Starting phenix.real_space_refine on Sun Oct 25 12:18:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wxl_21961/10_2026/6wxl_21961.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wxl_21961/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6wxl_21961/10_2026/6wxl_21961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wxl_21961/10_2026/6wxl_21961.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wxl_21961/10_2026/6wxl_21961.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wxl_21961/10_2026/6wxl_21961.cif" model { file = "/net/cci-nas-00/data/ceres_data/6wxl_21961/10_2026/6wxl_21961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wxl_21961/10_2026/6wxl_21961.cif" } 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-2.3rc1-6221/lib/python3.11/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 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 chiralities: 2 Restraints were copied for chains: C, G, D, I, E, J, F, K Time building chain proxies: 3.48, per 1000 atoms: 0.20 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 D 137 " - pdb=" SG CYS C 14 " distance=2.07 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 137 " - pdb=" SG CYS G 14 " distance=2.07 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 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 52 " - pdb=" SG CYS G 277 " distance=2.04 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " 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: 1.60 Conformation dependent library (CDL) restraints added in 896.4 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: 0.45 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: 3.64 Time building geometry restraints manager: 2.11 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: 9223 16.73 - 33.47: 822 33.47 - 50.20: 185 50.20 - 66.94: 39 66.94 - 83.67: 30 Dihedral angle restraints: 10299 sinusoidal: 4122 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 10296 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: 0.05 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: 5.740 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.180 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 14.131 83.674 6309 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/Z covalent geometry : bond 0.00470 / 0.21 (17352) covalent geometry : angle 0.70780 / 0.39 (23457) SS BOND : bond 0.01487 / 1.10 ( 24) SS BOND : angle 1.67037 / 0.95 ( 48) hydrogen bonds : bond 0.28214 / 19.30 ( 603) hydrogen bonds : angle 9.87591 / 6.81 ( 1728) link_NAG-ASN : bond 0.00182 / 0.11 ( 9) link_NAG-ASN : angle 1.57223 / 1.03 ( 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 : 0.618 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: 0.6807 time to fit residues: 237.1909 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 : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 212, 77] 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... 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 = 0.3271 r_free = 0.3271 target = 0.105972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.086062 restraints weight = 23607.929| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.07 r_work: 0.2859 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17385 Z= 0.231 Angle : 0.672 11.569 23532 Z= 0.353 Chirality : 0.048 0.217 2556 Planarity : 0.006 0.069 3060 Dihedral : 4.898 20.454 2376 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.73 % Allowed : 10.98 % Favored : 86.28 % 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: -2.76 (0.15), residues: 2151 helix: -1.34 (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 0.016 0.002 PHE G 251 TRP 0.015 0.002 TRP D 92 HIS 0.009 0.002 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.23 (17352) covalent geometry : angle 0.66187 / 0.35 (23457) SS BOND : bond 0.00569 / 0.33 ( 24) SS BOND : angle 2.31755 / 1.38 ( 48) hydrogen bonds : bond 0.05477 / 3.82 ( 603) hydrogen bonds : angle 5.88947 / 4.06 ( 1728) link_NAG-ASN : bond 0.00213 / 0.14 ( 9) link_NAG-ASN : angle 1.76646 / 1.15 ( 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 274 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: L 74 LYS cc_start: 0.7659 (ttmm) cc_final: 0.7366 (mmmt) REVERT: H 69 MET cc_start: 0.8936 (mtt) cc_final: 0.8639 (mtt) REVERT: D 74 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: E 34 ASP cc_start: 0.8227 (m-30) cc_final: 0.7569 (m-30) REVERT: E 69 THR cc_start: 0.8765 (p) cc_final: 0.8455 (m) REVERT: E 74 LYS cc_start: 0.7909 (ttmm) cc_final: 0.6912 (tptt) REVERT: E 107 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6704 (ttmm) REVERT: J 34 ASP cc_start: 0.8115 (m-30) cc_final: 0.7463 (m-30) REVERT: J 74 LYS cc_start: 0.7981 (ttmm) cc_final: 0.6860 (tmtm) REVERT: K 6 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8676 (mt0) REVERT: C 42 THR cc_start: 0.8349 (m) cc_final: 0.8103 (p) REVERT: C 140 ARG cc_start: 0.7890 (mmm160) cc_final: 0.7614 (mmm160) REVERT: C 190 GLU cc_start: 0.7366 (tp30) cc_final: 0.7094 (tt0) REVERT: G 208 ASN cc_start: 0.8104 (t0) cc_final: 0.7851 (t160) outliers start: 50 outliers final: 16 residues processed: 255 average time/residue: 0.6474 time to fit residues: 181.6912 Evaluate side-chains 224 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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: [84, 69, 170, 100, 35, 104, 117, 175, 73, 62, 169] chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 100 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 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: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3289 r_free = 0.3289 target = 0.107170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.086968 restraints weight = 23808.075| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.06 r_work: 0.2864 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17385 Z= 0.132 Angle : 0.543 8.004 23532 Z= 0.288 Chirality : 0.044 0.185 2556 Planarity : 0.004 0.056 3060 Dihedral : 4.438 20.568 2376 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.57 % Allowed : 12.68 % Favored : 84.75 % 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: -2.06 (0.16), residues: 2151 helix: -0.02 (0.29), residues: 333 sheet: -1.12 (0.19), residues: 723 loop : -1.96 (0.15), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 77 TYR 0.017 0.001 TYR E 49 PHE 0.008 0.001 PHE G 251 TRP 0.011 0.001 TRP D 92 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (17352) covalent geometry : angle 0.53337 / 0.28 (23457) SS BOND : bond 0.00369 / 0.21 ( 24) SS BOND : angle 2.13611 / 1.27 ( 48) hydrogen bonds : bond 0.04257 / 2.96 ( 603) hydrogen bonds : angle 5.17984 / 3.58 ( 1728) link_NAG-ASN : bond 0.00172 / 0.11 ( 9) link_NAG-ASN : angle 1.40298 / 0.84 ( 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 257 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8216 (tt0) cc_final: 0.7835 (mp0) REVERT: A 273 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: B 102 MET cc_start: 0.8041 (ttp) cc_final: 0.7785 (ttp) REVERT: L 24 ARG cc_start: 0.8283 (ptm160) cc_final: 0.7855 (mtp85) REVERT: L 74 LYS cc_start: 0.7554 (ttmm) cc_final: 0.7281 (mmmt) REVERT: L 89 MET cc_start: 0.8798 (ttp) cc_final: 0.8525 (ttp) REVERT: H 69 MET cc_start: 0.8955 (mtt) cc_final: 0.8524 (mtt) REVERT: D 30 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.5420 (mp10) REVERT: D 74 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: E 24 ARG cc_start: 0.8138 (ptm160) cc_final: 0.7886 (ptm160) REVERT: E 34 ASP cc_start: 0.8161 (m-30) cc_final: 0.7445 (m-30) REVERT: E 74 LYS cc_start: 0.7780 (ttmm) cc_final: 0.6764 (tptt) REVERT: F 80 MET cc_start: 0.8717 (tmm) cc_final: 0.8425 (tmm) REVERT: I 144 CYS cc_start: 0.6511 (t) cc_final: 0.6223 (t) REVERT: I 149 MET cc_start: 0.7572 (mmt) cc_final: 0.7179 (mmm) REVERT: I 168 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: J 34 ASP cc_start: 0.8039 (m-30) cc_final: 0.7581 (m-30) REVERT: J 74 LYS cc_start: 0.7922 (ttmm) cc_final: 0.6834 (tttp) REVERT: C 123 MET cc_start: 0.8383 (mtt) cc_final: 0.8147 (mtt) REVERT: C 150 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: C 151 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8481 (mmp) REVERT: C 243 VAL cc_start: 0.6814 (OUTLIER) cc_final: 0.6461 (t) REVERT: C 273 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: G 208 ASN cc_start: 0.7892 (t0) cc_final: 0.7624 (t160) outliers start: 47 outliers final: 16 residues processed: 241 average time/residue: 0.5643 time to fit residues: 152.4170 Evaluate side-chains 217 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 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 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: [205, 29, 203, 143, 2, 65, 98, 57, 37, 67, 209] chunk 205 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 203 optimal weight: 0.0970 chunk 143 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 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 = 0.3297 r_free = 0.3297 target = 0.107822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.087719 restraints weight = 23609.410| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.03 r_work: 0.2887 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17385 Z= 0.106 Angle : 0.497 6.053 23532 Z= 0.263 Chirality : 0.043 0.175 2556 Planarity : 0.004 0.052 3060 Dihedral : 4.122 17.822 2376 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.79 % Allowed : 13.83 % Favored : 83.39 % 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: -1.59 (0.17), residues: 2151 helix: 0.71 (0.29), residues: 333 sheet: -0.84 (0.19), residues: 717 loop : -1.77 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 24 TYR 0.014 0.001 TYR E 49 PHE 0.007 0.001 PHE A 245 TRP 0.010 0.001 TRP D 83 HIS 0.003 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (17352) covalent geometry : angle 0.48977 / 0.26 (23457) SS BOND : bond 0.00321 / 0.18 ( 24) SS BOND : angle 1.67622 / 1.04 ( 48) hydrogen bonds : bond 0.03681 / 2.55 ( 603) hydrogen bonds : angle 4.78006 / 3.31 ( 1728) link_NAG-ASN : bond 0.00155 / 0.09 ( 9) link_NAG-ASN : angle 1.33195 / 0.80 ( 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 260 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8164 (tt0) cc_final: 0.7872 (mp0) REVERT: A 241 ASP cc_start: 0.8441 (m-30) cc_final: 0.7856 (t0) REVERT: B 102 MET cc_start: 0.8132 (ttp) cc_final: 0.7915 (ttp) REVERT: B 123 LYS cc_start: 0.8190 (tttt) cc_final: 0.7730 (ttmt) REVERT: L 24 ARG cc_start: 0.8242 (ptm160) cc_final: 0.7983 (mtp-110) REVERT: L 74 LYS cc_start: 0.7562 (ttmm) cc_final: 0.7315 (mmmt) REVERT: H 69 MET cc_start: 0.8945 (mtt) cc_final: 0.8411 (mtt) REVERT: D 30 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.5395 (mp10) REVERT: D 74 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6818 (tt0) REVERT: D 171 ILE cc_start: 0.8206 (pt) cc_final: 0.7715 (mp) REVERT: E 34 ASP cc_start: 0.8125 (m-30) cc_final: 0.7429 (m-30) REVERT: E 74 LYS cc_start: 0.7801 (ttmm) cc_final: 0.6735 (tptt) REVERT: F 80 MET cc_start: 0.8699 (tmm) cc_final: 0.8420 (tmm) REVERT: I 144 CYS cc_start: 0.6567 (t) cc_final: 0.6240 (t) REVERT: I 149 MET cc_start: 0.7534 (mmt) cc_final: 0.7140 (mmm) REVERT: I 168 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: J 34 ASP cc_start: 0.8102 (m-30) cc_final: 0.7651 (m-30) REVERT: J 74 LYS cc_start: 0.7793 (ttmm) cc_final: 0.6763 (tptt) REVERT: K 3 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6502 (pp30) REVERT: K 43 GLN cc_start: 0.8381 (mt0) cc_final: 0.8111 (mm110) REVERT: C 123 MET cc_start: 0.8385 (mtt) cc_final: 0.8129 (mtt) REVERT: C 140 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7560 (mmm160) REVERT: C 150 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: C 243 VAL cc_start: 0.6865 (p) cc_final: 0.6573 (t) REVERT: C 273 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7858 (pt0) REVERT: G 208 ASN cc_start: 0.7879 (t0) cc_final: 0.7562 (t160) REVERT: G 307 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.6552 (mmt180) outliers start: 51 outliers final: 17 residues processed: 244 average time/residue: 0.5503 time to fit residues: 149.9491 Evaluate side-chains 207 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 277 CYS Chi-restraints excluded: chain A residue 299 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 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 168 GLN 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 214 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: [71, 132, 207, 53, 166, 92, 184, 208, 157, 95, 90] chunk 71 optimal weight: 0.0070 chunk 132 optimal weight: 3.9990 chunk 207 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 157 optimal weight: 0.0020 chunk 95 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.088367 restraints weight = 23685.372| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.05 r_work: 0.2904 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.002 0.036 17385 Z= 0.094 Angle : 0.491 7.913 23532 Z= 0.259 Chirality : 0.042 0.169 2556 Planarity : 0.003 0.049 3060 Dihedral : 4.003 18.996 2376 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.30 % Allowed : 15.08 % Favored : 82.62 % 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: -1.25 (0.17), residues: 2151 helix: 1.22 (0.29), residues: 333 sheet: -0.66 (0.19), residues: 705 loop : -1.58 (0.16), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 24 TYR 0.012 0.001 TYR E 49 PHE 0.007 0.001 PHE A 245 TRP 0.009 0.001 TRP D 83 HIS 0.003 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 (17352) covalent geometry : angle 0.48278 / 0.26 (23457) SS BOND : bond 0.00301 / 0.17 ( 24) SS BOND : angle 1.83151 / 1.09 ( 48) hydrogen bonds : bond 0.03410 / 2.36 ( 603) hydrogen bonds : angle 4.58557 / 3.17 ( 1728) link_NAG-ASN : bond 0.00143 / 0.08 ( 9) link_NAG-ASN : angle 1.35177 / 0.84 ( 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 240 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.492 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: 0.8104 (tt0) cc_final: 0.7723 (pt0) REVERT: A 273 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8310 (pt0) REVERT: B 102 MET cc_start: 0.8157 (ttp) cc_final: 0.7937 (ttp) REVERT: B 123 LYS cc_start: 0.8217 (tttt) cc_final: 0.7793 (ttmp) REVERT: B 171 ILE cc_start: 0.7815 (pt) cc_final: 0.7599 (mp) REVERT: L 24 ARG cc_start: 0.8181 (ptm160) cc_final: 0.7900 (mtp-110) REVERT: L 74 LYS cc_start: 0.7554 (ttmm) cc_final: 0.7342 (mmmt) REVERT: H 69 MET cc_start: 0.8923 (mtt) cc_final: 0.8308 (mtt) REVERT: D 30 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.5358 (mp10) REVERT: E 24 ARG cc_start: 0.8064 (mtp-110) cc_final: 0.7532 (mtm110) REVERT: E 34 ASP cc_start: 0.8109 (m-30) cc_final: 0.7462 (m-30) REVERT: E 74 LYS cc_start: 0.7800 (ttmm) cc_final: 0.6817 (tptt) REVERT: F 80 MET cc_start: 0.8647 (tmm) cc_final: 0.8347 (tmm) REVERT: J 34 ASP cc_start: 0.8023 (m-30) cc_final: 0.7602 (m-30) REVERT: J 74 LYS cc_start: 0.7850 (ttmm) cc_final: 0.6826 (tttp) REVERT: K 3 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6473 (pp30) REVERT: K 43 GLN cc_start: 0.8353 (mt0) cc_final: 0.8089 (mm110) REVERT: C 123 MET cc_start: 0.8379 (mtt) cc_final: 0.8168 (mtt) REVERT: C 150 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: C 243 VAL cc_start: 0.6863 (p) cc_final: 0.6643 (t) REVERT: G 208 ASN cc_start: 0.7759 (t0) cc_final: 0.7489 (t160) outliers start: 42 outliers final: 17 residues processed: 228 average time/residue: 0.6058 time to fit residues: 152.9391 Evaluate side-chains 209 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 D residue 30 GLN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 11 LEU 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 K residue 3 GLN Chi-restraints excluded: chain K residue 66 ARG 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 246 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 243 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: [92, 85, 140, 172, 190, 19, 202, 132, 197, 185, 50] chunk 92 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 211 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.084885 restraints weight = 23734.486| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.04 r_work: 0.2844 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17385 Z= 0.230 Angle : 0.637 8.700 23532 Z= 0.331 Chirality : 0.048 0.222 2556 Planarity : 0.005 0.055 3060 Dihedral : 4.511 20.224 2376 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.95 % Allowed : 15.30 % Favored : 81.75 % 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: -1.50 (0.17), residues: 2151 helix: 0.69 (0.29), residues: 327 sheet: -0.72 (0.20), residues: 723 loop : -1.72 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 54 TYR 0.023 0.002 TYR L 49 PHE 0.013 0.002 PHE C 294 TRP 0.015 0.002 TRP K 47 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.23 (17352) covalent geometry : angle 0.62536 / 0.33 (23457) SS BOND : bond 0.00468 / 0.26 ( 24) SS BOND : angle 2.42563 / 1.50 ( 48) hydrogen bonds : bond 0.04578 / 3.19 ( 603) hydrogen bonds : angle 5.00745 / 3.46 ( 1728) link_NAG-ASN : bond 0.00179 / 0.12 ( 9) link_NAG-ASN : angle 1.74600 / 1.15 ( 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 249 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.637 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 114 GLU cc_start: 0.8237 (tt0) cc_final: 0.7856 (pt0) REVERT: A 273 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8227 (pt0) REVERT: B 123 LYS cc_start: 0.8188 (tttt) cc_final: 0.7782 (ttmp) REVERT: B 167 MET cc_start: 0.8104 (tpt) cc_final: 0.7902 (tpp) REVERT: L 74 LYS cc_start: 0.7569 (ttmm) cc_final: 0.7313 (mmmt) REVERT: H 69 MET cc_start: 0.8904 (mtt) cc_final: 0.8236 (mtt) REVERT: D 147 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: E 34 ASP cc_start: 0.8134 (m-30) cc_final: 0.7425 (m-30) REVERT: F 45 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7642 (mt) REVERT: F 80 MET cc_start: 0.8506 (tmm) cc_final: 0.8265 (tmm) REVERT: I 144 CYS cc_start: 0.6670 (t) cc_final: 0.6398 (t) REVERT: I 149 MET cc_start: 0.7602 (mmt) cc_final: 0.7343 (mmm) REVERT: J 34 ASP cc_start: 0.8168 (m-30) cc_final: 0.7542 (m-30) REVERT: J 74 LYS cc_start: 0.7827 (ttmm) cc_final: 0.6802 (tttp) REVERT: K 3 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6543 (pp30) REVERT: K 43 GLN cc_start: 0.8300 (mt0) cc_final: 0.8059 (mm110) REVERT: C 123 MET cc_start: 0.8450 (mtt) cc_final: 0.8223 (mtt) REVERT: C 140 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7600 (mmm160) REVERT: C 150 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: G 208 ASN cc_start: 0.7969 (t0) cc_final: 0.7639 (t160) REVERT: G 273 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: G 275 ASP cc_start: 0.7737 (t0) cc_final: 0.7410 (t70) REVERT: G 307 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.6609 (mmt180) outliers start: 54 outliers final: 30 residues processed: 233 average time/residue: 0.5702 time to fit residues: 148.0973 Evaluate side-chains 223 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 94 THR Chi-restraints excluded: chain D residue 147 ASP 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 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 20 VAL 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 246 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 280 ASP 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 266 MET 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: [160, 152, 37, 170, 2, 166, 31, 161, 175, 60, 91] chunk 160 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 161 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 chunk 91 optimal weight: 4.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** ** I 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 = 0.3381 r_free = 0.3381 target = 0.112972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094891 restraints weight = 23264.757| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.67 r_work: 0.3015 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17385 Z= 0.101 Angle : 0.500 6.310 23532 Z= 0.264 Chirality : 0.042 0.174 2556 Planarity : 0.004 0.049 3060 Dihedral : 4.103 18.048 2376 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.08 % Allowed : 16.89 % Favored : 81.04 % 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: -1.09 (0.17), residues: 2151 helix: 1.42 (0.30), residues: 324 sheet: -0.55 (0.20), residues: 699 loop : -1.50 (0.16), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 24 TYR 0.036 0.001 TYR C 195 PHE 0.008 0.001 PHE C 245 TRP 0.008 0.001 TRP D 83 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (17352) covalent geometry : angle 0.49251 / 0.26 (23457) SS BOND : bond 0.00291 / 0.16 ( 24) SS BOND : angle 1.67496 / 1.02 ( 48) hydrogen bonds : bond 0.03514 / 2.43 ( 603) hydrogen bonds : angle 4.64459 / 3.21 ( 1728) link_NAG-ASN : bond 0.00136 / 0.07 ( 9) link_NAG-ASN : angle 1.35640 / 0.84 ( 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 231 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.703 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 273 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: A 320 MET cc_start: 0.8605 (ptp) cc_final: 0.8341 (ptp) REVERT: B 123 LYS cc_start: 0.8250 (tttt) cc_final: 0.7974 (ttmp) REVERT: H 69 MET cc_start: 0.8908 (mtt) cc_final: 0.8167 (mtm) REVERT: D 74 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: D 171 ILE cc_start: 0.8295 (pt) cc_final: 0.7829 (mp) REVERT: E 34 ASP cc_start: 0.7954 (m-30) cc_final: 0.7309 (m-30) REVERT: F 80 MET cc_start: 0.8487 (tmm) cc_final: 0.8265 (tmm) REVERT: J 34 ASP cc_start: 0.7787 (m-30) cc_final: 0.7485 (m-30) REVERT: J 74 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7054 (tttp) REVERT: K 3 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6664 (pp30) REVERT: C 114 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8047 (pt0) REVERT: C 123 MET cc_start: 0.8447 (mtt) cc_final: 0.8227 (mtt) REVERT: C 140 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7640 (mmm160) REVERT: C 150 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: G 208 ASN cc_start: 0.7770 (t0) cc_final: 0.7474 (t160) outliers start: 38 outliers final: 21 residues processed: 221 average time/residue: 0.5831 time to fit residues: 143.7157 Evaluate side-chains 211 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 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 K residue 66 ARG 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 G residue 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 277 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: [62, 44, 12, 150, 179, 189, 176, 115, 5, 201, 26] chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A 224 ASN B 60 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.093608 restraints weight = 23289.810| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.65 r_work: 0.2988 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17385 Z= 0.149 Angle : 0.553 6.582 23532 Z= 0.289 Chirality : 0.044 0.181 2556 Planarity : 0.004 0.056 3060 Dihedral : 4.222 18.403 2376 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.51 % Allowed : 16.28 % Favored : 81.20 % 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: -1.18 (0.17), residues: 2151 helix: 1.22 (0.29), residues: 327 sheet: -0.60 (0.20), residues: 708 loop : -1.52 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 24 TYR 0.032 0.002 TYR C 195 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/Z covalent geometry : bond 0.00368 / 0.15 (17352) covalent geometry : angle 0.54475 / 0.29 (23457) SS BOND : bond 0.00358 / 0.21 ( 24) SS BOND : angle 1.92184 / 1.17 ( 48) hydrogen bonds : bond 0.03909 / 2.70 ( 603) hydrogen bonds : angle 4.72135 / 3.26 ( 1728) link_NAG-ASN : bond 0.00098 / 0.06 ( 9) link_NAG-ASN : angle 1.47340 / 0.90 ( 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 234 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 0.547 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: 0.8533 (OUTLIER) cc_final: 0.8253 (pt0) REVERT: B 123 LYS cc_start: 0.8255 (tttt) cc_final: 0.7989 (ttmp) REVERT: L 24 ARG cc_start: 0.8111 (mtp85) cc_final: 0.7657 (mtp85) REVERT: H 69 MET cc_start: 0.8885 (mtt) cc_final: 0.8247 (mtt) REVERT: D 171 ILE cc_start: 0.8313 (pt) cc_final: 0.7823 (mp) REVERT: E 34 ASP cc_start: 0.7985 (m-30) cc_final: 0.7321 (m-30) REVERT: F 69 MET cc_start: 0.8797 (mtt) cc_final: 0.8350 (mtm) REVERT: F 80 MET cc_start: 0.8396 (tmm) cc_final: 0.8174 (tmm) REVERT: J 34 ASP cc_start: 0.7923 (m-30) cc_final: 0.7474 (m-30) REVERT: J 74 LYS cc_start: 0.7933 (ttmm) cc_final: 0.7046 (tttp) REVERT: K 3 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6697 (pp30) REVERT: C 114 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8055 (pt0) REVERT: C 123 MET cc_start: 0.8465 (mtt) cc_final: 0.8247 (mtt) REVERT: C 150 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: G 208 ASN cc_start: 0.7823 (t0) cc_final: 0.7528 (t160) REVERT: G 307 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.6669 (mmt180) outliers start: 46 outliers final: 29 residues processed: 220 average time/residue: 0.5900 time to fit residues: 144.0291 Evaluate side-chains 213 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 B residue 160 SER Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain D residue 113 SER 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 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 K residue 20 VAL Chi-restraints excluded: chain K residue 66 ARG 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 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 266 MET 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: [14, 187, 123, 165, 19, 21, 162, 124, 71, 95, 104] chunk 14 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 G 157 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.093697 restraints weight = 23339.725| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.66 r_work: 0.3002 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17385 Z= 0.137 Angle : 0.541 6.847 23532 Z= 0.283 Chirality : 0.044 0.180 2556 Planarity : 0.004 0.061 3060 Dihedral : 4.209 18.304 2376 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.80 % Allowed : 17.16 % Favored : 81.04 % 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: -1.14 (0.17), residues: 2151 helix: 1.25 (0.29), residues: 327 sheet: -0.60 (0.20), residues: 708 loop : -1.48 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 24 TYR 0.026 0.002 TYR C 195 PHE 0.008 0.001 PHE A 294 TRP 0.011 0.001 TRP D 92 HIS 0.003 0.001 HIS G 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (17352) covalent geometry : angle 0.53302 / 0.28 (23457) SS BOND : bond 0.00365 / 0.20 ( 24) SS BOND : angle 1.90809 / 1.14 ( 48) hydrogen bonds : bond 0.03803 / 2.63 ( 603) hydrogen bonds : angle 4.70022 / 3.25 ( 1728) link_NAG-ASN : bond 0.00100 / 0.06 ( 9) link_NAG-ASN : angle 1.42655 / 0.86 ( 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 220 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.664 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 273 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8220 (pt0) REVERT: B 123 LYS cc_start: 0.8258 (tttt) cc_final: 0.7997 (ttmp) REVERT: B 160 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8610 (m) REVERT: H 69 MET cc_start: 0.8836 (mtt) cc_final: 0.8221 (mtt) REVERT: D 149 MET cc_start: 0.7467 (mmm) cc_final: 0.7081 (mtm) REVERT: D 171 ILE cc_start: 0.8326 (pt) cc_final: 0.7838 (mp) REVERT: E 34 ASP cc_start: 0.7960 (m-30) cc_final: 0.7299 (m-30) REVERT: F 80 MET cc_start: 0.8387 (tmm) cc_final: 0.8169 (tmm) REVERT: F 86 ASP cc_start: 0.8065 (m-30) cc_final: 0.7577 (m-30) REVERT: J 34 ASP cc_start: 0.7916 (m-30) cc_final: 0.7482 (m-30) REVERT: J 74 LYS cc_start: 0.7927 (ttmm) cc_final: 0.7064 (tttp) REVERT: K 3 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6706 (pp30) REVERT: C 123 MET cc_start: 0.8484 (mtt) cc_final: 0.8272 (mtt) REVERT: C 140 ARG cc_start: 0.7940 (mmm160) cc_final: 0.7727 (mmm160) REVERT: C 150 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: G 208 ASN cc_start: 0.7810 (t0) cc_final: 0.7515 (t160) REVERT: G 307 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.6665 (mmt180) outliers start: 33 outliers final: 22 residues processed: 211 average time/residue: 0.5963 time to fit residues: 139.8562 Evaluate side-chains 210 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 I residue 98 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 100 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: [137, 155, 183, 4, 136, 211, 133, 108, 45, 127, 179] chunk 137 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 179 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN B 60 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092241 restraints weight = 23364.023| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.65 r_work: 0.2970 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17385 Z= 0.222 Angle : 0.633 7.463 23532 Z= 0.328 Chirality : 0.047 0.213 2556 Planarity : 0.005 0.067 3060 Dihedral : 4.534 20.039 2376 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.13 % Allowed : 16.89 % Favored : 80.98 % 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: -1.41 (0.17), residues: 2151 helix: 0.81 (0.29), residues: 333 sheet: -0.70 (0.20), residues: 726 loop : -1.66 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 24 TYR 0.035 0.002 TYR C 195 PHE 0.013 0.002 PHE C 294 TRP 0.014 0.002 TRP D 92 HIS 0.005 0.001 HIS G 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.22 (17352) covalent geometry : angle 0.62276 / 0.32 (23457) SS BOND : bond 0.00469 / 0.27 ( 24) SS BOND : angle 2.31012 / 1.41 ( 48) hydrogen bonds : bond 0.04493 / 3.12 ( 603) hydrogen bonds : angle 4.95560 / 3.42 ( 1728) link_NAG-ASN : bond 0.00181 / 0.12 ( 9) link_NAG-ASN : angle 1.67279 / 1.04 ( 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 223 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.712 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 273 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: B 123 LYS cc_start: 0.8281 (tttt) cc_final: 0.8012 (ttmp) REVERT: H 69 MET cc_start: 0.8850 (mtt) cc_final: 0.8205 (mtt) REVERT: D 149 MET cc_start: 0.7528 (mmm) cc_final: 0.6823 (mtm) REVERT: D 171 ILE cc_start: 0.8362 (pt) cc_final: 0.7844 (mp) REVERT: E 34 ASP cc_start: 0.7985 (m-30) cc_final: 0.7319 (m-30) REVERT: F 80 MET cc_start: 0.8402 (tmm) cc_final: 0.8041 (tmm) REVERT: F 86 ASP cc_start: 0.8111 (m-30) cc_final: 0.7565 (m-30) REVERT: J 34 ASP cc_start: 0.7976 (m-30) cc_final: 0.7499 (m-30) REVERT: J 74 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7040 (tttp) REVERT: K 3 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6682 (pp30) REVERT: C 140 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7713 (mmm160) REVERT: C 150 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: C 195 TYR cc_start: 0.7259 (m-10) cc_final: 0.6980 (m-10) REVERT: G 208 ASN cc_start: 0.7909 (t0) cc_final: 0.7599 (t160) REVERT: G 307 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.6684 (mmt180) outliers start: 39 outliers final: 28 residues processed: 211 average time/residue: 0.6174 time to fit residues: 144.6411 Evaluate side-chains 214 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 B residue 160 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 9 LEU 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 156 THR Chi-restraints excluded: chain I residue 160 SER 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 66 ARG 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 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 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: [78, 180, 99, 45, 47, 61, 90, 170, 182, 127, 146] chunk 78 optimal weight: 0.4980 chunk 180 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.094783 restraints weight = 23347.455| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.66 r_work: 0.3017 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17385 Z= 0.109 Angle : 0.508 5.785 23532 Z= 0.268 Chirality : 0.043 0.176 2556 Planarity : 0.004 0.062 3060 Dihedral : 4.140 17.190 2376 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.86 % Allowed : 17.05 % 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: -1.09 (0.17), residues: 2151 helix: 1.39 (0.29), residues: 333 sheet: -0.57 (0.20), residues: 720 loop : -1.50 (0.16), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 24 TYR 0.026 0.001 TYR C 195 PHE 0.010 0.001 PHE C 245 TRP 0.008 0.001 TRP D 83 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (17352) covalent geometry : angle 0.50095 / 0.27 (23457) SS BOND : bond 0.00318 / 0.17 ( 24) SS BOND : angle 1.69907 / 1.01 ( 48) hydrogen bonds : bond 0.03556 / 2.46 ( 603) hydrogen bonds : angle 4.62452 / 3.21 ( 1728) link_NAG-ASN : bond 0.00117 / 0.06 ( 9) link_NAG-ASN : angle 1.30096 / 0.77 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6009.87 seconds wall clock time: 103 minutes 4.82 seconds (6184.82 seconds total)