Starting phenix.real_space_refine on Wed Jun 18 20:25:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5a_29737/06_2025/8g5a_29737_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5a_29737/06_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_29737/06_2025/8g5a_29737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5a_29737/06_2025/8g5a_29737.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5a_29737/06_2025/8g5a_29737_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5a_29737/06_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-5710/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: 12.63, per 1000 atoms: 0.58 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: 5.23 Conformation dependent library (CDL) restraints added in 3.2 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: 3.72 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: 13.19 Time building geometry restraints manager: 6.26 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: 0.16 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: 146.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 53.680 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:4.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 206.650 ------------------------------------------------------------------------------- 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 : 2.506 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: 0.3809 time to fit residues: 174.2506 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 : 2.327 ------------------------------------------------------------------------------- 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 = 71)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097049 restraints weight = 36493.010| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.83 r_work: 0.3044 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 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 = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 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 : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 408 ASP cc_start: 0.8315 (m-30) cc_final: 0.7992 (m-30) REVERT: A 444 MET cc_start: 0.9072 (tpt) cc_final: 0.8747 (tpt) REVERT: A 470 TYR cc_start: 0.8438 (m-80) cc_final: 0.8042 (m-80) REVERT: B 338 PHE cc_start: 0.6287 (OUTLIER) cc_final: 0.5125 (m-80) REVERT: B 401 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8065 (mm-30) REVERT: B 444 MET cc_start: 0.9060 (tpt) cc_final: 0.8511 (tpt) REVERT: B 453 ARG cc_start: 0.8208 (mtm180) cc_final: 0.7963 (mtm180) REVERT: B 470 TYR cc_start: 0.8517 (m-80) cc_final: 0.8054 (m-80) REVERT: B 491 TYR cc_start: 0.8589 (m-80) cc_final: 0.8367 (m-80) REVERT: C 453 ARG cc_start: 0.8224 (mtm180) cc_final: 0.8001 (mtm180) REVERT: I 35 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8327 (mt-10) REVERT: I 39 GLN cc_start: 0.8334 (tt0) cc_final: 0.7900 (tt0) REVERT: J 35 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8272 (mt-10) REVERT: L 24 ARG cc_start: 0.6679 (ttm-80) cc_final: 0.6113 (ttm-80) REVERT: L 36 TYR cc_start: 0.8079 (m-80) cc_final: 0.7774 (m-80) REVERT: L 106 LEU cc_start: 0.5703 (OUTLIER) cc_final: 0.4697 (mt) REVERT: M 24 ARG cc_start: 0.6655 (ttm-80) cc_final: 0.6033 (ttp-110) REVERT: M 79 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6191 (mm-30) REVERT: M 106 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.4806 (mt) REVERT: N 24 ARG cc_start: 0.6669 (ttm-80) cc_final: 0.5989 (ttp-110) REVERT: N 106 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.4747 (mt) REVERT: N 148 TRP cc_start: 0.6384 (m100) cc_final: 0.5657 (m-10) outliers start: 36 outliers final: 24 residues processed: 267 average time/residue: 0.3432 time to fit residues: 146.4428 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 : 2.468 ------------------------------------------------------------------------------- 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: 8.9990 chunk 50 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 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: 2.1988 ------------------------------------------------------------------------------- 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 178 GLN ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN J 59 ASN L 147 GLN M 147 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.137306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094438 restraints weight = 36224.061| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.87 r_work: 0.2974 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22173 Z= 0.182 Angle : 0.567 7.991 30126 Z= 0.300 Chirality : 0.044 0.164 3357 Planarity : 0.004 0.048 3882 Dihedral : 5.267 48.039 3264 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.71 % Allowed : 7.65 % Favored : 90.63 % 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 (0.15), residues: 2763 helix: 1.88 (0.24), residues: 432 sheet: 0.01 (0.16), residues: 954 loop : -0.90 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.006 0.001 HIS J 207 PHE 0.015 0.002 PHE H 105 TYR 0.026 0.002 TYR M 94 ARG 0.004 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 12) link_NAG-ASN : angle 1.71458 ( 36) hydrogen bonds : bond 0.03501 ( 891) hydrogen bonds : angle 5.28804 ( 2412) SS BOND : bond 0.00380 ( 18) SS BOND : angle 0.90002 ( 36) covalent geometry : bond 0.00423 (22143) covalent geometry : angle 0.56333 (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 279 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.6196 (OUTLIER) cc_final: 0.5108 (m-80) REVERT: A 401 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7992 (mm-30) REVERT: B 338 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.5188 (m-80) REVERT: B 401 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8023 (mm-30) REVERT: B 444 MET cc_start: 0.9053 (tpt) cc_final: 0.8528 (tpt) REVERT: B 468 LYS cc_start: 0.8414 (ttpt) cc_final: 0.8157 (ttpt) REVERT: B 470 TYR cc_start: 0.8442 (m-80) cc_final: 0.8183 (m-80) REVERT: C 338 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5173 (m-80) REVERT: C 460 GLU cc_start: 0.7764 (tp30) cc_final: 0.7494 (tp30) REVERT: H 108 ASP cc_start: 0.8313 (p0) cc_final: 0.8109 (p0) REVERT: H 183 TYR cc_start: 0.7336 (m-10) cc_final: 0.7079 (m-10) REVERT: I 39 GLN cc_start: 0.8347 (tt0) cc_final: 0.7866 (tt0) REVERT: J 152 TYR cc_start: 0.7535 (p90) cc_final: 0.7237 (p90) REVERT: L 24 ARG cc_start: 0.6651 (ttm-80) cc_final: 0.6129 (ttm-80) REVERT: L 36 TYR cc_start: 0.8141 (m-80) cc_final: 0.7758 (m-80) REVERT: L 79 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6309 (tm-30) REVERT: L 106 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.4718 (mt) REVERT: L 148 TRP cc_start: 0.6313 (m100) cc_final: 0.5767 (m-10) REVERT: M 24 ARG cc_start: 0.6731 (ttm-80) cc_final: 0.6043 (ttm-80) REVERT: M 79 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6365 (tm-30) REVERT: M 106 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.4708 (mt) REVERT: M 148 TRP cc_start: 0.6263 (m100) cc_final: 0.5749 (m-10) REVERT: N 24 ARG cc_start: 0.6665 (ttm-80) cc_final: 0.6006 (ttm-80) REVERT: N 106 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.4700 (mt) REVERT: N 148 TRP cc_start: 0.6482 (m100) cc_final: 0.5758 (m-10) outliers start: 41 outliers final: 22 residues processed: 269 average time/residue: 0.3562 time to fit residues: 153.6931 Evaluate side-chains 244 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 3.318 ------------------------------------------------------------------------------- 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 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 246 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 182 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 235 optimal weight: 0.0070 chunk 91 optimal weight: 3.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 59 ASN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN J 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.138242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094042 restraints weight = 36487.765| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.91 r_work: 0.2995 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22173 Z= 0.138 Angle : 0.533 7.928 30126 Z= 0.281 Chirality : 0.043 0.154 3357 Planarity : 0.004 0.048 3882 Dihedral : 5.059 46.307 3264 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.92 % Allowed : 9.41 % Favored : 88.67 % 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: -0.12 (0.15), residues: 2763 helix: 2.02 (0.24), residues: 432 sheet: 0.06 (0.16), residues: 972 loop : -0.84 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 222 HIS 0.006 0.001 HIS J 207 PHE 0.013 0.002 PHE H 105 TYR 0.021 0.001 TYR L 94 ARG 0.007 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 12) link_NAG-ASN : angle 1.69301 ( 36) hydrogen bonds : bond 0.03216 ( 891) hydrogen bonds : angle 5.11241 ( 2412) SS BOND : bond 0.00323 ( 18) SS BOND : angle 1.02486 ( 36) covalent geometry : bond 0.00316 (22143) covalent geometry : angle 0.52897 (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 268 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.5251 (m-80) REVERT: A 401 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7921 (mm-30) REVERT: B 338 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5278 (m-80) REVERT: B 378 ASN cc_start: 0.7300 (m110) cc_final: 0.6875 (m-40) REVERT: B 401 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7954 (mm-30) REVERT: B 444 MET cc_start: 0.9032 (tpt) cc_final: 0.8553 (tpt) REVERT: B 468 LYS cc_start: 0.8351 (ttpt) cc_final: 0.8125 (ttpt) REVERT: B 469 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8159 (mm) REVERT: C 338 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5143 (m-80) REVERT: C 460 GLU cc_start: 0.7679 (tp30) cc_final: 0.7418 (tp30) REVERT: H 108 ASP cc_start: 0.8258 (p0) cc_final: 0.8054 (p0) REVERT: I 39 GLN cc_start: 0.8344 (tt0) cc_final: 0.7881 (tt0) REVERT: J 152 TYR cc_start: 0.7529 (p90) cc_final: 0.7248 (p90) REVERT: L 24 ARG cc_start: 0.6593 (ttm-80) cc_final: 0.5931 (ttm-80) REVERT: L 36 TYR cc_start: 0.8057 (m-80) cc_final: 0.7741 (m-80) REVERT: L 47 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8217 (mt) REVERT: L 79 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6161 (tm-30) REVERT: L 106 LEU cc_start: 0.5458 (OUTLIER) cc_final: 0.4656 (mt) REVERT: L 148 TRP cc_start: 0.6190 (m100) cc_final: 0.5883 (m-10) REVERT: M 24 ARG cc_start: 0.6689 (ttm-80) cc_final: 0.6016 (ttp-110) REVERT: M 79 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6348 (tm-30) REVERT: M 106 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.4653 (mt) REVERT: M 147 GLN cc_start: 0.6631 (OUTLIER) cc_final: 0.6074 (tt0) REVERT: M 148 TRP cc_start: 0.6230 (m100) cc_final: 0.5767 (m100) REVERT: N 24 ARG cc_start: 0.6499 (ttm-80) cc_final: 0.5953 (ttp-110) REVERT: N 106 LEU cc_start: 0.5562 (OUTLIER) cc_final: 0.4694 (mt) REVERT: N 148 TRP cc_start: 0.6555 (m100) cc_final: 0.5959 (m100) outliers start: 46 outliers final: 26 residues processed: 260 average time/residue: 0.3032 time to fit residues: 129.1731 Evaluate side-chains 241 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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 B residue 110 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain 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 I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 112 GLN 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 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: 0.9990 chunk 129 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 273 optimal weight: 20.0000 chunk 230 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 245 optimal weight: 30.0000 chunk 176 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN ** 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** ** 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 = 0.3804 r_free = 0.3804 target = 0.134322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091419 restraints weight = 36605.632| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.82 r_work: 0.2917 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 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 = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 22173 Z= 0.331 Angle : 0.659 8.253 30126 Z= 0.349 Chirality : 0.048 0.207 3357 Planarity : 0.005 0.049 3882 Dihedral : 5.715 50.454 3262 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.80 % Allowed : 10.04 % Favored : 87.16 % 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: -0.36 (0.15), residues: 2763 helix: 1.84 (0.24), residues: 414 sheet: -0.15 (0.16), residues: 960 loop : -0.92 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 222 HIS 0.008 0.002 HIS B 435 PHE 0.026 0.002 PHE J 105 TYR 0.047 0.002 TYR L 94 ARG 0.004 0.001 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 12) link_NAG-ASN : angle 2.24109 ( 36) hydrogen bonds : bond 0.04018 ( 891) hydrogen bonds : angle 5.45238 ( 2412) SS BOND : bond 0.00602 ( 18) SS BOND : angle 1.01525 ( 36) covalent geometry : bond 0.00780 (22143) covalent geometry : angle 0.65381 (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 289 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 222 time to evaluate : 2.434 Fit side-chains REVERT: A 338 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5815 (m-80) REVERT: A 378 ASN cc_start: 0.7798 (m110) cc_final: 0.7442 (m-40) REVERT: A 401 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8091 (mm-30) REVERT: A 445 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8149 (t0) REVERT: A 468 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8212 (ttpt) REVERT: B 338 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.6135 (m-80) REVERT: B 378 ASN cc_start: 0.7502 (m110) cc_final: 0.7087 (m-40) REVERT: B 444 MET cc_start: 0.9039 (tpt) cc_final: 0.8549 (tpt) REVERT: B 468 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8026 (ttpt) REVERT: B 469 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8323 (mm) REVERT: B 470 TYR cc_start: 0.8556 (m-80) cc_final: 0.8330 (m-80) REVERT: C 338 PHE cc_start: 0.6380 (OUTLIER) cc_final: 0.5605 (m-80) REVERT: C 408 ASP cc_start: 0.8523 (m-30) cc_final: 0.8207 (m-30) REVERT: C 460 GLU cc_start: 0.7745 (tp30) cc_final: 0.7449 (tp30) REVERT: I 39 GLN cc_start: 0.8450 (tt0) cc_final: 0.7970 (tt0) REVERT: J 152 TYR cc_start: 0.7628 (p90) cc_final: 0.7249 (p90) REVERT: L 24 ARG cc_start: 0.6758 (ttm-80) cc_final: 0.6127 (ttm-80) REVERT: L 47 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8320 (mt) REVERT: L 106 LEU cc_start: 0.5639 (OUTLIER) cc_final: 0.4783 (mt) REVERT: L 148 TRP cc_start: 0.6618 (m100) cc_final: 0.6050 (m-10) REVERT: M 24 ARG cc_start: 0.6722 (ttm-80) cc_final: 0.6070 (ttp-110) REVERT: M 106 LEU cc_start: 0.5546 (OUTLIER) cc_final: 0.4715 (mt) REVERT: M 148 TRP cc_start: 0.6474 (m100) cc_final: 0.6085 (m100) REVERT: N 24 ARG cc_start: 0.6539 (ttm-80) cc_final: 0.6042 (ttp-110) REVERT: N 78 LEU cc_start: 0.6865 (mt) cc_final: 0.6660 (tt) REVERT: N 106 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.4721 (mt) REVERT: N 148 TRP cc_start: 0.6647 (m100) cc_final: 0.6065 (m100) outliers start: 67 outliers final: 40 residues processed: 280 average time/residue: 0.3062 time to fit residues: 138.3835 Evaluate side-chains 255 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 445 ASN 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 318 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 338 PHE 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 114 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 96 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 167 optimal weight: 30.0000 chunk 158 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 221 optimal weight: 0.9990 chunk 207 optimal weight: 0.3980 chunk 265 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 356 GLN C 189 GLN H 112 GLN H 178 GLN I 162 ASN I 178 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.137684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094400 restraints weight = 36523.950| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.11 r_work: 0.2970 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- 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 = 0.72 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 = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22173 Z= 0.112 Angle : 0.539 11.026 30126 Z= 0.279 Chirality : 0.043 0.299 3357 Planarity : 0.004 0.052 3882 Dihedral : 5.104 47.496 3262 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.13 % Allowed : 11.08 % Favored : 86.78 % 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: -0.12 (0.16), residues: 2763 helix: 2.06 (0.25), residues: 432 sheet: 0.03 (0.16), residues: 960 loop : -0.84 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.008 0.001 HIS A 471 PHE 0.016 0.001 PHE J 153 TYR 0.031 0.001 TYR L 94 ARG 0.004 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00975 ( 12) link_NAG-ASN : angle 3.16315 ( 36) hydrogen bonds : bond 0.03012 ( 891) hydrogen bonds : angle 5.05142 ( 2412) SS BOND : bond 0.00306 ( 18) SS BOND : angle 0.94605 ( 36) covalent geometry : bond 0.00246 (22143) covalent geometry : angle 0.52708 (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 279 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 468 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8156 (ttpt) REVERT: B 378 ASN cc_start: 0.7394 (m110) cc_final: 0.6953 (m-40) REVERT: B 444 MET cc_start: 0.8983 (tpt) cc_final: 0.8571 (tpt) REVERT: B 468 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8020 (ttpt) REVERT: B 469 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8177 (mm) REVERT: C 460 GLU cc_start: 0.7710 (tp30) cc_final: 0.7482 (tp30) REVERT: H 39 GLN cc_start: 0.8415 (tt0) cc_final: 0.8074 (tt0) REVERT: H 131 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6663 (mt) REVERT: I 39 GLN cc_start: 0.8416 (tt0) cc_final: 0.7982 (tt0) REVERT: J 35 GLU cc_start: 0.8877 (mp0) cc_final: 0.8633 (mp0) REVERT: J 152 TYR cc_start: 0.7656 (p90) cc_final: 0.7404 (p90) REVERT: L 24 ARG cc_start: 0.6686 (ttm-80) cc_final: 0.5967 (ttm-80) REVERT: L 47 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8185 (mt) REVERT: L 79 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6237 (tm-30) REVERT: L 106 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.4649 (mt) REVERT: L 148 TRP cc_start: 0.6623 (m100) cc_final: 0.6015 (m-10) REVERT: L 175 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7625 (tt) REVERT: M 24 ARG cc_start: 0.6697 (ttm-80) cc_final: 0.6077 (ttp-110) REVERT: M 106 LEU cc_start: 0.5465 (OUTLIER) cc_final: 0.4771 (mt) REVERT: M 148 TRP cc_start: 0.6472 (m100) cc_final: 0.6272 (m100) REVERT: N 24 ARG cc_start: 0.6594 (ttm-80) cc_final: 0.6218 (ttm-80) REVERT: N 79 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6313 (tm-30) REVERT: N 106 LEU cc_start: 0.5480 (OUTLIER) cc_final: 0.4780 (mt) REVERT: N 148 TRP cc_start: 0.6611 (m100) cc_final: 0.5775 (m-10) REVERT: N 154 LEU cc_start: 0.4523 (OUTLIER) cc_final: 0.4105 (mt) outliers start: 51 outliers final: 28 residues processed: 268 average time/residue: 0.3026 time to fit residues: 131.3300 Evaluate side-chains 244 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 192 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 106 LEU Chi-restraints excluded: chain M residue 110 VAL 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: 10.0000 chunk 158 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 187 optimal weight: 20.0000 chunk 13 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** H 6 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.135829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092592 restraints weight = 36586.839| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.24 r_work: 0.2936 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22173 Z= 0.219 Angle : 0.586 7.994 30126 Z= 0.306 Chirality : 0.045 0.183 3357 Planarity : 0.004 0.048 3882 Dihedral : 5.225 47.718 3252 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.09 % Allowed : 12.25 % Favored : 85.65 % 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: -0.20 (0.16), residues: 2763 helix: 2.15 (0.25), residues: 414 sheet: -0.09 (0.17), residues: 951 loop : -0.84 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 222 HIS 0.006 0.001 HIS A 17 PHE 0.020 0.002 PHE I 105 TYR 0.054 0.002 TYR M 94 ARG 0.003 0.000 ARG C 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 12) link_NAG-ASN : angle 2.70994 ( 36) hydrogen bonds : bond 0.03442 ( 891) hydrogen bonds : angle 5.14683 ( 2412) SS BOND : bond 0.00475 ( 18) SS BOND : angle 0.96529 ( 36) covalent geometry : bond 0.00515 (22143) covalent geometry : angle 0.57829 (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 255 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 2.538 Fit side-chains REVERT: A 378 ASN cc_start: 0.7665 (m110) cc_final: 0.7320 (m-40) REVERT: A 401 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7971 (mm-30) REVERT: A 468 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8101 (ttpt) REVERT: A 470 TYR cc_start: 0.8713 (m-80) cc_final: 0.8408 (m-80) REVERT: B 378 ASN cc_start: 0.7403 (m110) cc_final: 0.6960 (m-40) REVERT: B 444 MET cc_start: 0.9039 (tpt) cc_final: 0.8498 (tpt) REVERT: B 468 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8022 (ttpt) REVERT: B 469 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8225 (mm) REVERT: B 470 TYR cc_start: 0.8412 (m-80) cc_final: 0.7924 (m-10) REVERT: C 408 ASP cc_start: 0.8522 (m-30) cc_final: 0.8217 (m-30) REVERT: H 90 ASP cc_start: 0.7906 (t0) cc_final: 0.7675 (t0) REVERT: I 39 GLN cc_start: 0.8486 (tt0) cc_final: 0.8029 (tt0) REVERT: J 152 TYR cc_start: 0.7667 (p90) cc_final: 0.7394 (p90) REVERT: L 24 ARG cc_start: 0.6785 (ttm-80) cc_final: 0.5828 (ttp-110) REVERT: L 47 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8302 (mt) REVERT: L 106 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.4751 (mt) REVERT: L 148 TRP cc_start: 0.6741 (m100) cc_final: 0.6146 (m-10) REVERT: L 175 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7677 (tt) REVERT: M 24 ARG cc_start: 0.6778 (ttm-80) cc_final: 0.6116 (ttp-110) REVERT: M 106 LEU cc_start: 0.5516 (OUTLIER) cc_final: 0.4806 (mt) REVERT: M 148 TRP cc_start: 0.6725 (m100) cc_final: 0.6237 (m100) REVERT: N 24 ARG cc_start: 0.6638 (ttm-80) cc_final: 0.6078 (ttm-80) REVERT: N 106 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.4810 (mt) REVERT: N 148 TRP cc_start: 0.6654 (m100) cc_final: 0.6064 (m100) REVERT: N 154 LEU cc_start: 0.4494 (OUTLIER) cc_final: 0.4132 (mt) REVERT: N 175 LEU cc_start: 0.7666 (tt) cc_final: 0.7459 (tt) outliers start: 50 outliers final: 32 residues processed: 248 average time/residue: 0.2928 time to fit residues: 119.6774 Evaluate side-chains 240 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 2.576 ------------------------------------------------------------------------------- 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 182 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain 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 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 175 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 93 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.0070 chunk 175 optimal weight: 3.9990 chunk 241 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 178 GLN ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 GLN I 178 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.138139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094623 restraints weight = 36653.854| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.04 r_work: 0.2977 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 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 = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22173 Z= 0.127 Angle : 0.531 9.495 30126 Z= 0.275 Chirality : 0.043 0.159 3357 Planarity : 0.004 0.050 3882 Dihedral : 4.923 44.586 3252 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.01 % Allowed : 12.71 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.11 (0.16), residues: 2763 helix: 2.11 (0.25), residues: 432 sheet: 0.03 (0.17), residues: 942 loop : -0.83 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 47 HIS 0.004 0.001 HIS A 17 PHE 0.017 0.001 PHE L 118 TYR 0.035 0.001 TYR M 94 ARG 0.003 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 12) link_NAG-ASN : angle 2.31702 ( 36) hydrogen bonds : bond 0.03012 ( 891) hydrogen bonds : angle 4.93044 ( 2412) SS BOND : bond 0.00324 ( 18) SS BOND : angle 1.02624 ( 36) covalent geometry : bond 0.00291 (22143) covalent geometry : angle 0.52477 (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 269 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASN cc_start: 0.7514 (m110) cc_final: 0.7222 (m-40) REVERT: A 401 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7837 (mm-30) REVERT: A 468 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8126 (ttpt) REVERT: A 470 TYR cc_start: 0.8638 (m-80) cc_final: 0.8406 (m-80) REVERT: B 378 ASN cc_start: 0.7339 (m110) cc_final: 0.6883 (m-40) REVERT: B 444 MET cc_start: 0.8992 (tpt) cc_final: 0.8523 (tpt) REVERT: B 468 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8145 (ttpt) REVERT: H 90 ASP cc_start: 0.7870 (t0) cc_final: 0.7631 (t0) REVERT: I 39 GLN cc_start: 0.8458 (tt0) cc_final: 0.8004 (tt0) REVERT: J 3 GLN cc_start: 0.7376 (pt0) cc_final: 0.7167 (tt0) REVERT: J 152 TYR cc_start: 0.7618 (p90) cc_final: 0.7327 (p90) REVERT: L 24 ARG cc_start: 0.6701 (ttm-80) cc_final: 0.5905 (ttm-80) REVERT: L 47 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8121 (mt) REVERT: L 78 LEU cc_start: 0.6817 (mt) cc_final: 0.6508 (tt) REVERT: L 79 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6316 (tm-30) REVERT: L 106 LEU cc_start: 0.5436 (OUTLIER) cc_final: 0.4666 (mt) REVERT: L 148 TRP cc_start: 0.6700 (m100) cc_final: 0.6110 (m-10) REVERT: M 24 ARG cc_start: 0.6640 (ttm-80) cc_final: 0.6079 (ttp-110) REVERT: M 79 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6373 (tm-30) REVERT: M 106 LEU cc_start: 0.5507 (OUTLIER) cc_final: 0.4817 (mt) REVERT: M 148 TRP cc_start: 0.6775 (m100) cc_final: 0.6302 (m100) REVERT: N 24 ARG cc_start: 0.6508 (ttm-80) cc_final: 0.6021 (ttm-80) REVERT: N 106 LEU cc_start: 0.5448 (OUTLIER) cc_final: 0.4769 (mt) REVERT: N 148 TRP cc_start: 0.6625 (m100) cc_final: 0.5873 (m-10) REVERT: N 154 LEU cc_start: 0.4470 (OUTLIER) cc_final: 0.4051 (mt) outliers start: 48 outliers final: 33 residues processed: 262 average time/residue: 0.2956 time to fit residues: 126.9034 Evaluate side-chains 251 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 2.841 ------------------------------------------------------------------------------- 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 318 THR 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 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 335 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain J 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 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 M residue 110 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 144 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 230 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 267 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 178 GLN I 207 HIS ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.138669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.093381 restraints weight = 36320.928| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.09 r_work: 0.2988 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22173 Z= 0.121 Angle : 0.532 9.529 30126 Z= 0.275 Chirality : 0.043 0.201 3357 Planarity : 0.004 0.049 3882 Dihedral : 4.831 43.953 3252 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.80 % Allowed : 12.63 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.03 (0.16), residues: 2763 helix: 2.18 (0.25), residues: 432 sheet: 0.09 (0.17), residues: 942 loop : -0.79 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS I 207 PHE 0.015 0.001 PHE J 153 TYR 0.030 0.001 TYR M 94 ARG 0.005 0.000 ARG B 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 12) link_NAG-ASN : angle 2.16164 ( 36) hydrogen bonds : bond 0.02980 ( 891) hydrogen bonds : angle 4.87341 ( 2412) SS BOND : bond 0.00357 ( 18) SS BOND : angle 1.07365 ( 36) covalent geometry : bond 0.00277 (22143) covalent geometry : angle 0.52620 (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 261 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASN cc_start: 0.7431 (m110) cc_final: 0.7138 (m-40) REVERT: A 468 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8118 (ttpt) REVERT: A 470 TYR cc_start: 0.8623 (m-80) cc_final: 0.8404 (m-80) REVERT: B 378 ASN cc_start: 0.7298 (m110) cc_final: 0.6834 (m-40) REVERT: B 444 MET cc_start: 0.9003 (tpt) cc_final: 0.8477 (tpt) REVERT: B 468 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8094 (ttpt) REVERT: B 469 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8062 (mm) REVERT: C 462 MET cc_start: 0.8201 (mmm) cc_final: 0.7950 (mmm) REVERT: H 50 GLU cc_start: 0.8462 (pt0) cc_final: 0.8251 (pt0) REVERT: H 90 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7640 (t0) REVERT: I 39 GLN cc_start: 0.8419 (tt0) cc_final: 0.7984 (tt0) REVERT: J 152 TYR cc_start: 0.7614 (p90) cc_final: 0.7313 (p90) REVERT: L 24 ARG cc_start: 0.6583 (ttm-80) cc_final: 0.5740 (ttp-110) REVERT: L 78 LEU cc_start: 0.6874 (mt) cc_final: 0.6621 (tt) REVERT: L 79 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6259 (tm-30) REVERT: L 106 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.4744 (mt) REVERT: L 148 TRP cc_start: 0.6659 (m100) cc_final: 0.6108 (m-10) REVERT: M 24 ARG cc_start: 0.6656 (ttm-80) cc_final: 0.6070 (ttp-110) REVERT: M 79 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6349 (tm-30) REVERT: M 106 LEU cc_start: 0.5465 (OUTLIER) cc_final: 0.4759 (mt) REVERT: M 148 TRP cc_start: 0.6822 (m100) cc_final: 0.6367 (m100) REVERT: N 24 ARG cc_start: 0.6495 (ttm-80) cc_final: 0.5936 (ttm-80) REVERT: N 106 LEU cc_start: 0.5473 (OUTLIER) cc_final: 0.4819 (mt) REVERT: N 148 TRP cc_start: 0.6629 (m100) cc_final: 0.5937 (m-10) REVERT: N 154 LEU cc_start: 0.4454 (OUTLIER) cc_final: 0.4056 (mt) outliers start: 43 outliers final: 30 residues processed: 254 average time/residue: 0.2707 time to fit residues: 114.4843 Evaluate side-chains 249 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 90 ASP 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 117 THR Chi-restraints excluded: chain J residue 176 VAL 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 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 110 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 195 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 chunk 124 optimal weight: 0.0270 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 0.0870 chunk 65 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 overall best weight: 1.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 112 GLN I 178 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.137763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091738 restraints weight = 36660.696| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.14 r_work: 0.2972 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 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 = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22173 Z= 0.154 Angle : 0.550 9.214 30126 Z= 0.284 Chirality : 0.043 0.178 3357 Planarity : 0.004 0.053 3882 Dihedral : 4.925 44.458 3252 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.84 % Allowed : 12.42 % Favored : 85.74 % 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: -0.04 (0.16), residues: 2763 helix: 2.32 (0.25), residues: 414 sheet: 0.07 (0.17), residues: 942 loop : -0.78 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 222 HIS 0.004 0.001 HIS B 435 PHE 0.027 0.002 PHE N 118 TYR 0.034 0.002 TYR M 94 ARG 0.005 0.000 ARG B 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 12) link_NAG-ASN : angle 2.10189 ( 36) hydrogen bonds : bond 0.03111 ( 891) hydrogen bonds : angle 4.92478 ( 2412) SS BOND : bond 0.00357 ( 18) SS BOND : angle 1.04827 ( 36) covalent geometry : bond 0.00359 (22143) covalent geometry : angle 0.54464 (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 252 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 2.499 Fit side-chains revert: symmetry clash REVERT: A 378 ASN cc_start: 0.7413 (m110) cc_final: 0.7136 (m-40) REVERT: A 444 MET cc_start: 0.9040 (tpt) cc_final: 0.8718 (tpt) REVERT: A 468 LYS cc_start: 0.8488 (ttpt) cc_final: 0.8121 (ttpt) REVERT: B 378 ASN cc_start: 0.7302 (m110) cc_final: 0.6851 (m-40) REVERT: B 444 MET cc_start: 0.9023 (tpt) cc_final: 0.8418 (tpt) REVERT: B 468 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8069 (ttpt) REVERT: B 469 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8134 (mm) REVERT: C 408 ASP cc_start: 0.8513 (m-30) cc_final: 0.8212 (m-30) REVERT: C 462 MET cc_start: 0.8215 (mmm) cc_final: 0.7967 (mmm) REVERT: H 89 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: H 90 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7610 (t0) REVERT: I 39 GLN cc_start: 0.8469 (tt0) cc_final: 0.8018 (tt0) REVERT: J 152 TYR cc_start: 0.7597 (p90) cc_final: 0.7302 (p90) REVERT: L 24 ARG cc_start: 0.6621 (ttm-80) cc_final: 0.5860 (ttm-80) REVERT: L 47 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8209 (mt) REVERT: L 78 LEU cc_start: 0.6749 (mt) cc_final: 0.6498 (tt) REVERT: L 79 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6327 (tm-30) REVERT: L 106 LEU cc_start: 0.5560 (OUTLIER) cc_final: 0.4779 (mt) REVERT: L 148 TRP cc_start: 0.6706 (m100) cc_final: 0.6180 (m-10) REVERT: M 24 ARG cc_start: 0.6654 (ttm-80) cc_final: 0.6070 (ttp-110) REVERT: M 79 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6429 (tm-30) REVERT: M 106 LEU cc_start: 0.5413 (OUTLIER) cc_final: 0.4732 (mt) REVERT: M 148 TRP cc_start: 0.6852 (m100) cc_final: 0.6400 (m100) REVERT: N 24 ARG cc_start: 0.6425 (ttm-80) cc_final: 0.5902 (ttm-80) REVERT: N 106 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.4832 (mt) REVERT: N 148 TRP cc_start: 0.6659 (m100) cc_final: 0.5978 (m-10) REVERT: N 154 LEU cc_start: 0.4309 (OUTLIER) cc_final: 0.3926 (mt) outliers start: 44 outliers final: 33 residues processed: 244 average time/residue: 0.2791 time to fit residues: 114.6055 Evaluate side-chains 246 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain 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 166 VAL 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 455 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 90 ASP 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 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 106 LEU 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 110 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 260 optimal weight: 0.0370 chunk 102 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 240 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 178 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.137050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.091315 restraints weight = 36473.212| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.08 r_work: 0.2965 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22173 Z= 0.184 Angle : 0.567 8.997 30126 Z= 0.293 Chirality : 0.044 0.182 3357 Planarity : 0.004 0.048 3882 Dihedral : 5.032 45.218 3252 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.80 % Allowed : 12.55 % Favored : 85.65 % 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: -0.08 (0.16), residues: 2763 helix: 2.26 (0.25), residues: 414 sheet: -0.02 (0.17), residues: 963 loop : -0.76 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 222 HIS 0.005 0.001 HIS B 435 PHE 0.016 0.002 PHE I 105 TYR 0.037 0.002 TYR M 94 ARG 0.005 0.000 ARG B 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 12) link_NAG-ASN : angle 2.11921 ( 36) hydrogen bonds : bond 0.03226 ( 891) hydrogen bonds : angle 4.97813 ( 2412) SS BOND : bond 0.00411 ( 18) SS BOND : angle 1.04205 ( 36) covalent geometry : bond 0.00431 (22143) covalent geometry : angle 0.56157 (30054) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15271.82 seconds wall clock time: 264 minutes 53.83 seconds (15893.83 seconds total)