Starting phenix.real_space_refine on Wed May 21 15:56:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5a_29737/05_2025/8g5a_29737_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5a_29737/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5a_29737/05_2025/8g5a_29737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5a_29737/05_2025/8g5a_29737.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5a_29737/05_2025/8g5a_29737_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5a_29737/05_2025/8g5a_29737_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: "I" 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: "M" 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: C, B, L, N, H, J 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: 12.06, per 1000 atoms: 0.56 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 C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 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: 4.96 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 3.64 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: 8.87 Time building geometry restraints manager: 5.87 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'M' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 4.590 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: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 48.800 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.100 ------------------------------------------------------------------------------- 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 : 6.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (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 TRP 0.011 0.001 TRP J 47 HIS 0.004 0.001 HIS I 207 PHE 0.015 0.001 PHE N 116 TYR 0.030 0.002 TYR N 192 ARG 0.005 0.000 ARG M 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 12) link_NAG-ASN : angle 1.72431 ( 36) hydrogen bonds : bond 0.12086 ( 891) hydrogen bonds : angle 6.64901 ( 2412) SS BOND : bond 0.00278 ( 18) SS BOND : angle 1.20516 ( 36) covalent geometry : bond 0.00499 (22143) covalent geometry : angle 0.69310 (30054) *********************** 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 : 2.424 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: 0.5088 (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: 0.6399 (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: 0.6393 (mm-30) REVERT: N 81 GLU cc_start: 0.6951 (pt0) cc_final: 0.5761 (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: 0.3592 time to fit residues: 164.2427 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 : 2.291 ------------------------------------------------------------------------------- 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 233 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 216 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 chunk 250 optimal weight: 0.8980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 216 ASN B 435 HIS ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN H 178 GLN I 178 GLN I 207 HIS J 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.140060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097025 restraints weight = 36493.011| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.83 r_work: 0.3043 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22173 Z= 0.219 Angle : 0.620 7.701 30126 Z= 0.332 Chirality : 0.047 0.185 3357 Planarity : 0.005 0.043 3882 Dihedral : 5.619 53.509 3264 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.51 % Allowed : 5.40 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 2763 helix: 1.67 (0.25), residues: 432 sheet: -0.09 (0.16), residues: 993 loop : -0.77 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 222 HIS 0.007 0.001 HIS C 435 PHE 0.017 0.002 PHE H 105 TYR 0.031 0.002 TYR M 94 ARG 0.004 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 12) link_NAG-ASN : angle 1.75615 ( 36) hydrogen bonds : bond 0.03778 ( 891) hydrogen bonds : angle 5.52488 ( 2412) SS BOND : bond 0.00531 ( 18) SS BOND : angle 1.18146 ( 36) covalent geometry : bond 0.00508 (22143) covalent geometry : angle 0.61680 (30054) *********************** 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: 36 poor density : 240 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8078 (mm-30) REVERT: A 408 ASP cc_start: 0.8306 (m-30) cc_final: 0.7984 (m-30) REVERT: A 444 MET cc_start: 0.9077 (tpt) cc_final: 0.8752 (tpt) REVERT: A 470 TYR cc_start: 0.8439 (m-80) cc_final: 0.8042 (m-80) REVERT: B 338 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5126 (m-80) REVERT: B 401 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 444 MET cc_start: 0.9065 (tpt) cc_final: 0.8517 (tpt) REVERT: B 453 ARG cc_start: 0.8205 (mtm180) cc_final: 0.7961 (mtm180) REVERT: B 470 TYR cc_start: 0.8517 (m-80) cc_final: 0.8053 (m-80) REVERT: B 491 TYR cc_start: 0.8587 (m-80) cc_final: 0.8364 (m-80) REVERT: C 453 ARG cc_start: 0.8221 (mtm180) cc_final: 0.7998 (mtm180) REVERT: I 35 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8328 (mt-10) REVERT: I 39 GLN cc_start: 0.8341 (tt0) cc_final: 0.7906 (tt0) REVERT: J 35 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8272 (mt-10) REVERT: L 24 ARG cc_start: 0.6694 (ttm-80) cc_final: 0.6122 (ttm-80) REVERT: L 36 TYR cc_start: 0.8081 (m-80) cc_final: 0.7776 (m-80) REVERT: L 106 LEU cc_start: 0.5703 (OUTLIER) cc_final: 0.4699 (mt) REVERT: M 24 ARG cc_start: 0.6662 (ttm-80) cc_final: 0.6035 (ttp-110) REVERT: M 79 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6188 (mm-30) REVERT: M 106 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.4812 (mt) REVERT: N 24 ARG cc_start: 0.6679 (ttm-80) cc_final: 0.5990 (ttp-110) REVERT: N 106 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.4748 (mt) REVERT: N 148 TRP cc_start: 0.6382 (m100) cc_final: 0.5654 (m-10) outliers start: 36 outliers final: 24 residues processed: 267 average time/residue: 0.3185 time to fit residues: 134.8751 Evaluate side-chains 241 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 2.365 ------------------------------------------------------------------------------- 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 455 LEU Chi-restraints excluded: chain C residue 155 THR 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 H residue 176 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 4 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 189 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 ASN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 59 ASN I 178 GLN J 59 ASN L 147 GLN M 147 GLN N 152 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.136700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090832 restraints weight = 36274.403| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.89 r_work: 0.2969 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22173 Z= 0.217 Angle : 0.588 8.065 30126 Z= 0.311 Chirality : 0.045 0.171 3357 Planarity : 0.004 0.047 3882 Dihedral : 5.408 48.897 3264 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.80 % Allowed : 7.86 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 2763 helix: 1.78 (0.24), residues: 432 sheet: -0.07 (0.16), residues: 969 loop : -0.88 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 222 HIS 0.006 0.001 HIS J 207 PHE 0.017 0.002 PHE H 105 TYR 0.028 0.002 TYR M 94 ARG 0.003 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 12) link_NAG-ASN : angle 1.82552 ( 36) hydrogen bonds : bond 0.03663 ( 891) hydrogen bonds : angle 5.35830 ( 2412) SS BOND : bond 0.00429 ( 18) SS BOND : angle 0.91651 ( 36) covalent geometry : bond 0.00507 (22143) covalent geometry : angle 0.58443 (30054) *********************** 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: 43 poor density : 231 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5128 (m-80) REVERT: A 401 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8008 (mm-30) REVERT: A 408 ASP cc_start: 0.8396 (m-30) cc_final: 0.8192 (m-30) REVERT: A 470 TYR cc_start: 0.8407 (m-80) cc_final: 0.8160 (m-80) REVERT: B 338 PHE cc_start: 0.6077 (OUTLIER) cc_final: 0.5179 (m-80) REVERT: B 401 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8015 (mm-30) REVERT: B 444 MET cc_start: 0.9057 (tpt) cc_final: 0.8534 (tpt) REVERT: B 468 LYS cc_start: 0.8397 (ttpt) cc_final: 0.8157 (ttpt) REVERT: C 338 PHE cc_start: 0.6218 (OUTLIER) cc_final: 0.5141 (m-80) REVERT: C 460 GLU cc_start: 0.7747 (tp30) cc_final: 0.7439 (tp30) REVERT: I 39 GLN cc_start: 0.8365 (tt0) cc_final: 0.7874 (tt0) REVERT: J 152 TYR cc_start: 0.7611 (p90) cc_final: 0.7293 (p90) REVERT: L 24 ARG cc_start: 0.6586 (ttm-80) cc_final: 0.6014 (ttm-80) REVERT: L 36 TYR cc_start: 0.8148 (m-80) cc_final: 0.7759 (m-80) REVERT: L 79 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6303 (tm-30) REVERT: L 106 LEU cc_start: 0.5550 (OUTLIER) cc_final: 0.4718 (mt) REVERT: L 148 TRP cc_start: 0.6389 (m100) cc_final: 0.5851 (m-10) REVERT: M 24 ARG cc_start: 0.6721 (ttm-80) cc_final: 0.6037 (ttm-80) REVERT: M 79 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6383 (tm-30) REVERT: M 106 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.4699 (mt) REVERT: M 148 TRP cc_start: 0.6299 (m100) cc_final: 0.5783 (m-10) REVERT: N 24 ARG cc_start: 0.6644 (ttm-80) cc_final: 0.6182 (ttm-80) REVERT: N 106 LEU cc_start: 0.5577 (OUTLIER) cc_final: 0.4683 (mt) REVERT: N 148 TRP cc_start: 0.6505 (m100) cc_final: 0.5748 (m-10) REVERT: N 152 ASN cc_start: 0.3526 (OUTLIER) cc_final: 0.3322 (p0) outliers start: 43 outliers final: 22 residues processed: 264 average time/residue: 0.3079 time to fit residues: 128.6274 Evaluate side-chains 240 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 182 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 335 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 I residue 117 THR 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 93 GLU 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 M residue 147 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 246 optimal weight: 0.0870 chunk 156 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 235 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 59 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.136875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.091733 restraints weight = 36530.456| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.02 r_work: 0.2956 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22173 Z= 0.183 Angle : 0.560 7.994 30126 Z= 0.297 Chirality : 0.044 0.160 3357 Planarity : 0.004 0.047 3882 Dihedral : 5.265 47.840 3264 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.30 % Allowed : 9.20 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2763 helix: 1.83 (0.24), residues: 432 sheet: -0.01 (0.16), residues: 954 loop : -0.92 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 222 HIS 0.005 0.001 HIS J 207 PHE 0.016 0.002 PHE I 105 TYR 0.023 0.002 TYR L 94 ARG 0.006 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 12) link_NAG-ASN : angle 1.86241 ( 36) hydrogen bonds : bond 0.03435 ( 891) hydrogen bonds : angle 5.23808 ( 2412) SS BOND : bond 0.00381 ( 18) SS BOND : angle 1.11717 ( 36) covalent geometry : bond 0.00426 (22143) covalent geometry : angle 0.55558 (30054) *********************** 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 269 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.6195 (OUTLIER) cc_final: 0.5326 (m-80) REVERT: A 378 ASN cc_start: 0.7690 (m110) cc_final: 0.7336 (m-40) REVERT: A 401 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8012 (mm-30) REVERT: A 408 ASP cc_start: 0.8498 (m-30) cc_final: 0.8223 (m-30) REVERT: B 338 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5370 (m-80) REVERT: B 378 ASN cc_start: 0.7450 (m110) cc_final: 0.7031 (m-40) REVERT: B 401 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8037 (mm-30) REVERT: B 408 ASP cc_start: 0.8497 (m-30) cc_final: 0.8227 (m-30) REVERT: B 444 MET cc_start: 0.9039 (tpt) cc_final: 0.8590 (tpt) REVERT: B 468 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8111 (ttpt) REVERT: B 469 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8174 (mm) REVERT: C 338 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.5251 (m-80) REVERT: C 460 GLU cc_start: 0.7769 (tp30) cc_final: 0.7469 (tp30) REVERT: I 39 GLN cc_start: 0.8403 (tt0) cc_final: 0.7922 (tt0) REVERT: J 152 TYR cc_start: 0.7575 (p90) cc_final: 0.7287 (p90) REVERT: L 24 ARG cc_start: 0.6685 (ttm-80) cc_final: 0.6075 (ttm-80) REVERT: L 36 TYR cc_start: 0.8166 (m-80) cc_final: 0.7793 (m-80) REVERT: L 47 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8297 (mt) REVERT: L 79 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6118 (tm-30) REVERT: L 106 LEU cc_start: 0.5542 (OUTLIER) cc_final: 0.4728 (mt) REVERT: L 148 TRP cc_start: 0.6218 (m100) cc_final: 0.5833 (m-10) REVERT: M 24 ARG cc_start: 0.6708 (ttm-80) cc_final: 0.6073 (ttp-110) REVERT: M 106 LEU cc_start: 0.5483 (OUTLIER) cc_final: 0.4672 (mt) REVERT: M 147 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6176 (tt0) REVERT: M 148 TRP cc_start: 0.6222 (m100) cc_final: 0.5748 (m100) REVERT: N 24 ARG cc_start: 0.6581 (ttm-80) cc_final: 0.6155 (ttm-80) REVERT: N 79 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6307 (tm-30) REVERT: N 106 LEU cc_start: 0.5545 (OUTLIER) cc_final: 0.4686 (mt) REVERT: N 148 TRP cc_start: 0.6559 (m100) cc_final: 0.5806 (m-10) outliers start: 55 outliers final: 31 residues processed: 258 average time/residue: 0.2968 time to fit residues: 124.4273 Evaluate side-chains 246 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 2.700 ------------------------------------------------------------------------------- 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 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 346 MET 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 335 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 496 LEU 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 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 93 GLU Chi-restraints excluded: chain L residue 106 LEU 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 M residue 147 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 193 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 230 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 245 optimal weight: 30.0000 chunk 176 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** ** B 471 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN M 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090168 restraints weight = 36595.163| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.94 r_work: 0.2891 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 22173 Z= 0.368 Angle : 0.686 8.374 30126 Z= 0.363 Chirality : 0.049 0.214 3357 Planarity : 0.005 0.053 3882 Dihedral : 5.905 51.330 3264 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.05 % Allowed : 10.87 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 2763 helix: 1.68 (0.24), residues: 414 sheet: -0.20 (0.16), residues: 960 loop : -1.00 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 222 HIS 0.009 0.002 HIS B 435 PHE 0.025 0.003 PHE J 105 TYR 0.026 0.003 TYR L 94 ARG 0.004 0.001 ARG A 492 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 12) link_NAG-ASN : angle 2.40834 ( 36) hydrogen bonds : bond 0.04184 ( 891) hydrogen bonds : angle 5.56650 ( 2412) SS BOND : bond 0.00655 ( 18) SS BOND : angle 1.04836 ( 36) covalent geometry : bond 0.00867 (22143) covalent geometry : angle 0.68104 (30054) *********************** 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 293 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 220 time to evaluate : 2.532 Fit side-chains revert: symmetry clash REVERT: A 338 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.5969 (m-80) REVERT: A 378 ASN cc_start: 0.7880 (m110) cc_final: 0.7521 (m-40) REVERT: A 401 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8105 (mm-30) REVERT: A 408 ASP cc_start: 0.8545 (m-30) cc_final: 0.8275 (m-30) REVERT: A 445 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8132 (t0) REVERT: B 338 PHE cc_start: 0.6442 (OUTLIER) cc_final: 0.6242 (m-80) REVERT: B 378 ASN cc_start: 0.7557 (m110) cc_final: 0.7325 (m110) REVERT: B 444 MET cc_start: 0.9039 (tpt) cc_final: 0.8544 (tpt) REVERT: B 468 LYS cc_start: 0.8475 (ttpt) cc_final: 0.7982 (ttpt) REVERT: B 470 TYR cc_start: 0.8534 (m-80) cc_final: 0.8187 (m-10) REVERT: C 338 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.5707 (m-80) REVERT: C 408 ASP cc_start: 0.8603 (m-30) cc_final: 0.8279 (m-30) REVERT: C 460 GLU cc_start: 0.7770 (tp30) cc_final: 0.7448 (tp30) REVERT: H 35 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8539 (mp0) REVERT: H 90 ASP cc_start: 0.7983 (t0) cc_final: 0.7773 (t0) REVERT: I 39 GLN cc_start: 0.8505 (tt0) cc_final: 0.8072 (tt0) REVERT: J 152 TYR cc_start: 0.7741 (p90) cc_final: 0.7272 (p90) REVERT: L 24 ARG cc_start: 0.6856 (ttm-80) cc_final: 0.6148 (ttm-80) REVERT: L 47 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8357 (mt) REVERT: L 106 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.4782 (mt) REVERT: L 132 VAL cc_start: 0.7829 (t) cc_final: 0.7563 (m) REVERT: L 148 TRP cc_start: 0.6600 (m100) cc_final: 0.6044 (m-10) REVERT: L 175 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7574 (tt) REVERT: M 24 ARG cc_start: 0.6815 (ttm-80) cc_final: 0.6145 (ttp-110) REVERT: M 106 LEU cc_start: 0.5516 (OUTLIER) cc_final: 0.4729 (mt) REVERT: M 148 TRP cc_start: 0.6527 (m100) cc_final: 0.6107 (m100) REVERT: N 24 ARG cc_start: 0.6597 (ttm-80) cc_final: 0.5996 (ttp-110) REVERT: N 78 LEU cc_start: 0.6952 (mt) cc_final: 0.6662 (tt) REVERT: N 106 LEU cc_start: 0.5658 (OUTLIER) cc_final: 0.4755 (mt) REVERT: N 148 TRP cc_start: 0.6655 (m100) cc_final: 0.6043 (m100) outliers start: 73 outliers final: 47 residues processed: 280 average time/residue: 0.3084 time to fit residues: 139.7674 Evaluate side-chains 266 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 2.377 ------------------------------------------------------------------------------- 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 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 445 ASN 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 346 MET Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 439 LEU 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 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 455 LEU 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 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 93 GLU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain M residue 4 MET 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 M residue 147 GLN Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 23 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 96 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN C 189 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 178 GLN I 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091415 restraints weight = 36495.997| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.23 r_work: 0.2916 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22173 Z= 0.137 Angle : 0.540 7.896 30126 Z= 0.285 Chirality : 0.043 0.173 3357 Planarity : 0.004 0.050 3882 Dihedral : 5.184 46.634 3264 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.09 % Allowed : 12.30 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2763 helix: 2.15 (0.25), residues: 414 sheet: -0.14 (0.16), residues: 975 loop : -0.84 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.007 0.001 HIS A 471 PHE 0.020 0.001 PHE J 129 TYR 0.025 0.002 TYR L 94 ARG 0.004 0.000 ARG A 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 12) link_NAG-ASN : angle 1.93378 ( 36) hydrogen bonds : bond 0.03191 ( 891) hydrogen bonds : angle 5.14514 ( 2412) SS BOND : bond 0.00351 ( 18) SS BOND : angle 0.95187 ( 36) covalent geometry : bond 0.00315 (22143) covalent geometry : angle 0.53577 (30054) *********************** 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 268 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASN cc_start: 0.7733 (m110) cc_final: 0.7381 (m-40) REVERT: A 401 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8009 (mm-30) REVERT: A 408 ASP cc_start: 0.8610 (m-30) cc_final: 0.8342 (m-30) REVERT: A 468 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8144 (ttpt) REVERT: B 378 ASN cc_start: 0.7469 (m110) cc_final: 0.7059 (m-40) REVERT: B 401 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8033 (tp30) REVERT: B 408 ASP cc_start: 0.8635 (m-30) cc_final: 0.8377 (m-30) REVERT: B 444 MET cc_start: 0.8988 (tpt) cc_final: 0.8518 (tpt) REVERT: B 468 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8072 (ttpt) REVERT: B 469 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8290 (mm) REVERT: B 470 TYR cc_start: 0.8475 (m-80) cc_final: 0.8247 (m-80) REVERT: C 460 GLU cc_start: 0.7849 (tp30) cc_final: 0.7608 (tp30) REVERT: H 39 GLN cc_start: 0.8465 (tt0) cc_final: 0.8127 (tt0) REVERT: H 90 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7747 (t0) REVERT: I 39 GLN cc_start: 0.8488 (tt0) cc_final: 0.8026 (tt0) REVERT: J 152 TYR cc_start: 0.7733 (p90) cc_final: 0.7414 (p90) REVERT: L 24 ARG cc_start: 0.6747 (ttm-80) cc_final: 0.5984 (ttm-80) REVERT: L 47 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8235 (mt) REVERT: L 106 LEU cc_start: 0.5477 (OUTLIER) cc_final: 0.4695 (mt) REVERT: L 148 TRP cc_start: 0.6659 (m100) cc_final: 0.6074 (m-10) REVERT: M 24 ARG cc_start: 0.6791 (ttm-80) cc_final: 0.6092 (ttp-110) REVERT: M 106 LEU cc_start: 0.5394 (OUTLIER) cc_final: 0.4753 (mt) REVERT: M 148 TRP cc_start: 0.6290 (m100) cc_final: 0.5777 (m100) REVERT: N 24 ARG cc_start: 0.6571 (ttm-80) cc_final: 0.6144 (ttm-80) REVERT: N 106 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.4758 (mt) REVERT: N 148 TRP cc_start: 0.6607 (m100) cc_final: 0.5817 (m-10) REVERT: N 154 LEU cc_start: 0.4327 (OUTLIER) cc_final: 0.3989 (mt) REVERT: N 167 ASP cc_start: 0.4482 (t70) cc_final: 0.4155 (t0) REVERT: N 175 LEU cc_start: 0.7636 (tt) cc_final: 0.7436 (tt) outliers start: 50 outliers final: 28 residues processed: 260 average time/residue: 0.3022 time to fit residues: 126.5973 Evaluate side-chains 238 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 2.329 ------------------------------------------------------------------------------- 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 182 ILE Chi-restraints excluded: chain B residue 335 ILE 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 182 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 112 GLN 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 M residue 4 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 102 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 252 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 178 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.135989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092415 restraints weight = 36523.836| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.23 r_work: 0.2937 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22173 Z= 0.196 Angle : 0.570 9.302 30126 Z= 0.298 Chirality : 0.044 0.203 3357 Planarity : 0.004 0.050 3882 Dihedral : 5.117 47.952 3252 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.43 % Allowed : 12.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2763 helix: 2.09 (0.25), residues: 414 sheet: -0.22 (0.16), residues: 990 loop : -0.82 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 222 HIS 0.005 0.001 HIS B 435 PHE 0.017 0.002 PHE I 105 TYR 0.025 0.002 TYR A 470 ARG 0.006 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 12) link_NAG-ASN : angle 2.01528 ( 36) hydrogen bonds : bond 0.03388 ( 891) hydrogen bonds : angle 5.17000 ( 2412) SS BOND : bond 0.00431 ( 18) SS BOND : angle 1.06512 ( 36) covalent geometry : bond 0.00459 (22143) covalent geometry : angle 0.56480 (30054) *********************** 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 261 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 2.702 Fit side-chains REVERT: A 378 ASN cc_start: 0.7706 (m110) cc_final: 0.7347 (m-40) REVERT: A 401 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8002 (mm-30) REVERT: A 408 ASP cc_start: 0.8585 (m-30) cc_final: 0.8313 (m-30) REVERT: B 378 ASN cc_start: 0.7461 (m110) cc_final: 0.7022 (m-40) REVERT: B 408 ASP cc_start: 0.8549 (m-30) cc_final: 0.8274 (m-30) REVERT: B 444 MET cc_start: 0.9009 (tpt) cc_final: 0.8468 (tpt) REVERT: B 468 LYS cc_start: 0.8502 (ttpt) cc_final: 0.8039 (ttpt) REVERT: B 469 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8292 (mm) REVERT: B 470 TYR cc_start: 0.8425 (m-80) cc_final: 0.8161 (m-10) REVERT: C 408 ASP cc_start: 0.8567 (m-30) cc_final: 0.8258 (m-30) REVERT: C 460 GLU cc_start: 0.7733 (tp30) cc_final: 0.7470 (tp30) REVERT: H 39 GLN cc_start: 0.8415 (tt0) cc_final: 0.8029 (tt0) REVERT: H 90 ASP cc_start: 0.7922 (t0) cc_final: 0.7719 (t0) REVERT: I 39 GLN cc_start: 0.8471 (tt0) cc_final: 0.8020 (tt0) REVERT: J 3 GLN cc_start: 0.7539 (pt0) cc_final: 0.7250 (tt0) REVERT: J 152 TYR cc_start: 0.7834 (p90) cc_final: 0.7560 (p90) REVERT: L 24 ARG cc_start: 0.6860 (ttm-80) cc_final: 0.5890 (ttp-110) REVERT: L 47 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8278 (mt) REVERT: L 106 LEU cc_start: 0.5520 (OUTLIER) cc_final: 0.4776 (mt) REVERT: L 148 TRP cc_start: 0.6673 (m100) cc_final: 0.6110 (m-10) REVERT: M 24 ARG cc_start: 0.6828 (ttm-80) cc_final: 0.6147 (ttp-110) REVERT: M 106 LEU cc_start: 0.5486 (OUTLIER) cc_final: 0.4825 (mt) REVERT: M 148 TRP cc_start: 0.6358 (m100) cc_final: 0.5860 (m-10) REVERT: N 24 ARG cc_start: 0.6514 (ttm-80) cc_final: 0.5938 (ttm-80) REVERT: N 106 LEU cc_start: 0.5619 (OUTLIER) cc_final: 0.4841 (mt) REVERT: N 148 TRP cc_start: 0.6603 (m100) cc_final: 0.5852 (m-10) REVERT: N 154 LEU cc_start: 0.4260 (OUTLIER) cc_final: 0.3893 (mt) REVERT: N 175 LEU cc_start: 0.7768 (tt) cc_final: 0.7541 (tt) outliers start: 58 outliers final: 37 residues processed: 253 average time/residue: 0.2898 time to fit residues: 120.9022 Evaluate side-chains 244 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 2.462 ------------------------------------------------------------------------------- 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 318 THR Chi-restraints excluded: chain B residue 335 ILE 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 182 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL 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 117 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 93 GLU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 4 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 75 optimal weight: 0.0870 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 187 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- 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 356 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 112 GLN I 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.135755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092594 restraints weight = 36632.351| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.93 r_work: 0.2947 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22173 Z= 0.208 Angle : 0.582 9.206 30126 Z= 0.302 Chirality : 0.045 0.231 3357 Planarity : 0.004 0.049 3882 Dihedral : 5.139 47.717 3252 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.47 % Allowed : 13.17 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2763 helix: 2.04 (0.25), residues: 414 sheet: -0.27 (0.16), residues: 990 loop : -0.94 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 222 HIS 0.005 0.001 HIS B 435 PHE 0.020 0.002 PHE L 118 TYR 0.047 0.002 TYR N 94 ARG 0.004 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 12) link_NAG-ASN : angle 2.03242 ( 36) hydrogen bonds : bond 0.03414 ( 891) hydrogen bonds : angle 5.12764 ( 2412) SS BOND : bond 0.00450 ( 18) SS BOND : angle 1.00302 ( 36) covalent geometry : bond 0.00487 (22143) covalent geometry : angle 0.57779 (30054) *********************** 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 257 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 2.484 Fit side-chains REVERT: A 378 ASN cc_start: 0.7619 (m110) cc_final: 0.7289 (m-40) REVERT: A 401 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8011 (mm-30) REVERT: A 408 ASP cc_start: 0.8498 (m-30) cc_final: 0.8239 (m-30) REVERT: B 408 ASP cc_start: 0.8485 (m-30) cc_final: 0.8189 (m-30) REVERT: B 444 MET cc_start: 0.9009 (tpt) cc_final: 0.8498 (tpt) REVERT: B 468 LYS cc_start: 0.8490 (ttpt) cc_final: 0.8029 (ttpt) REVERT: B 469 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8305 (mm) REVERT: B 470 TYR cc_start: 0.8419 (m-80) cc_final: 0.8140 (m-10) REVERT: C 408 ASP cc_start: 0.8480 (m-30) cc_final: 0.8168 (m-30) REVERT: H 90 ASP cc_start: 0.7829 (t0) cc_final: 0.7618 (t0) REVERT: I 39 GLN cc_start: 0.8496 (tt0) cc_final: 0.8059 (tt0) REVERT: J 3 GLN cc_start: 0.7477 (pt0) cc_final: 0.7213 (tt0) REVERT: J 35 GLU cc_start: 0.8902 (mp0) cc_final: 0.8636 (mp0) REVERT: L 24 ARG cc_start: 0.6790 (ttm-80) cc_final: 0.5948 (ttm-80) REVERT: L 47 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8269 (mt) REVERT: L 106 LEU cc_start: 0.5448 (OUTLIER) cc_final: 0.4690 (mt) REVERT: L 148 TRP cc_start: 0.6704 (m100) cc_final: 0.6147 (m-10) REVERT: M 24 ARG cc_start: 0.6685 (ttm-80) cc_final: 0.6128 (ttp-110) REVERT: M 106 LEU cc_start: 0.5467 (OUTLIER) cc_final: 0.4820 (mt) REVERT: M 148 TRP cc_start: 0.6461 (m100) cc_final: 0.6081 (m100) REVERT: N 24 ARG cc_start: 0.6355 (ttm-80) cc_final: 0.5901 (ttm-80) REVERT: N 106 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.4821 (mt) REVERT: N 148 TRP cc_start: 0.6662 (m100) cc_final: 0.5907 (m-10) REVERT: N 154 LEU cc_start: 0.4279 (OUTLIER) cc_final: 0.3931 (mt) REVERT: N 175 LEU cc_start: 0.7680 (tt) cc_final: 0.7457 (tt) outliers start: 59 outliers final: 41 residues processed: 249 average time/residue: 0.2669 time to fit residues: 110.9771 Evaluate side-chains 241 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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 A residue 388 THR 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 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 182 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL 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 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 93 GLU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 4 MET 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 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 144 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 230 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 270 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 267 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 GLN B 378 ASN ** B 471 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.138500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094226 restraints weight = 36264.473| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.04 r_work: 0.2982 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 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 = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22173 Z= 0.110 Angle : 0.532 10.098 30126 Z= 0.275 Chirality : 0.042 0.186 3357 Planarity : 0.004 0.060 3882 Dihedral : 4.765 44.650 3252 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.80 % Allowed : 13.76 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2763 helix: 2.13 (0.25), residues: 432 sheet: -0.06 (0.17), residues: 972 loop : -0.94 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 47 HIS 0.004 0.001 HIS J 207 PHE 0.014 0.001 PHE M 118 TYR 0.027 0.001 TYR N 94 ARG 0.004 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 12) link_NAG-ASN : angle 1.72447 ( 36) hydrogen bonds : bond 0.02950 ( 891) hydrogen bonds : angle 4.89786 ( 2412) SS BOND : bond 0.00299 ( 18) SS BOND : angle 0.97318 ( 36) covalent geometry : bond 0.00249 (22143) covalent geometry : angle 0.52817 (30054) *********************** 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 258 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 2.298 Fit side-chains revert: symmetry clash REVERT: A 408 ASP cc_start: 0.8499 (m-30) cc_final: 0.8261 (m-30) REVERT: B 408 ASP cc_start: 0.8526 (m-30) cc_final: 0.8271 (m-30) REVERT: B 444 MET cc_start: 0.8983 (tpt) cc_final: 0.8476 (tpt) REVERT: B 468 LYS cc_start: 0.8513 (ttpt) cc_final: 0.8053 (ttpt) REVERT: B 469 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8154 (mm) REVERT: B 470 TYR cc_start: 0.8349 (m-80) cc_final: 0.8076 (m-10) REVERT: C 462 MET cc_start: 0.8201 (mmm) cc_final: 0.7945 (mmm) REVERT: H 3 GLN cc_start: 0.7746 (pt0) cc_final: 0.7544 (pm20) REVERT: I 39 GLN cc_start: 0.8432 (tt0) cc_final: 0.7997 (tt0) REVERT: J 3 GLN cc_start: 0.7393 (pt0) cc_final: 0.7140 (tt0) REVERT: L 24 ARG cc_start: 0.6654 (ttm-80) cc_final: 0.5724 (ttp-110) REVERT: L 47 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8127 (mt) REVERT: L 78 LEU cc_start: 0.6782 (mt) cc_final: 0.6491 (tt) REVERT: L 106 LEU cc_start: 0.5431 (OUTLIER) cc_final: 0.4690 (mt) REVERT: L 148 TRP cc_start: 0.6579 (m100) cc_final: 0.6056 (m-10) REVERT: L 175 LEU cc_start: 0.7928 (tt) cc_final: 0.7683 (tt) REVERT: M 24 ARG cc_start: 0.6668 (ttm-80) cc_final: 0.6052 (ttp-110) REVERT: M 79 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6348 (tm-30) REVERT: M 106 LEU cc_start: 0.5492 (OUTLIER) cc_final: 0.4811 (mt) REVERT: M 148 TRP cc_start: 0.6440 (m100) cc_final: 0.6036 (m-10) REVERT: N 24 ARG cc_start: 0.6295 (ttm-80) cc_final: 0.5773 (ttm-80) REVERT: N 106 LEU cc_start: 0.5463 (OUTLIER) cc_final: 0.4795 (mt) REVERT: N 148 TRP cc_start: 0.6599 (m100) cc_final: 0.5854 (m-10) REVERT: N 154 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.4018 (mt) REVERT: N 175 LEU cc_start: 0.7694 (tt) cc_final: 0.7492 (tt) REVERT: N 192 TYR cc_start: 0.3596 (OUTLIER) cc_final: 0.3316 (m-10) outliers start: 43 outliers final: 33 residues processed: 251 average time/residue: 0.2697 time to fit residues: 113.5224 Evaluate side-chains 240 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 2.333 ------------------------------------------------------------------------------- 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 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 2 VAL 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 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 93 GLU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 4 MET 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 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 Chi-restraints excluded: chain N residue 192 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 195 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 126 optimal weight: 0.4980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 C 189 GLN H 112 GLN H 178 GLN I 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.137514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091611 restraints weight = 36664.201| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.15 r_work: 0.2979 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 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 = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22173 Z= 0.149 Angle : 0.550 10.015 30126 Z= 0.285 Chirality : 0.043 0.199 3357 Planarity : 0.004 0.049 3882 Dihedral : 4.811 45.539 3252 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.01 % Allowed : 13.59 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2763 helix: 2.35 (0.25), residues: 414 sheet: -0.01 (0.17), residues: 930 loop : -0.80 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 47 HIS 0.005 0.001 HIS B 435 PHE 0.025 0.002 PHE L 118 TYR 0.039 0.002 TYR M 94 ARG 0.005 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 12) link_NAG-ASN : angle 1.80374 ( 36) hydrogen bonds : bond 0.03099 ( 891) hydrogen bonds : angle 4.93508 ( 2412) SS BOND : bond 0.00351 ( 18) SS BOND : angle 1.01050 ( 36) covalent geometry : bond 0.00349 (22143) covalent geometry : angle 0.54563 (30054) ********************** 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 240 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 2.426 Fit side-chains REVERT: A 378 ASN cc_start: 0.7530 (m110) cc_final: 0.7203 (m-40) REVERT: A 408 ASP cc_start: 0.8486 (m-30) cc_final: 0.8237 (m-30) REVERT: B 408 ASP cc_start: 0.8498 (m-30) cc_final: 0.8216 (m-30) REVERT: B 444 MET cc_start: 0.8995 (tpt) cc_final: 0.8478 (tpt) REVERT: B 468 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8023 (ttpt) REVERT: B 469 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8166 (mm) REVERT: B 470 TYR cc_start: 0.8355 (m-80) cc_final: 0.8044 (m-10) REVERT: C 408 ASP cc_start: 0.8519 (m-30) cc_final: 0.8220 (m-30) REVERT: C 462 MET cc_start: 0.8228 (mmm) cc_final: 0.7962 (mmm) REVERT: H 90 ASP cc_start: 0.7839 (t0) cc_final: 0.7637 (t0) REVERT: I 39 GLN cc_start: 0.8437 (tt0) cc_final: 0.7983 (tt0) REVERT: J 3 GLN cc_start: 0.7326 (pt0) cc_final: 0.7121 (tt0) REVERT: L 24 ARG cc_start: 0.6717 (ttm-80) cc_final: 0.5847 (ttp-110) REVERT: L 47 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8234 (mt) REVERT: L 106 LEU cc_start: 0.5480 (OUTLIER) cc_final: 0.4772 (mt) REVERT: L 148 TRP cc_start: 0.6622 (m100) cc_final: 0.6098 (m-10) REVERT: M 24 ARG cc_start: 0.6765 (ttm-80) cc_final: 0.6105 (ttp-110) REVERT: M 106 LEU cc_start: 0.5410 (OUTLIER) cc_final: 0.4763 (mt) REVERT: M 148 TRP cc_start: 0.6468 (m100) cc_final: 0.6066 (m-10) REVERT: N 24 ARG cc_start: 0.6384 (ttm-80) cc_final: 0.5803 (ttm-80) REVERT: N 106 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.4875 (mt) REVERT: N 148 TRP cc_start: 0.6617 (m100) cc_final: 0.5923 (m-10) REVERT: N 154 LEU cc_start: 0.4292 (OUTLIER) cc_final: 0.3894 (mt) REVERT: N 175 LEU cc_start: 0.7810 (tt) cc_final: 0.7595 (tt) REVERT: N 192 TYR cc_start: 0.3461 (OUTLIER) cc_final: 0.3121 (m-10) outliers start: 48 outliers final: 37 residues processed: 233 average time/residue: 0.2772 time to fit residues: 108.2710 Evaluate side-chains 234 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 2.419 ------------------------------------------------------------------------------- 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 A residue 388 THR 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 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 436 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 112 GLN 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 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 93 GLU Chi-restraints excluded: chain L residue 106 LEU 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 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 Chi-restraints excluded: chain N residue 192 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 130 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 260 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 240 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN H 178 GLN I 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091332 restraints weight = 36475.228| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.91 r_work: 0.2950 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22173 Z= 0.213 Angle : 0.588 9.561 30126 Z= 0.307 Chirality : 0.045 0.215 3357 Planarity : 0.004 0.053 3882 Dihedral : 5.038 46.888 3252 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.17 % Allowed : 13.47 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2763 helix: 2.18 (0.25), residues: 414 sheet: -0.16 (0.17), residues: 960 loop : -0.77 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 222 HIS 0.006 0.001 HIS B 435 PHE 0.023 0.002 PHE L 118 TYR 0.051 0.002 TYR M 94 ARG 0.005 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 12) link_NAG-ASN : angle 1.95963 ( 36) hydrogen bonds : bond 0.03383 ( 891) hydrogen bonds : angle 5.06386 ( 2412) SS BOND : bond 0.00451 ( 18) SS BOND : angle 1.05387 ( 36) covalent geometry : bond 0.00501 (22143) covalent geometry : angle 0.58411 (30054) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14445.28 seconds wall clock time: 250 minutes 35.84 seconds (15035.84 seconds total)