Starting phenix.real_space_refine on Wed Mar 4 23:20:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l0l_23098/03_2026/7l0l_23098.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l0l_23098/03_2026/7l0l_23098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l0l_23098/03_2026/7l0l_23098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l0l_23098/03_2026/7l0l_23098.map" model { file = "/net/cci-nas-00/data/ceres_data/7l0l_23098/03_2026/7l0l_23098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l0l_23098/03_2026/7l0l_23098.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.049 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 10782 2.51 5 N 2955 2.21 5 O 3378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17211 Number of models: 1 Model: "" Number of chains: 18 Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "A" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2521 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 18, 'TRANS': 303} Chain: "B" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "J" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "C" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2521 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 18, 'TRANS': 303} Chain: "E" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain: "G" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "D" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2521 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 18, 'TRANS': 303} Chain: "F" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain: "I" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} 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 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" 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 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.08, per 1000 atoms: 0.24 Number of scatterers: 17211 At special positions: 0 Unit cell: (139.707, 125.628, 150.537, 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 3378 8.00 N 2955 7.00 C 10782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS F 47 " 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 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS E 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " 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 401 " - " ASN A 33 " " NAG A 402 " - " ASN A 169 " " NAG A 403 " - " ASN A 21 " " NAG A 404 " - " ASN A 289 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 33 " " NAG C 402 " - " ASN C 169 " " NAG C 403 " - " ASN C 21 " " NAG C 404 " - " ASN C 289 " " NAG D 401 " - " ASN D 33 " " NAG D 402 " - " ASN D 169 " " NAG D 403 " - " ASN D 21 " " NAG D 404 " - " ASN D 289 " " NAG E 301 " - " ASN E 154 " " NAG F 301 " - " ASN F 154 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 665.9 milliseconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 48 sheets defined 20.3% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'L' and resid 28 through 31 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.547A pdb=" N ARG A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 127' Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.660A pdb=" N MET B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 74 through 124 removed outlier: 3.806A pdb=" N VAL B 115 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 172 removed outlier: 3.619A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 31 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.944A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ARG C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.641A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'E' and resid 37 through 59 removed outlier: 3.507A pdb=" N MET E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 74 through 124 removed outlier: 3.756A pdb=" N VAL E 115 " --> pdb=" O HIS E 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 116 " --> pdb=" O ASP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 154 Processing helix chain 'E' and resid 158 through 172 removed outlier: 3.546A pdb=" N TYR E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU E 165 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.705A pdb=" N GLN G 64 " --> pdb=" O GLN G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'K' and resid 28 through 31 Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.761A pdb=" N ASP D 77 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG D 78 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.595A pdb=" N TRP D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'F' and resid 37 through 59 removed outlier: 3.636A pdb=" N MET F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 62 No H-bonds generated for 'chain 'F' and resid 60 through 62' Processing helix chain 'F' and resid 74 through 126 removed outlier: 3.551A pdb=" N VAL F 115 " --> pdb=" O HIS F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 158 through 172 removed outlier: 3.660A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.513A pdb=" N VAL L 85 " --> pdb=" O HIS L 38 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'A' and resid 51 through 53A removed outlier: 7.875A pdb=" N LEU A 51 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR A 279 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS A 53 " --> pdb=" O THR A 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.568A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.624A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N HIS A 116A" --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG A 263 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 115 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.624A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.467A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB4, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.591A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.515A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.702A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.605A pdb=" N VAL J 85 " --> pdb=" O HIS J 38 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 36 Processing sheet with id=AC2, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 53A removed outlier: 6.067A pdb=" N LEU C 51 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.614A pdb=" N LEU C 59 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.698A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS C 116A" --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG C 263 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 115 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.698A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.725A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AD3, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.601A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.692A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.489A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.570A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL K 85 " --> pdb=" O HIS K 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 32 through 36 Processing sheet with id=AD9, first strand: chain 'D' and resid 25 through 26 Processing sheet with id=AE1, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AE2, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'D' and resid 51 through 53A removed outlier: 7.955A pdb=" N LEU D 51 " --> pdb=" O CYS D 277 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N THR D 279 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS D 53 " --> pdb=" O THR D 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.592A pdb=" N LEU D 59 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE D 87 " --> pdb=" O MET D 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.705A pdb=" N SER D 101 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N TRP D 234 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE D 179 " --> pdb=" O TYR D 256 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR D 256 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS D 116A" --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG D 263 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL D 115 " --> pdb=" O ARG D 263 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.705A pdb=" N SER D 101 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N TRP D 234 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 136 through 141 removed outlier: 4.774A pdb=" N CYS D 139 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 146 " --> pdb=" O CYS D 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 164 through 169 Processing sheet with id=AE9, first strand: chain 'D' and resid 281 through 282 Processing sheet with id=AF1, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.525A pdb=" N LEU I 82 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.530A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.582A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1818 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: 3.17 Time building geometry restraints manager: 1.79 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: 5651 1.34 - 1.46: 4301 1.46 - 1.58: 7505 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 17595 Sorted by residual: bond pdb=" C1 NAG C 404 " pdb=" O5 NAG C 404 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 NAG A 404 " pdb=" O5 NAG A 404 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 NAG D 404 " pdb=" O5 NAG D 404 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG D 401 " pdb=" O5 NAG D 401 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG B 301 " pdb=" O5 NAG B 301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 ... (remaining 17590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 22876 1.21 - 2.42: 779 2.42 - 3.64: 126 3.64 - 4.85: 33 4.85 - 6.06: 3 Bond angle restraints: 23817 Sorted by residual: angle pdb=" C TYR A 195 " pdb=" N GLN A 196 " pdb=" CA GLN A 196 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.11e+00 angle pdb=" C TYR D 195 " pdb=" N GLN D 196 " pdb=" CA GLN D 196 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.80e+00 angle pdb=" N GLY H 106 " pdb=" CA GLY H 106 " pdb=" C GLY H 106 " ideal model delta sigma weight residual 111.72 114.79 -3.07 1.31e+00 5.83e-01 5.49e+00 angle pdb=" C LEU E 126 " pdb=" N ARG E 127 " pdb=" CA ARG E 127 " ideal model delta sigma weight residual 120.82 124.07 -3.25 1.50e+00 4.44e-01 4.70e+00 angle pdb=" C LEU F 126 " pdb=" N ARG F 127 " pdb=" CA ARG F 127 " ideal model delta sigma weight residual 120.82 124.03 -3.21 1.50e+00 4.44e-01 4.59e+00 ... (remaining 23812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 9742 17.62 - 35.25: 737 35.25 - 52.87: 163 52.87 - 70.49: 20 70.49 - 88.11: 15 Dihedral angle restraints: 10677 sinusoidal: 4497 harmonic: 6180 Sorted by residual: dihedral pdb=" CB CYS A 30 " pdb=" SG CYS A 30 " pdb=" SG CYS F 47 " pdb=" CB CYS F 47 " ideal model delta sinusoidal sigma weight residual -86.00 -45.15 -40.85 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS E 47 " pdb=" SG CYS E 47 " pdb=" SG CYS D 30 " pdb=" CB CYS D 30 " ideal model delta sinusoidal sigma weight residual -86.00 -47.19 -38.81 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CA LEU E 126 " pdb=" C LEU E 126 " pdb=" N ARG E 127 " pdb=" CA ARG E 127 " ideal model delta harmonic sigma weight residual -180.00 -162.37 -17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 10674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1508 0.027 - 0.054: 649 0.054 - 0.081: 214 0.081 - 0.108: 152 0.108 - 0.135: 75 Chirality restraints: 2598 Sorted by residual: chirality pdb=" CA ILE K 48 " pdb=" N ILE K 48 " pdb=" C ILE K 48 " pdb=" CB ILE K 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE C 260 " pdb=" N ILE C 260 " pdb=" C ILE C 260 " pdb=" CB ILE C 260 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2595 not shown) Planarity restraints: 3090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 73 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 74 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 73 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO C 74 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 13 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO I 14 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO I 14 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 14 " -0.027 5.00e-02 4.00e+02 ... (remaining 3087 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1194 2.74 - 3.28: 16017 3.28 - 3.82: 27752 3.82 - 4.36: 34852 4.36 - 4.90: 60950 Nonbonded interactions: 140765 Sorted by model distance: nonbonded pdb=" OG1 THR C 283 " pdb=" O GLY C 286 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR D 283 " pdb=" O GLY D 286 " model vdw 2.236 3.040 nonbonded pdb=" NH2 ARG A 126 " pdb=" O GLN A 165 " model vdw 2.254 3.120 nonbonded pdb=" OH TYR J 96 " pdb=" O ILE G 100 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR K 96 " pdb=" O ILE I 100 " model vdw 2.257 3.040 ... (remaining 140760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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=1.00 max=1.00 mean=1.00 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: 2.340 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: 0.040 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.210 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.003 0.030 17634 Z= 0.146 Angle : 0.524 6.058 23910 Z= 0.298 Chirality : 0.042 0.135 2598 Planarity : 0.004 0.051 3075 Dihedral : 13.077 88.114 6675 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 2142 helix: 1.45 (0.25), residues: 357 sheet: 0.35 (0.24), residues: 507 loop : 0.32 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.032 0.001 TYR E 22 PHE 0.009 0.001 PHE D 232 TRP 0.022 0.001 TRP D 69 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00315 (17595) covalent geometry : angle 0.52162 (23817) SS BOND : bond 0.00183 ( 24) SS BOND : angle 0.80149 ( 48) hydrogen bonds : bond 0.22970 ( 640) hydrogen bonds : angle 7.98173 ( 1818) link_NAG-ASN : bond 0.00111 ( 15) link_NAG-ASN : angle 1.13450 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8600 (t80) cc_final: 0.8393 (t80) REVERT: A 187 ASP cc_start: 0.7230 (p0) cc_final: 0.7016 (p0) REVERT: C 211 LYS cc_start: 0.7480 (tttm) cc_final: 0.7083 (ttpt) REVERT: E 75 ARG cc_start: 0.7954 (mmp-170) cc_final: 0.7721 (mmp-170) REVERT: G 23 LYS cc_start: 0.8645 (tttp) cc_final: 0.8403 (ttpp) REVERT: F 40 SER cc_start: 0.8690 (m) cc_final: 0.8473 (m) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.6490 time to fit residues: 182.1040 Evaluate side-chains 190 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN B 60 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN F 125 GLN F 169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.083881 restraints weight = 25627.365| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.59 r_work: 0.2958 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17634 Z= 0.228 Angle : 0.599 8.523 23910 Z= 0.319 Chirality : 0.046 0.148 2598 Planarity : 0.004 0.052 3075 Dihedral : 4.850 54.489 2661 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.68 % Allowed : 7.49 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.18), residues: 2142 helix: 2.18 (0.25), residues: 357 sheet: 0.55 (0.24), residues: 495 loop : 0.06 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 82B TYR 0.039 0.002 TYR E 22 PHE 0.017 0.003 PHE D 232 TRP 0.015 0.002 TRP B 21 HIS 0.010 0.002 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00568 (17595) covalent geometry : angle 0.59478 (23817) SS BOND : bond 0.00372 ( 24) SS BOND : angle 1.22425 ( 48) hydrogen bonds : bond 0.05428 ( 640) hydrogen bonds : angle 5.43208 ( 1818) link_NAG-ASN : bond 0.00131 ( 15) link_NAG-ASN : angle 1.24241 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 37 ARG cc_start: 0.7565 (ttp-170) cc_final: 0.7335 (ttp-170) REVERT: L 45 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7807 (ttt90) REVERT: A 187 ASP cc_start: 0.7284 (p0) cc_final: 0.7016 (p0) REVERT: A 312 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8208 (tp30) REVERT: B 57 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: H 105 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7138 (pp30) REVERT: C 211 LYS cc_start: 0.7855 (tttm) cc_final: 0.7396 (ttpt) REVERT: C 304 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: G 3 GLN cc_start: 0.8184 (pm20) cc_final: 0.7612 (pm20) REVERT: G 23 LYS cc_start: 0.8552 (tttp) cc_final: 0.8118 (ttmm) REVERT: K 37 ARG cc_start: 0.7744 (ttp-170) cc_final: 0.7476 (ttp80) REVERT: K 103 LYS cc_start: 0.6709 (tptp) cc_final: 0.6460 (tptp) REVERT: D 304 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7973 (mt-10) outliers start: 50 outliers final: 16 residues processed: 225 average time/residue: 0.6651 time to fit residues: 165.3237 Evaluate side-chains 210 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain I residue 86 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 41 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 160 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 GLN A 224 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** 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 = 0.3462 r_free = 0.3462 target = 0.109953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.084463 restraints weight = 25776.889| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.61 r_work: 0.2962 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17634 Z= 0.140 Angle : 0.525 12.134 23910 Z= 0.279 Chirality : 0.043 0.191 2598 Planarity : 0.004 0.052 3075 Dihedral : 4.486 51.268 2661 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.98 % Allowed : 10.27 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.18), residues: 2142 helix: 2.57 (0.26), residues: 360 sheet: 0.54 (0.24), residues: 495 loop : 0.06 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 82B TYR 0.027 0.001 TYR E 22 PHE 0.012 0.002 PHE D 232 TRP 0.012 0.001 TRP B 21 HIS 0.005 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00336 (17595) covalent geometry : angle 0.52130 (23817) SS BOND : bond 0.00520 ( 24) SS BOND : angle 1.02773 ( 48) hydrogen bonds : bond 0.04348 ( 640) hydrogen bonds : angle 4.83728 ( 1818) link_NAG-ASN : bond 0.00062 ( 15) link_NAG-ASN : angle 1.20579 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.474 Fit side-chains REVERT: A 91 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7896 (mp0) REVERT: A 187 ASP cc_start: 0.7260 (p0) cc_final: 0.7054 (p0) REVERT: A 312 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8190 (tp30) REVERT: A 325 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7696 (tp40) REVERT: B 102 MET cc_start: 0.8462 (mtm) cc_final: 0.8148 (mtm) REVERT: H 105 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7067 (pp30) REVERT: C 211 LYS cc_start: 0.7909 (tttm) cc_final: 0.7700 (tttt) REVERT: C 304 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7898 (mt-10) REVERT: G 3 GLN cc_start: 0.8292 (pm20) cc_final: 0.7803 (pm20) REVERT: G 23 LYS cc_start: 0.8541 (tttp) cc_final: 0.8097 (ttmm) REVERT: D 198 VAL cc_start: 0.8170 (t) cc_final: 0.7791 (t) REVERT: F 156 THR cc_start: 0.8788 (m) cc_final: 0.8359 (p) REVERT: I 64 GLN cc_start: 0.7456 (mt0) cc_final: 0.7136 (mt0) outliers start: 37 outliers final: 21 residues processed: 227 average time/residue: 0.6456 time to fit residues: 162.2809 Evaluate side-chains 212 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 86 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 19 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.083569 restraints weight = 25716.022| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.61 r_work: 0.2944 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17634 Z= 0.165 Angle : 0.533 8.311 23910 Z= 0.280 Chirality : 0.044 0.146 2598 Planarity : 0.004 0.051 3075 Dihedral : 4.354 50.536 2661 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.94 % Allowed : 11.40 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2142 helix: 2.66 (0.26), residues: 360 sheet: 0.48 (0.24), residues: 495 loop : -0.00 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 82B TYR 0.012 0.001 TYR E 22 PHE 0.014 0.002 PHE D 232 TRP 0.013 0.001 TRP B 21 HIS 0.007 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00407 (17595) covalent geometry : angle 0.52849 (23817) SS BOND : bond 0.00407 ( 24) SS BOND : angle 1.11441 ( 48) hydrogen bonds : bond 0.04175 ( 640) hydrogen bonds : angle 4.64358 ( 1818) link_NAG-ASN : bond 0.00073 ( 15) link_NAG-ASN : angle 1.29664 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7928 (mp0) REVERT: A 187 ASP cc_start: 0.7386 (p0) cc_final: 0.7045 (p0) REVERT: A 304 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: A 312 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8192 (tp30) REVERT: A 325 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7698 (tp40) REVERT: B 102 MET cc_start: 0.8469 (mtm) cc_final: 0.8127 (mtm) REVERT: H 105 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7104 (pp30) REVERT: C 211 LYS cc_start: 0.7914 (tttm) cc_final: 0.7693 (tttt) REVERT: C 304 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: E 43 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8521 (mttt) REVERT: G 3 GLN cc_start: 0.8330 (pm20) cc_final: 0.7767 (pm20) REVERT: G 23 LYS cc_start: 0.8527 (tttp) cc_final: 0.8095 (ttmm) REVERT: F 22 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: F 59 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7780 (mtp) REVERT: F 156 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8363 (p) REVERT: I 105 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7893 (pm20) outliers start: 55 outliers final: 26 residues processed: 225 average time/residue: 0.6425 time to fit residues: 160.5318 Evaluate side-chains 222 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 61 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 170 optimal weight: 0.0060 chunk 131 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.083695 restraints weight = 25506.993| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.59 r_work: 0.2955 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17634 Z= 0.158 Angle : 0.524 8.068 23910 Z= 0.275 Chirality : 0.043 0.145 2598 Planarity : 0.004 0.050 3075 Dihedral : 4.193 47.367 2661 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.00 % Allowed : 12.73 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.18), residues: 2142 helix: 2.71 (0.26), residues: 360 sheet: 0.37 (0.23), residues: 504 loop : -0.05 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 82B TYR 0.015 0.001 TYR C 256 PHE 0.013 0.002 PHE D 232 TRP 0.012 0.001 TRP B 21 HIS 0.006 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00391 (17595) covalent geometry : angle 0.52006 (23817) SS BOND : bond 0.00364 ( 24) SS BOND : angle 0.97310 ( 48) hydrogen bonds : bond 0.04004 ( 640) hydrogen bonds : angle 4.51440 ( 1818) link_NAG-ASN : bond 0.00067 ( 15) link_NAG-ASN : angle 1.29418 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 0.673 Fit side-chains REVERT: L 60 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8498 (m-30) REVERT: A 91 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7935 (mp0) REVERT: A 304 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8460 (mp0) REVERT: A 312 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8177 (tp30) REVERT: A 325 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7743 (tp40) REVERT: B 102 MET cc_start: 0.8470 (mtm) cc_final: 0.8228 (mtm) REVERT: H 105 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.6981 (pp30) REVERT: C 116 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: C 211 LYS cc_start: 0.7917 (tttm) cc_final: 0.7688 (tttt) REVERT: C 304 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: G 3 GLN cc_start: 0.8328 (pm20) cc_final: 0.7747 (pm20) REVERT: G 23 LYS cc_start: 0.8533 (tttp) cc_final: 0.8116 (ttmm) REVERT: F 22 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: F 59 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7923 (mtp) REVERT: F 156 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8343 (p) REVERT: I 105 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7864 (pm20) outliers start: 56 outliers final: 27 residues processed: 223 average time/residue: 0.6314 time to fit residues: 156.4342 Evaluate side-chains 218 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 206 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 92 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.084776 restraints weight = 25365.651| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.58 r_work: 0.2974 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17634 Z= 0.109 Angle : 0.490 6.894 23910 Z= 0.258 Chirality : 0.042 0.146 2598 Planarity : 0.004 0.051 3075 Dihedral : 3.980 43.946 2661 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.35 % Allowed : 14.02 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2142 helix: 2.95 (0.26), residues: 360 sheet: 0.40 (0.24), residues: 507 loop : -0.02 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG L 61 TYR 0.010 0.001 TYR A 17 PHE 0.008 0.001 PHE F 110 TRP 0.011 0.001 TRP B 21 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00255 (17595) covalent geometry : angle 0.48660 (23817) SS BOND : bond 0.00308 ( 24) SS BOND : angle 0.77270 ( 48) hydrogen bonds : bond 0.03630 ( 640) hydrogen bonds : angle 4.35105 ( 1818) link_NAG-ASN : bond 0.00088 ( 15) link_NAG-ASN : angle 1.19132 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7931 (mp0) REVERT: A 304 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: A 325 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7610 (tp40) REVERT: B 102 MET cc_start: 0.8461 (mtm) cc_final: 0.8232 (mtm) REVERT: C 116 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: C 211 LYS cc_start: 0.7927 (tttm) cc_final: 0.7699 (tttt) REVERT: G 3 GLN cc_start: 0.8347 (pm20) cc_final: 0.7823 (pm20) REVERT: G 23 LYS cc_start: 0.8515 (tttp) cc_final: 0.8099 (ttmm) REVERT: D 187 ASP cc_start: 0.7412 (p0) cc_final: 0.7152 (p0) REVERT: F 22 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: F 59 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7898 (mtp) REVERT: F 156 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8255 (p) REVERT: I 105 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7865 (pm20) outliers start: 44 outliers final: 22 residues processed: 219 average time/residue: 0.6128 time to fit residues: 149.5937 Evaluate side-chains 209 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 0.0070 chunk 111 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.083945 restraints weight = 25570.653| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.59 r_work: 0.2957 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17634 Z= 0.168 Angle : 0.527 8.286 23910 Z= 0.275 Chirality : 0.043 0.144 2598 Planarity : 0.004 0.051 3075 Dihedral : 3.955 36.186 2661 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.89 % Allowed : 14.07 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2142 helix: 2.80 (0.26), residues: 360 sheet: 0.34 (0.24), residues: 507 loop : -0.08 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 61 TYR 0.014 0.001 TYR C 256 PHE 0.014 0.002 PHE A 232 TRP 0.012 0.002 TRP B 21 HIS 0.006 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00419 (17595) covalent geometry : angle 0.52334 (23817) SS BOND : bond 0.00341 ( 24) SS BOND : angle 0.88189 ( 48) hydrogen bonds : bond 0.03886 ( 640) hydrogen bonds : angle 4.39058 ( 1818) link_NAG-ASN : bond 0.00088 ( 15) link_NAG-ASN : angle 1.27164 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: L 61 ARG cc_start: 0.6756 (ttp-110) cc_final: 0.6527 (ttp-110) REVERT: A 91 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7962 (mp0) REVERT: A 304 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8496 (mp0) REVERT: A 312 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: A 325 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7677 (tp40) REVERT: B 102 MET cc_start: 0.8497 (mtm) cc_final: 0.8263 (mtm) REVERT: C 116 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: C 211 LYS cc_start: 0.7948 (tttm) cc_final: 0.7506 (ttpt) REVERT: G 3 GLN cc_start: 0.8325 (pm20) cc_final: 0.7727 (pm20) REVERT: G 23 LYS cc_start: 0.8505 (tttp) cc_final: 0.8117 (ttmm) REVERT: G 105 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: F 22 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: F 59 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8037 (mtp) REVERT: F 156 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8345 (p) REVERT: F 168 LEU cc_start: 0.8561 (mp) cc_final: 0.8205 (tt) REVERT: I 105 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7861 (pm20) outliers start: 54 outliers final: 29 residues processed: 222 average time/residue: 0.6167 time to fit residues: 152.2599 Evaluate side-chains 219 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.083351 restraints weight = 25629.741| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.58 r_work: 0.2948 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17634 Z= 0.191 Angle : 0.554 8.887 23910 Z= 0.289 Chirality : 0.044 0.145 2598 Planarity : 0.004 0.050 3075 Dihedral : 3.963 20.728 2661 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.57 % Allowed : 14.71 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 2142 helix: 2.65 (0.26), residues: 360 sheet: 0.28 (0.23), residues: 507 loop : -0.17 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 82B TYR 0.016 0.002 TYR A 17 PHE 0.026 0.002 PHE H 63 TRP 0.014 0.002 TRP E 21 HIS 0.007 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00479 (17595) covalent geometry : angle 0.55056 (23817) SS BOND : bond 0.00357 ( 24) SS BOND : angle 0.92356 ( 48) hydrogen bonds : bond 0.04055 ( 640) hydrogen bonds : angle 4.45383 ( 1818) link_NAG-ASN : bond 0.00084 ( 15) link_NAG-ASN : angle 1.36757 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.555 Fit side-chains REVERT: L 61 ARG cc_start: 0.6819 (ttp-110) cc_final: 0.6590 (ttp-110) REVERT: A 91 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7922 (mp0) REVERT: A 304 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: A 312 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8168 (tp30) REVERT: A 325 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7667 (tp40) REVERT: B 102 MET cc_start: 0.8498 (mtm) cc_final: 0.8268 (mtm) REVERT: C 116 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: C 211 LYS cc_start: 0.7976 (tttm) cc_final: 0.7538 (ttpt) REVERT: C 304 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: G 3 GLN cc_start: 0.8331 (pm20) cc_final: 0.7735 (pm20) REVERT: G 23 LYS cc_start: 0.8502 (tttp) cc_final: 0.8119 (ttmm) REVERT: G 105 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7356 (pm20) REVERT: D 239 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7122 (mmm) REVERT: F 22 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: F 59 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8120 (mtp) REVERT: F 156 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8370 (p) REVERT: F 168 LEU cc_start: 0.8570 (mp) cc_final: 0.8202 (tt) REVERT: I 105 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7857 (pm20) REVERT: I 108 LEU cc_start: 0.8654 (tt) cc_final: 0.8454 (tt) outliers start: 48 outliers final: 30 residues processed: 213 average time/residue: 0.6137 time to fit residues: 144.9337 Evaluate side-chains 219 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 153 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 188 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN D 12 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.083881 restraints weight = 25684.805| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.59 r_work: 0.2947 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17634 Z= 0.155 Angle : 0.523 7.973 23910 Z= 0.273 Chirality : 0.043 0.145 2598 Planarity : 0.004 0.052 3075 Dihedral : 3.863 20.448 2661 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.51 % Allowed : 14.71 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 2142 helix: 2.75 (0.26), residues: 360 sheet: 0.26 (0.23), residues: 507 loop : -0.17 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 82B TYR 0.018 0.001 TYR A 17 PHE 0.028 0.002 PHE H 63 TRP 0.012 0.001 TRP E 21 HIS 0.005 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00384 (17595) covalent geometry : angle 0.51974 (23817) SS BOND : bond 0.00325 ( 24) SS BOND : angle 0.86027 ( 48) hydrogen bonds : bond 0.03813 ( 640) hydrogen bonds : angle 4.36973 ( 1818) link_NAG-ASN : bond 0.00080 ( 15) link_NAG-ASN : angle 1.27789 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 0.633 Fit side-chains REVERT: A 91 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7910 (mp0) REVERT: A 304 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8541 (mp0) REVERT: A 312 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8163 (tp30) REVERT: A 325 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7668 (tp40) REVERT: B 102 MET cc_start: 0.8491 (mtm) cc_final: 0.8229 (mtm) REVERT: C 116 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: C 211 LYS cc_start: 0.8020 (tttm) cc_final: 0.7552 (ttpt) REVERT: G 3 GLN cc_start: 0.8373 (pm20) cc_final: 0.7764 (pm20) REVERT: G 23 LYS cc_start: 0.8512 (tttp) cc_final: 0.8137 (ttmm) REVERT: G 105 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7360 (pm20) REVERT: K 42 GLN cc_start: 0.7461 (mm-40) cc_final: 0.7123 (mp10) REVERT: D 239 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7043 (mmm) REVERT: F 22 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: F 156 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8365 (p) REVERT: F 168 LEU cc_start: 0.8553 (mp) cc_final: 0.8194 (tt) REVERT: I 105 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7867 (pm20) outliers start: 47 outliers final: 29 residues processed: 210 average time/residue: 0.6236 time to fit residues: 145.4407 Evaluate side-chains 217 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 161 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 191 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.108999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.083819 restraints weight = 25471.193| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.58 r_work: 0.2944 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17634 Z= 0.157 Angle : 0.527 8.111 23910 Z= 0.275 Chirality : 0.043 0.144 2598 Planarity : 0.004 0.052 3075 Dihedral : 3.865 20.425 2661 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.14 % Allowed : 15.14 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2142 helix: 2.75 (0.26), residues: 360 sheet: 0.28 (0.24), residues: 504 loop : -0.16 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 61 TYR 0.016 0.001 TYR A 17 PHE 0.030 0.002 PHE H 63 TRP 0.013 0.002 TRP E 21 HIS 0.006 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00390 (17595) covalent geometry : angle 0.52376 (23817) SS BOND : bond 0.00323 ( 24) SS BOND : angle 0.86519 ( 48) hydrogen bonds : bond 0.03823 ( 640) hydrogen bonds : angle 4.35774 ( 1818) link_NAG-ASN : bond 0.00080 ( 15) link_NAG-ASN : angle 1.29986 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7912 (mp0) REVERT: A 304 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8554 (mp0) REVERT: A 312 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8166 (tp30) REVERT: A 325 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7607 (tp40) REVERT: B 102 MET cc_start: 0.8502 (mtm) cc_final: 0.8295 (mtm) REVERT: H 105 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.6829 (pp30) REVERT: C 116 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: C 211 LYS cc_start: 0.8020 (tttm) cc_final: 0.7549 (ttpt) REVERT: G 3 GLN cc_start: 0.8389 (pm20) cc_final: 0.7778 (pm20) REVERT: G 23 LYS cc_start: 0.8510 (tttp) cc_final: 0.8138 (ttmm) REVERT: G 105 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: D 239 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7104 (mmm) REVERT: F 22 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: F 156 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8350 (p) REVERT: F 168 LEU cc_start: 0.8543 (mp) cc_final: 0.8192 (tt) REVERT: I 105 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7855 (pm20) outliers start: 40 outliers final: 28 residues processed: 202 average time/residue: 0.6518 time to fit residues: 145.9495 Evaluate side-chains 214 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 174 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.083692 restraints weight = 25667.924| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.58 r_work: 0.2953 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17634 Z= 0.164 Angle : 0.537 8.184 23910 Z= 0.279 Chirality : 0.044 0.196 2598 Planarity : 0.004 0.052 3075 Dihedral : 3.879 20.493 2661 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.14 % Allowed : 15.25 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2142 helix: 2.71 (0.26), residues: 360 sheet: 0.27 (0.24), residues: 504 loop : -0.17 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 61 TYR 0.018 0.001 TYR A 17 PHE 0.030 0.002 PHE H 63 TRP 0.014 0.002 TRP E 21 HIS 0.006 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00409 (17595) covalent geometry : angle 0.53356 (23817) SS BOND : bond 0.00332 ( 24) SS BOND : angle 0.87971 ( 48) hydrogen bonds : bond 0.03847 ( 640) hydrogen bonds : angle 4.36255 ( 1818) link_NAG-ASN : bond 0.00080 ( 15) link_NAG-ASN : angle 1.30915 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5806.71 seconds wall clock time: 99 minutes 53.38 seconds (5993.38 seconds total)