Starting phenix.real_space_refine on Wed Mar 4 22:41:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wxl_21961/03_2026/6wxl_21961.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wxl_21961/03_2026/6wxl_21961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wxl_21961/03_2026/6wxl_21961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wxl_21961/03_2026/6wxl_21961.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wxl_21961/03_2026/6wxl_21961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wxl_21961/03_2026/6wxl_21961.map" } resolution = 2.76 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= 0.006 sd= 0.220 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 102 5.16 5 C 10593 2.51 5 N 2970 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 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: 17016 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2415 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "B" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1380 Classifications: {'peptide': 170} Link IDs: {'TRANS': 169} Chain: "L" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 863 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 105} Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "A" 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, G, D, I, E, J, F, K Time building chain proxies: 3.31, per 1000 atoms: 0.19 Number of scatterers: 17016 At special positions: 0 Unit cell: (129.96, 133.209, 148.371, 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 102 16.00 O 3351 8.00 N 2970 7.00 C 10593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.07 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.07 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS I 137 " distance=2.07 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 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 38 " " NAG B 301 " - " ASN B 82 " " NAG B 302 " - " ASN B 154 " " NAG C 401 " - " ASN C 38 " " NAG D 301 " - " ASN D 82 " " NAG D 302 " - " ASN D 154 " " NAG G 401 " - " ASN G 38 " " NAG I 301 " - " ASN I 82 " " NAG I 302 " - " ASN I 154 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 783.4 milliseconds 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 51 sheets defined 18.6% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.840A pdb=" N THR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.837A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.623A pdb=" N THR A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 54 removed outlier: 3.700A pdb=" N GLN B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.689A pdb=" N ASN B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.576A pdb=" N ARG B 153 " --> pdb=" O MET B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 161 removed outlier: 3.507A pdb=" N LYS B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 161' Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.830A pdb=" N GLN B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100G Processing helix chain 'D' and resid 38 through 54 removed outlier: 3.700A pdb=" N GLN D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 126 removed outlier: 3.689A pdb=" N ASN D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 removed outlier: 3.577A pdb=" N ARG D 153 " --> pdb=" O MET D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.508A pdb=" N LYS D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.830A pdb=" N GLN D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN D 172 " --> pdb=" O GLN D 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 100B through 100G Processing helix chain 'I' and resid 38 through 54 removed outlier: 3.700A pdb=" N GLN I 47 " --> pdb=" O SER I 43 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG I 54 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 126 removed outlier: 3.689A pdb=" N ASN I 82 " --> pdb=" O GLY I 78 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN I 105 " --> pdb=" O ALA I 101 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP I 116 " --> pdb=" O ASP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 154 removed outlier: 3.578A pdb=" N ARG I 153 " --> pdb=" O MET I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 161 removed outlier: 3.508A pdb=" N LYS I 161 " --> pdb=" O ASP I 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 158 through 161' Processing helix chain 'I' and resid 162 through 172 removed outlier: 3.830A pdb=" N GLN I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN I 169 " --> pdb=" O GLU I 165 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG I 170 " --> pdb=" O ALA I 166 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 100B through 100G Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.840A pdb=" N THR C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.837A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 187 through 196 removed outlier: 3.622A pdb=" N THR C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 3.839A pdb=" N THR G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.838A pdb=" N ASP G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 187 through 196 removed outlier: 3.621A pdb=" N THR G 192 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 37 removed outlier: 3.501A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.655A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.847A pdb=" N VAL A 59 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.778A pdb=" N LYS A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP A 234 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 179 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG A 256 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.778A pdb=" N LYS A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP A 234 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 140 removed outlier: 3.582A pdb=" N SER A 146 " --> pdb=" O THR A 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.511A pdb=" N GLY A 286 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.721A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.605A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.557A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.638A pdb=" N LEU H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'D' and resid 31 through 37 removed outlier: 3.501A pdb=" N GLY D 33 " --> pdb=" O HIS D 26 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.720A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.513A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.605A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.555A pdb=" N VAL F 5 " --> pdb=" O LYS F 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.637A pdb=" N LEU F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AC7, first strand: chain 'I' and resid 31 through 37 removed outlier: 3.501A pdb=" N GLY I 33 " --> pdb=" O HIS I 26 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR I 22 " --> pdb=" O ASP I 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.719A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.513A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.605A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.557A pdb=" N VAL K 5 " --> pdb=" O LYS K 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.638A pdb=" N LEU K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AD5, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AD6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD8, first strand: chain 'C' and resid 51 through 52 removed outlier: 5.655A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.848A pdb=" N VAL C 59 " --> pdb=" O ILE C 88 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.779A pdb=" N LYS C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP C 234 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL C 179 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ARG C 256 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.779A pdb=" N LYS C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP C 234 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.582A pdb=" N SER C 146 " --> pdb=" O THR C 136 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AE5, first strand: chain 'C' and resid 286 through 287 removed outlier: 3.512A pdb=" N GLY C 286 " --> pdb=" O TYR C 283 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 24 through 26 Processing sheet with id=AE7, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AE8, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AE9, first strand: chain 'G' and resid 51 through 52 removed outlier: 5.655A pdb=" N ILE G 51 " --> pdb=" O ASP G 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.850A pdb=" N VAL G 59 " --> pdb=" O ILE G 88 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 100 through 102 removed outlier: 6.780A pdb=" N LYS G 101 " --> pdb=" O PHE G 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP G 234 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL G 179 " --> pdb=" O ARG G 256 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ARG G 256 " --> pdb=" O VAL G 179 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 100 through 102 removed outlier: 6.780A pdb=" N LYS G 101 " --> pdb=" O PHE G 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP G 234 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 136 through 140 removed outlier: 3.581A pdb=" N SER G 146 " --> pdb=" O THR G 136 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AF6, first strand: chain 'G' and resid 286 through 287 removed outlier: 3.511A pdb=" N GLY G 286 " --> pdb=" O TYR G 283 " (cutoff:3.500A) 663 hydrogen bonds defined for protein. 1728 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: 3.12 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5683 1.35 - 1.47: 4309 1.47 - 1.60: 7204 1.60 - 1.72: 0 1.72 - 1.85: 156 Bond restraints: 17352 Sorted by residual: bond pdb=" C1 NAG I 301 " pdb=" O5 NAG I 301 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C1 NAG B 301 " pdb=" O5 NAG B 301 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.39e+00 bond pdb=" C1 NAG D 301 " pdb=" O5 NAG D 301 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C1 NAG D 302 " pdb=" O5 NAG D 302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.06e+00 ... (remaining 17347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 22932 2.00 - 4.00: 466 4.00 - 6.00: 34 6.00 - 8.00: 19 8.00 - 10.00: 6 Bond angle restraints: 23457 Sorted by residual: angle pdb=" N THR J 94 " pdb=" CA THR J 94 " pdb=" C THR J 94 " ideal model delta sigma weight residual 109.81 118.18 -8.37 2.21e+00 2.05e-01 1.43e+01 angle pdb=" N THR L 94 " pdb=" CA THR L 94 " pdb=" C THR L 94 " ideal model delta sigma weight residual 109.81 118.17 -8.36 2.21e+00 2.05e-01 1.43e+01 angle pdb=" N THR E 94 " pdb=" CA THR E 94 " pdb=" C THR E 94 " ideal model delta sigma weight residual 109.81 118.15 -8.34 2.21e+00 2.05e-01 1.42e+01 angle pdb=" CA THR E 94 " pdb=" C THR E 94 " pdb=" N PRO E 95 " ideal model delta sigma weight residual 118.44 123.84 -5.40 1.59e+00 3.96e-01 1.15e+01 angle pdb=" CA THR L 94 " pdb=" C THR L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 118.44 123.73 -5.29 1.59e+00 3.96e-01 1.11e+01 ... (remaining 23452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 9382 16.73 - 33.47: 836 33.47 - 50.20: 198 50.20 - 66.94: 42 66.94 - 83.67: 30 Dihedral angle restraints: 10488 sinusoidal: 4311 harmonic: 6177 Sorted by residual: dihedral pdb=" CB CYS A 52 " pdb=" SG CYS A 52 " pdb=" SG CYS A 277 " pdb=" CB CYS A 277 " ideal model delta sinusoidal sigma weight residual -86.00 -10.81 -75.19 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -10.83 -75.17 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CB CYS G 52 " pdb=" SG CYS G 52 " pdb=" SG CYS G 277 " pdb=" CB CYS G 277 " ideal model delta sinusoidal sigma weight residual -86.00 -10.85 -75.15 1 1.00e+01 1.00e-02 7.14e+01 ... (remaining 10485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2039 0.060 - 0.119: 456 0.119 - 0.179: 55 0.179 - 0.239: 0 0.239 - 0.298: 6 Chirality restraints: 2556 Sorted by residual: chirality pdb=" CA THR L 94 " pdb=" N THR L 94 " pdb=" C THR L 94 " pdb=" CB THR L 94 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA THR J 94 " pdb=" N THR J 94 " pdb=" C THR J 94 " pdb=" CB THR J 94 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA THR E 94 " pdb=" N THR E 94 " pdb=" C THR E 94 " pdb=" CB THR E 94 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 2553 not shown) Planarity restraints: 3069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 95 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO E 95A" 0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 95A" -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 95A" -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO L 95A" 0.128 5.00e-02 4.00e+02 pdb=" CA PRO L 95A" -0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 95A" -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 95 " -0.049 5.00e-02 4.00e+02 7.37e-02 8.70e+00 pdb=" N PRO J 95A" 0.128 5.00e-02 4.00e+02 pdb=" CA PRO J 95A" -0.037 5.00e-02 4.00e+02 pdb=" CD PRO J 95A" -0.042 5.00e-02 4.00e+02 ... (remaining 3066 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4531 2.80 - 3.33: 12971 3.33 - 3.85: 28159 3.85 - 4.38: 33460 4.38 - 4.90: 58587 Nonbonded interactions: 137708 Sorted by model distance: nonbonded pdb=" OH TYR H 27 " pdb=" O LYS H 95 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR F 27 " pdb=" O LYS F 95 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR K 27 " pdb=" O LYS K 95 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR K 100D" pdb=" OD2 ASP K 101 " model vdw 2.307 3.040 nonbonded pdb=" OH TYR F 100D" pdb=" OD2 ASP F 101 " model vdw 2.308 3.040 ... (remaining 137703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'F' selection = chain 'K' } 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: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.830 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17385 Z= 0.211 Angle : 0.713 9.995 23532 Z= 0.395 Chirality : 0.050 0.298 2556 Planarity : 0.006 0.074 3060 Dihedral : 14.176 83.674 6498 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.16 % Allowed : 3.99 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -3.74 (0.14), residues: 2151 helix: -4.18 (0.13), residues: 324 sheet: -1.45 (0.19), residues: 624 loop : -2.61 (0.13), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 57 TYR 0.023 0.002 TYR L 49 PHE 0.018 0.002 PHE G 294 TRP 0.006 0.002 TRP C 180 HIS 0.009 0.002 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00470 (17352) covalent geometry : angle 0.70780 (23457) SS BOND : bond 0.01487 ( 24) SS BOND : angle 1.67037 ( 48) hydrogen bonds : bond 0.28214 ( 603) hydrogen bonds : angle 9.87591 ( 1728) link_NAG-ASN : bond 0.00182 ( 9) link_NAG-ASN : angle 1.57223 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 316 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: B 62 GLN cc_start: 0.8465 (tt0) cc_final: 0.8234 (tt0) REVERT: B 102 MET cc_start: 0.7570 (ttp) cc_final: 0.7327 (ttp) REVERT: B 123 LYS cc_start: 0.8188 (tttm) cc_final: 0.7890 (ttpt) REVERT: L 74 LYS cc_start: 0.7364 (ttmm) cc_final: 0.6580 (tptt) REVERT: L 79 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7426 (mt-10) REVERT: H 80 MET cc_start: 0.8133 (tmm) cc_final: 0.7798 (ttp) REVERT: D 61 GLN cc_start: 0.8175 (tp40) cc_final: 0.7835 (tp-100) REVERT: D 62 GLN cc_start: 0.8462 (tt0) cc_final: 0.8218 (mt0) REVERT: D 155 ASN cc_start: 0.8446 (t0) cc_final: 0.8201 (t0) REVERT: E 34 ASP cc_start: 0.7518 (m-30) cc_final: 0.6899 (m-30) REVERT: E 74 LYS cc_start: 0.7368 (ttmm) cc_final: 0.6651 (tptt) REVERT: F 100 MET cc_start: 0.8586 (tpp) cc_final: 0.8364 (tpp) REVERT: I 60 ASN cc_start: 0.7960 (m110) cc_final: 0.7722 (m110) REVERT: I 61 GLN cc_start: 0.8247 (tp40) cc_final: 0.8042 (tp-100) REVERT: I 62 GLN cc_start: 0.8400 (tt0) cc_final: 0.8125 (tt0) REVERT: J 34 ASP cc_start: 0.7316 (m-30) cc_final: 0.6655 (m-30) REVERT: J 74 LYS cc_start: 0.7675 (ttmm) cc_final: 0.6708 (tptt) REVERT: K 72 ASP cc_start: 0.7730 (t70) cc_final: 0.7221 (t70) REVERT: K 100 TYR cc_start: 0.8688 (t80) cc_final: 0.8483 (t80) REVERT: C 42 THR cc_start: 0.8277 (m) cc_final: 0.7882 (p) REVERT: C 151 MET cc_start: 0.8640 (mmm) cc_final: 0.7692 (mmt) REVERT: C 190 GLU cc_start: 0.7135 (tp30) cc_final: 0.6912 (tt0) REVERT: G 70 ILE cc_start: 0.7372 (mm) cc_final: 0.7129 (mm) outliers start: 3 outliers final: 0 residues processed: 318 average time/residue: 0.7514 time to fit residues: 260.3195 Evaluate side-chains 218 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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: 3.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 211 GLN A 224 ASN B 60 ASN H 6 GLN H 35 HIS H 78 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 60 ASN E 27 HIS F 6 GLN F 35 HIS F 78 HIS I 125 GLN J 27 HIS K 6 GLN K 35 HIS K 78 HIS C 208 ASN C 224 ASN G 208 ASN G 224 ASN G 240 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.086800 restraints weight = 23552.263| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.06 r_work: 0.2855 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17385 Z= 0.234 Angle : 0.673 11.522 23532 Z= 0.354 Chirality : 0.048 0.219 2556 Planarity : 0.006 0.070 3060 Dihedral : 5.878 53.530 2565 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.90 % Allowed : 10.77 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.77 (0.15), residues: 2151 helix: -1.37 (0.25), residues: 333 sheet: -1.51 (0.19), residues: 693 loop : -2.19 (0.14), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 96 TYR 0.023 0.002 TYR L 49 PHE 0.015 0.002 PHE G 251 TRP 0.016 0.002 TRP D 92 HIS 0.008 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00581 (17352) covalent geometry : angle 0.66367 (23457) SS BOND : bond 0.00711 ( 24) SS BOND : angle 2.31242 ( 48) hydrogen bonds : bond 0.05444 ( 603) hydrogen bonds : angle 5.87414 ( 1728) link_NAG-ASN : bond 0.00357 ( 9) link_NAG-ASN : angle 1.72259 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: B 123 LYS cc_start: 0.8191 (tttm) cc_final: 0.7956 (ttpt) REVERT: B 167 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7801 (tpp) REVERT: L 74 LYS cc_start: 0.7644 (ttmm) cc_final: 0.7347 (mmmt) REVERT: H 69 MET cc_start: 0.8943 (mtt) cc_final: 0.8517 (mtt) REVERT: D 74 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: E 34 ASP cc_start: 0.8224 (m-30) cc_final: 0.7500 (m-30) REVERT: E 69 THR cc_start: 0.8734 (p) cc_final: 0.8419 (m) REVERT: E 74 LYS cc_start: 0.7897 (ttmm) cc_final: 0.6884 (tptt) REVERT: E 107 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6535 (ttmm) REVERT: F 80 MET cc_start: 0.8591 (tmm) cc_final: 0.8355 (tmm) REVERT: J 34 ASP cc_start: 0.8113 (m-30) cc_final: 0.7466 (m-30) REVERT: J 74 LYS cc_start: 0.7968 (ttmm) cc_final: 0.6827 (tmtm) REVERT: K 6 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8678 (mt0) REVERT: C 42 THR cc_start: 0.8345 (m) cc_final: 0.8110 (p) REVERT: C 190 GLU cc_start: 0.7338 (tp30) cc_final: 0.7070 (tt0) REVERT: G 208 ASN cc_start: 0.8069 (t0) cc_final: 0.7845 (t160) outliers start: 53 outliers final: 16 residues processed: 259 average time/residue: 0.6948 time to fit residues: 197.9432 Evaluate side-chains 223 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain G residue 273 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 224 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 125 GLN L 45 GLN H 6 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN F 6 GLN I 27 GLN K 6 GLN C 208 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.086907 restraints weight = 23812.812| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.06 r_work: 0.2868 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17385 Z= 0.124 Angle : 0.538 8.234 23532 Z= 0.285 Chirality : 0.044 0.185 2556 Planarity : 0.004 0.056 3060 Dihedral : 5.340 52.338 2565 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.51 % Allowed : 12.84 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.02 (0.16), residues: 2151 helix: -0.00 (0.29), residues: 333 sheet: -1.11 (0.19), residues: 717 loop : -1.92 (0.15), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 77 TYR 0.016 0.001 TYR E 49 PHE 0.008 0.001 PHE A 294 TRP 0.010 0.001 TRP D 92 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00297 (17352) covalent geometry : angle 0.52802 (23457) SS BOND : bond 0.00385 ( 24) SS BOND : angle 2.13374 ( 48) hydrogen bonds : bond 0.04185 ( 603) hydrogen bonds : angle 5.18233 ( 1728) link_NAG-ASN : bond 0.00381 ( 9) link_NAG-ASN : angle 1.34595 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8216 (tt0) cc_final: 0.7837 (mp0) REVERT: A 273 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8262 (pt0) REVERT: B 102 MET cc_start: 0.8145 (ttp) cc_final: 0.7921 (ttp) REVERT: L 24 ARG cc_start: 0.8279 (ptm160) cc_final: 0.7847 (mtp85) REVERT: L 74 LYS cc_start: 0.7551 (ttmm) cc_final: 0.7285 (mmmt) REVERT: H 69 MET cc_start: 0.8961 (mtt) cc_final: 0.8522 (mtt) REVERT: D 30 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.5401 (mp10) REVERT: D 74 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: E 24 ARG cc_start: 0.8182 (ptm160) cc_final: 0.7607 (ptp90) REVERT: E 34 ASP cc_start: 0.8209 (m-30) cc_final: 0.7509 (m-30) REVERT: E 74 LYS cc_start: 0.7779 (ttmm) cc_final: 0.6760 (tptt) REVERT: F 80 MET cc_start: 0.8530 (tmm) cc_final: 0.8262 (tmm) REVERT: I 144 CYS cc_start: 0.6503 (t) cc_final: 0.6206 (t) REVERT: I 149 MET cc_start: 0.7573 (mmt) cc_final: 0.7175 (mmm) REVERT: I 168 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: J 34 ASP cc_start: 0.8056 (m-30) cc_final: 0.7609 (m-30) REVERT: J 74 LYS cc_start: 0.7921 (ttmm) cc_final: 0.6804 (tptt) REVERT: C 123 MET cc_start: 0.8386 (mtt) cc_final: 0.8148 (mtt) REVERT: C 150 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: C 151 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8471 (mmp) REVERT: C 243 VAL cc_start: 0.6820 (OUTLIER) cc_final: 0.6468 (t) REVERT: C 273 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: G 208 ASN cc_start: 0.7889 (t0) cc_final: 0.7630 (t160) outliers start: 46 outliers final: 18 residues processed: 236 average time/residue: 0.6194 time to fit residues: 162.3194 Evaluate side-chains 217 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 168 GLN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain G residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 205 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 209 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 224 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 125 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.087106 restraints weight = 23611.498| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.03 r_work: 0.2866 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17385 Z= 0.140 Angle : 0.539 6.822 23532 Z= 0.284 Chirality : 0.044 0.184 2556 Planarity : 0.004 0.054 3060 Dihedral : 5.171 52.832 2565 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.90 % Allowed : 14.10 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.71 (0.17), residues: 2151 helix: 0.49 (0.29), residues: 333 sheet: -0.91 (0.19), residues: 717 loop : -1.81 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 24 TYR 0.018 0.002 TYR J 49 PHE 0.009 0.001 PHE A 294 TRP 0.011 0.001 TRP D 92 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00341 (17352) covalent geometry : angle 0.53092 (23457) SS BOND : bond 0.00376 ( 24) SS BOND : angle 1.88009 ( 48) hydrogen bonds : bond 0.04067 ( 603) hydrogen bonds : angle 4.96809 ( 1728) link_NAG-ASN : bond 0.00243 ( 9) link_NAG-ASN : angle 1.44666 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8271 (tt0) cc_final: 0.7909 (mp0) REVERT: A 273 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: B 102 MET cc_start: 0.8160 (ttp) cc_final: 0.7887 (ttp) REVERT: B 123 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7566 (ttmp) REVERT: L 24 ARG cc_start: 0.8230 (ptm160) cc_final: 0.7902 (mtp85) REVERT: L 74 LYS cc_start: 0.7547 (ttmm) cc_final: 0.7287 (mmmt) REVERT: H 69 MET cc_start: 0.8958 (mtt) cc_final: 0.8397 (mtt) REVERT: D 74 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6921 (tt0) REVERT: D 171 ILE cc_start: 0.8119 (pt) cc_final: 0.7577 (mp) REVERT: E 34 ASP cc_start: 0.8159 (m-30) cc_final: 0.7446 (m-30) REVERT: E 74 LYS cc_start: 0.7811 (ttmm) cc_final: 0.6734 (tptt) REVERT: F 80 MET cc_start: 0.8526 (tmm) cc_final: 0.8288 (tmm) REVERT: I 144 CYS cc_start: 0.6583 (t) cc_final: 0.6325 (t) REVERT: I 149 MET cc_start: 0.7518 (mmt) cc_final: 0.7233 (mmm) REVERT: J 34 ASP cc_start: 0.8153 (m-30) cc_final: 0.7670 (m-30) REVERT: J 74 LYS cc_start: 0.7805 (ttmm) cc_final: 0.6791 (tttp) REVERT: K 3 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6461 (pp30) REVERT: K 43 GLN cc_start: 0.8349 (mt0) cc_final: 0.8083 (mm110) REVERT: C 114 GLU cc_start: 0.7950 (tt0) cc_final: 0.7419 (pt0) REVERT: C 150 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: C 243 VAL cc_start: 0.6814 (OUTLIER) cc_final: 0.6500 (t) REVERT: C 273 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7836 (pt0) REVERT: G 208 ASN cc_start: 0.7905 (t0) cc_final: 0.7611 (t160) REVERT: G 307 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.6564 (mmt180) outliers start: 53 outliers final: 21 residues processed: 240 average time/residue: 0.6030 time to fit residues: 161.1246 Evaluate side-chains 221 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 307 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 71 optimal weight: 0.0020 chunk 132 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 224 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 125 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.093652 restraints weight = 23290.999| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.65 r_work: 0.2989 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17385 Z= 0.136 Angle : 0.531 6.207 23532 Z= 0.278 Chirality : 0.044 0.179 2556 Planarity : 0.004 0.052 3060 Dihedral : 5.045 52.368 2565 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.01 % Allowed : 14.64 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.47 (0.17), residues: 2151 helix: 0.86 (0.29), residues: 333 sheet: -0.78 (0.19), residues: 717 loop : -1.69 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 24 TYR 0.016 0.001 TYR L 49 PHE 0.009 0.001 PHE A 251 TRP 0.011 0.001 TRP D 92 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00334 (17352) covalent geometry : angle 0.52314 (23457) SS BOND : bond 0.00355 ( 24) SS BOND : angle 1.76802 ( 48) hydrogen bonds : bond 0.03932 ( 603) hydrogen bonds : angle 4.84039 ( 1728) link_NAG-ASN : bond 0.00222 ( 9) link_NAG-ASN : angle 1.48666 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8198 (tt0) cc_final: 0.7940 (pt0) REVERT: A 273 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8269 (pt0) REVERT: B 102 MET cc_start: 0.8235 (ttp) cc_final: 0.8001 (ttp) REVERT: B 123 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7737 (ttmp) REVERT: H 69 MET cc_start: 0.8941 (mtt) cc_final: 0.8296 (mtt) REVERT: D 74 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6976 (tt0) REVERT: D 171 ILE cc_start: 0.8343 (pt) cc_final: 0.7889 (mp) REVERT: E 34 ASP cc_start: 0.7998 (m-30) cc_final: 0.7350 (m-30) REVERT: F 80 MET cc_start: 0.8432 (tmm) cc_final: 0.8065 (tmm) REVERT: J 34 ASP cc_start: 0.7964 (m-30) cc_final: 0.7503 (m-30) REVERT: J 74 LYS cc_start: 0.7879 (ttmm) cc_final: 0.7036 (tptt) REVERT: K 3 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6663 (pp30) REVERT: C 114 GLU cc_start: 0.8014 (tt0) cc_final: 0.7722 (pt0) REVERT: C 150 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: C 273 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7890 (pt0) REVERT: G 208 ASN cc_start: 0.7868 (t0) cc_final: 0.7563 (t160) REVERT: G 273 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: G 307 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.6633 (mmt180) outliers start: 55 outliers final: 27 residues processed: 238 average time/residue: 0.6076 time to fit residues: 160.6603 Evaluate side-chains 224 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 273 GLN Chi-restraints excluded: chain G residue 307 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 92 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 190 optimal weight: 0.0070 chunk 19 optimal weight: 0.0170 chunk 202 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 224 ASN B 60 ASN B 125 GLN L 27 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN C 208 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.092554 restraints weight = 23281.512| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.66 r_work: 0.2983 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17385 Z= 0.187 Angle : 0.597 9.138 23532 Z= 0.311 Chirality : 0.046 0.200 2556 Planarity : 0.004 0.054 3060 Dihedral : 5.244 52.463 2565 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.55 % Allowed : 14.75 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.49 (0.17), residues: 2151 helix: 0.77 (0.29), residues: 327 sheet: -0.75 (0.19), residues: 723 loop : -1.71 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 54 TYR 0.021 0.002 TYR L 49 PHE 0.011 0.002 PHE A 251 TRP 0.013 0.002 TRP D 92 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00471 (17352) covalent geometry : angle 0.58525 (23457) SS BOND : bond 0.00440 ( 24) SS BOND : angle 2.40703 ( 48) hydrogen bonds : bond 0.04303 ( 603) hydrogen bonds : angle 4.93251 ( 1728) link_NAG-ASN : bond 0.00229 ( 9) link_NAG-ASN : angle 1.63152 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 191 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8209 (tt0) cc_final: 0.8004 (pt0) REVERT: A 273 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: B 102 MET cc_start: 0.8198 (ttp) cc_final: 0.7958 (ttp) REVERT: B 123 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7748 (ttmp) REVERT: H 69 MET cc_start: 0.8905 (mtt) cc_final: 0.8226 (mtt) REVERT: D 74 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6996 (tt0) REVERT: D 149 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.6831 (mpt) REVERT: D 171 ILE cc_start: 0.8369 (pt) cc_final: 0.7871 (mp) REVERT: E 34 ASP cc_start: 0.7991 (m-30) cc_final: 0.7309 (m-30) REVERT: F 45 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7618 (mt) REVERT: I 144 CYS cc_start: 0.6951 (t) cc_final: 0.6690 (t) REVERT: I 149 MET cc_start: 0.7804 (mmt) cc_final: 0.7601 (mmm) REVERT: J 34 ASP cc_start: 0.8000 (m-30) cc_final: 0.7420 (m-30) REVERT: J 74 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7038 (tttp) REVERT: K 3 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6658 (pp30) REVERT: C 114 GLU cc_start: 0.8123 (tt0) cc_final: 0.7791 (pt0) REVERT: C 140 ARG cc_start: 0.7925 (mmm160) cc_final: 0.7648 (mmm160) REVERT: C 150 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: C 273 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: G 208 ASN cc_start: 0.7885 (t0) cc_final: 0.7555 (t160) REVERT: G 273 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8031 (pt0) REVERT: G 307 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6666 (mmt180) outliers start: 65 outliers final: 37 residues processed: 237 average time/residue: 0.6198 time to fit residues: 162.5082 Evaluate side-chains 235 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 273 GLN Chi-restraints excluded: chain G residue 277 CYS Chi-restraints excluded: chain G residue 307 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 160 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 60 ASN B 125 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN C 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.093004 restraints weight = 23314.322| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.69 r_work: 0.2990 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17385 Z= 0.150 Angle : 0.556 7.362 23532 Z= 0.291 Chirality : 0.044 0.181 2556 Planarity : 0.004 0.051 3060 Dihedral : 5.138 52.178 2565 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.22 % Allowed : 15.36 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.37 (0.17), residues: 2151 helix: 1.01 (0.29), residues: 327 sheet: -0.70 (0.19), residues: 723 loop : -1.65 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 24 TYR 0.038 0.002 TYR C 195 PHE 0.009 0.001 PHE A 294 TRP 0.011 0.001 TRP D 92 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00370 (17352) covalent geometry : angle 0.54661 (23457) SS BOND : bond 0.00369 ( 24) SS BOND : angle 2.09523 ( 48) hydrogen bonds : bond 0.04000 ( 603) hydrogen bonds : angle 4.82731 ( 1728) link_NAG-ASN : bond 0.00226 ( 9) link_NAG-ASN : angle 1.52033 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8170 (tt0) cc_final: 0.7963 (pt0) REVERT: A 273 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: B 102 MET cc_start: 0.8162 (ttp) cc_final: 0.7922 (ttp) REVERT: B 123 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7710 (ttmp) REVERT: L 74 LYS cc_start: 0.7986 (mttt) cc_final: 0.7771 (mmmt) REVERT: H 69 MET cc_start: 0.8906 (mtt) cc_final: 0.8242 (mtt) REVERT: D 74 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: D 149 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.6916 (mpt) REVERT: D 171 ILE cc_start: 0.8299 (pt) cc_final: 0.7846 (mp) REVERT: E 34 ASP cc_start: 0.7995 (m-30) cc_final: 0.7327 (m-30) REVERT: F 80 MET cc_start: 0.8631 (tmm) cc_final: 0.8278 (tmm) REVERT: J 34 ASP cc_start: 0.7942 (m-30) cc_final: 0.7521 (m-30) REVERT: J 74 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7040 (tttp) REVERT: K 3 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6639 (pp30) REVERT: C 114 GLU cc_start: 0.8081 (tt0) cc_final: 0.7749 (pt0) REVERT: C 140 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7626 (mmm160) REVERT: C 150 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: C 295 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7686 (pp30) REVERT: G 208 ASN cc_start: 0.7886 (t0) cc_final: 0.7591 (t160) REVERT: G 307 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.6671 (mmt180) outliers start: 59 outliers final: 29 residues processed: 236 average time/residue: 0.6393 time to fit residues: 166.8869 Evaluate side-chains 224 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 277 CYS Chi-restraints excluded: chain G residue 307 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 224 ASN B 60 ASN B 125 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN G 157 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.092770 restraints weight = 23288.082| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.66 r_work: 0.2976 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17385 Z= 0.170 Angle : 0.577 7.532 23532 Z= 0.302 Chirality : 0.045 0.188 2556 Planarity : 0.004 0.056 3060 Dihedral : 5.200 52.229 2565 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.95 % Allowed : 15.90 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.38 (0.17), residues: 2151 helix: 0.95 (0.29), residues: 333 sheet: -0.69 (0.20), residues: 726 loop : -1.66 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 24 TYR 0.030 0.002 TYR C 195 PHE 0.010 0.001 PHE A 251 TRP 0.012 0.002 TRP D 92 HIS 0.004 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00425 (17352) covalent geometry : angle 0.56860 (23457) SS BOND : bond 0.00413 ( 24) SS BOND : angle 2.03319 ( 48) hydrogen bonds : bond 0.04162 ( 603) hydrogen bonds : angle 4.87480 ( 1728) link_NAG-ASN : bond 0.00234 ( 9) link_NAG-ASN : angle 1.55496 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: A 273 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: B 123 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7729 (ttmp) REVERT: L 74 LYS cc_start: 0.7982 (mttt) cc_final: 0.7755 (mmmt) REVERT: H 69 MET cc_start: 0.8883 (mtt) cc_final: 0.8208 (mtt) REVERT: D 74 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: D 149 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.6943 (mpt) REVERT: D 171 ILE cc_start: 0.8338 (pt) cc_final: 0.7881 (mp) REVERT: E 34 ASP cc_start: 0.8000 (m-30) cc_final: 0.7330 (m-30) REVERT: F 45 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7630 (mt) REVERT: I 168 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: J 34 ASP cc_start: 0.7960 (m-30) cc_final: 0.7512 (m-30) REVERT: J 74 LYS cc_start: 0.7928 (ttmm) cc_final: 0.7019 (tttp) REVERT: K 3 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6662 (pp30) REVERT: C 114 GLU cc_start: 0.8044 (tt0) cc_final: 0.7741 (pt0) REVERT: C 150 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: C 295 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7695 (pp30) REVERT: G 208 ASN cc_start: 0.7893 (t0) cc_final: 0.7599 (t160) REVERT: G 307 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6668 (mmt180) outliers start: 54 outliers final: 34 residues processed: 230 average time/residue: 0.6446 time to fit residues: 163.8091 Evaluate side-chains 231 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 168 GLN Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 275 ASP Chi-restraints excluded: chain G residue 277 CYS Chi-restraints excluded: chain G residue 307 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 14 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 224 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 125 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN C 208 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.093504 restraints weight = 23359.213| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.66 r_work: 0.2989 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17385 Z= 0.136 Angle : 0.538 6.216 23532 Z= 0.282 Chirality : 0.044 0.180 2556 Planarity : 0.004 0.060 3060 Dihedral : 5.056 51.737 2565 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.46 % Allowed : 16.45 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.26 (0.17), residues: 2151 helix: 1.18 (0.29), residues: 333 sheet: -0.65 (0.19), residues: 726 loop : -1.62 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 24 TYR 0.030 0.002 TYR C 195 PHE 0.009 0.001 PHE A 294 TRP 0.010 0.001 TRP D 92 HIS 0.005 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00332 (17352) covalent geometry : angle 0.52957 (23457) SS BOND : bond 0.00347 ( 24) SS BOND : angle 1.84783 ( 48) hydrogen bonds : bond 0.03858 ( 603) hydrogen bonds : angle 4.76819 ( 1728) link_NAG-ASN : bond 0.00219 ( 9) link_NAG-ASN : angle 1.46494 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: B 123 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7748 (ttmp) REVERT: L 74 LYS cc_start: 0.7965 (mttt) cc_final: 0.7756 (mmmt) REVERT: H 69 MET cc_start: 0.8886 (mtt) cc_final: 0.8214 (mtt) REVERT: D 74 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: D 149 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7638 (mmm) REVERT: D 171 ILE cc_start: 0.8291 (pt) cc_final: 0.7852 (mp) REVERT: E 34 ASP cc_start: 0.8008 (m-30) cc_final: 0.7330 (m-30) REVERT: F 45 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7565 (mt) REVERT: F 80 MET cc_start: 0.8594 (tmm) cc_final: 0.8315 (tmm) REVERT: I 168 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: J 34 ASP cc_start: 0.7908 (m-30) cc_final: 0.7499 (m-30) REVERT: J 60 ASP cc_start: 0.7881 (m-30) cc_final: 0.7451 (t0) REVERT: J 74 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7045 (tttp) REVERT: K 3 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6662 (pp30) REVERT: C 114 GLU cc_start: 0.8057 (tt0) cc_final: 0.7763 (pt0) REVERT: C 140 ARG cc_start: 0.7912 (mmm160) cc_final: 0.7598 (mmm160) REVERT: C 150 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: C 295 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7700 (pp30) REVERT: G 208 ASN cc_start: 0.7821 (t0) cc_final: 0.7516 (t160) REVERT: G 307 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6664 (mmt180) outliers start: 45 outliers final: 30 residues processed: 222 average time/residue: 0.6394 time to fit residues: 157.0170 Evaluate side-chains 225 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 168 GLN Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 277 CYS Chi-restraints excluded: chain G residue 307 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 137 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 133 optimal weight: 0.0670 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 125 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093330 restraints weight = 23292.881| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.65 r_work: 0.2986 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17385 Z= 0.153 Angle : 0.559 6.431 23532 Z= 0.292 Chirality : 0.044 0.181 2556 Planarity : 0.004 0.066 3060 Dihedral : 5.094 51.825 2565 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.62 % Allowed : 16.67 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.29 (0.17), residues: 2151 helix: 1.12 (0.29), residues: 333 sheet: -0.66 (0.19), residues: 726 loop : -1.63 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 24 TYR 0.028 0.002 TYR C 195 PHE 0.009 0.001 PHE A 251 TRP 0.012 0.001 TRP D 92 HIS 0.005 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00378 (17352) covalent geometry : angle 0.55047 (23457) SS BOND : bond 0.00394 ( 24) SS BOND : angle 1.90216 ( 48) hydrogen bonds : bond 0.03990 ( 603) hydrogen bonds : angle 4.79811 ( 1728) link_NAG-ASN : bond 0.00225 ( 9) link_NAG-ASN : angle 1.50641 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: A 273 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: B 123 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7776 (ttmp) REVERT: L 74 LYS cc_start: 0.7995 (mttt) cc_final: 0.7780 (mmmt) REVERT: H 69 MET cc_start: 0.8876 (mtt) cc_final: 0.8220 (mtt) REVERT: D 74 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: D 149 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7690 (mmm) REVERT: D 171 ILE cc_start: 0.8322 (pt) cc_final: 0.7882 (mp) REVERT: E 34 ASP cc_start: 0.7979 (m-30) cc_final: 0.7309 (m-30) REVERT: F 45 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7621 (mt) REVERT: F 69 MET cc_start: 0.8769 (mtt) cc_final: 0.8275 (mtm) REVERT: I 168 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: J 34 ASP cc_start: 0.7897 (m-30) cc_final: 0.7381 (m-30) REVERT: J 60 ASP cc_start: 0.7867 (m-30) cc_final: 0.7450 (t0) REVERT: J 74 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7063 (tttp) REVERT: K 3 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6723 (pp30) REVERT: C 114 GLU cc_start: 0.8052 (tt0) cc_final: 0.7815 (pt0) REVERT: C 140 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7595 (mmm160) REVERT: C 150 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: C 295 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7700 (pp30) REVERT: G 208 ASN cc_start: 0.7825 (t0) cc_final: 0.7531 (t160) REVERT: G 307 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.6672 (mmt180) outliers start: 48 outliers final: 34 residues processed: 217 average time/residue: 0.6465 time to fit residues: 155.1897 Evaluate side-chains 228 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 168 GLN Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 277 CYS Chi-restraints excluded: chain G residue 307 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 78 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 125 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.093242 restraints weight = 23377.875| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.66 r_work: 0.2986 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17385 Z= 0.153 Angle : 0.557 6.348 23532 Z= 0.291 Chirality : 0.044 0.183 2556 Planarity : 0.004 0.065 3060 Dihedral : 5.096 51.754 2565 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.57 % Allowed : 16.72 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.29 (0.17), residues: 2151 helix: 1.13 (0.29), residues: 333 sheet: -0.67 (0.19), residues: 726 loop : -1.62 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 24 TYR 0.027 0.002 TYR C 195 PHE 0.009 0.001 PHE A 251 TRP 0.011 0.001 TRP D 92 HIS 0.005 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00378 (17352) covalent geometry : angle 0.54847 (23457) SS BOND : bond 0.00397 ( 24) SS BOND : angle 1.89278 ( 48) hydrogen bonds : bond 0.03989 ( 603) hydrogen bonds : angle 4.80206 ( 1728) link_NAG-ASN : bond 0.00223 ( 9) link_NAG-ASN : angle 1.50279 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6033.19 seconds wall clock time: 103 minutes 15.39 seconds (6195.39 seconds total)