAG-ASN : angle 1.65866 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6948.13 seconds wall clock time: 119 minutes 52.57 seconds (7192.57 seconds total)