Starting phenix.real_space_refine on Sat Sep 12 16:27:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wxl_21961/09_2026/6wxl_21961.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wxl_21961/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6wxl_21961/09_2026/6wxl_21961.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wxl_21961/09_2026/6wxl_21961.cif" model { file = "/net/cci-nas-00/data/ceres_data/6wxl_21961/09_2026/6wxl_21961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wxl_21961/09_2026/6wxl_21961.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wxl_21961/09_2026/6wxl_21961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wxl_21961/09_2026/6wxl_21961.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.220 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 10593 2.51 5 N 2970 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 3.45, 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 C 14 " - pdb=" SG CYS D 137 " distance=2.07 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS I 137 " distance=2.07 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 38 " " NAG B 301 " - " ASN B 82 " " NAG B 302 " - " ASN B 154 " " NAG C 401 " - " ASN C 38 " " NAG D 301 " - " ASN D 82 " " NAG D 302 " - " ASN D 154 " " NAG G 401 " - " ASN G 38 " " NAG I 301 " - " ASN I 82 " " NAG I 302 " - " ASN I 154 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 726.6 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: 0.39 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: 3.16 Time building geometry restraints manager: 1.86 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: 824 33.47 - 50.20: 183 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: 5.020 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.640 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- 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 / 1.03 ( 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 : 0.673 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: 0.7489 time to fit residues: 260.4267 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 : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 2.48 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- 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 / 1.43 ( 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 : 0.674 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: 0.7661 (ttmm) cc_final: 0.7368 (mmmt) REVERT: H 69 MET cc_start: 0.8936 (mtt) cc_final: 0.8640 (mtt) REVERT: D 74 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: E 34 ASP cc_start: 0.8227 (m-30) cc_final: 0.7567 (m-30) REVERT: E 69 THR cc_start: 0.8765 (p) cc_final: 0.8455 (m) REVERT: E 74 LYS cc_start: 0.7910 (ttmm) cc_final: 0.6914 (tptt) REVERT: E 107 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6704 (ttmm) REVERT: J 34 ASP cc_start: 0.8116 (m-30) cc_final: 0.7464 (m-30) REVERT: J 74 LYS cc_start: 0.7982 (ttmm) cc_final: 0.6862 (tmtm) REVERT: K 6 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8676 (mt0) REVERT: C 42 THR cc_start: 0.8348 (m) cc_final: 0.8103 (p) REVERT: C 140 ARG cc_start: 0.7890 (mmm160) cc_final: 0.7613 (mmm160) REVERT: C 190 GLU cc_start: 0.7366 (tp30) cc_final: 0.7095 (tt0) REVERT: G 208 ASN cc_start: 0.8103 (t0) cc_final: 0.7850 (t160) outliers start: 50 outliers final: 16 residues processed: 255 average time/residue: 0.7082 time to fit residues: 198.9003 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 : 0.718 ------------------------------------------------------------------------------- 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: 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: 0.7980 chunk 73 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.107208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.087019 restraints weight = 23803.199| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.05 r_work: 0.2864 rms_B_bonded: 2.47 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: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17385 Z= 0.129 Angle : 0.541 7.991 23532 Z= 0.287 Chirality : 0.044 0.183 2556 Planarity : 0.004 0.056 3060 Dihedral : 4.436 20.783 2376 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.62 % Allowed : 12.57 % Favored : 84.81 % 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: -0.01 (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 0.016 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 0.00309 / 0.13 (17352) covalent geometry : angle 0.53082 / 0.28 (23457) SS BOND : bond 0.00384 / 0.21 ( 24) SS BOND : angle 2.12279 / 1.27 ( 48) hydrogen bonds : bond 0.04229 / 2.94 ( 603) hydrogen bonds : angle 5.18452 / 3.58 ( 1728) link_NAG-ASN : bond 0.00176 / 0.11 ( 9) link_NAG-ASN : angle 1.38953 / 0.83 ( 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 258 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8189 (tt0) cc_final: 0.7818 (mp0) REVERT: A 273 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: B 102 MET cc_start: 0.8040 (ttp) cc_final: 0.7785 (ttp) REVERT: L 24 ARG cc_start: 0.8288 (ptm160) cc_final: 0.7855 (mtp85) REVERT: L 74 LYS cc_start: 0.7554 (ttmm) cc_final: 0.7285 (mmmt) REVERT: L 89 MET cc_start: 0.8796 (ttp) cc_final: 0.8531 (ttp) REVERT: H 69 MET cc_start: 0.8954 (mtt) cc_final: 0.8523 (mtt) REVERT: D 30 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.5421 (mp10) REVERT: D 74 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: E 24 ARG cc_start: 0.8143 (ptm160) cc_final: 0.7889 (ptm160) REVERT: E 34 ASP cc_start: 0.8162 (m-30) cc_final: 0.7446 (m-30) REVERT: E 74 LYS cc_start: 0.7779 (ttmm) cc_final: 0.6762 (tptt) REVERT: F 80 MET cc_start: 0.8715 (tmm) cc_final: 0.8417 (tmm) REVERT: I 144 CYS cc_start: 0.6503 (t) cc_final: 0.6218 (t) REVERT: I 149 MET cc_start: 0.7561 (mmt) cc_final: 0.7163 (mmm) REVERT: J 34 ASP cc_start: 0.8032 (m-30) cc_final: 0.7573 (m-30) REVERT: J 74 LYS cc_start: 0.7924 (ttmm) cc_final: 0.6838 (tttp) REVERT: C 123 MET cc_start: 0.8381 (mtt) cc_final: 0.8146 (mtt) REVERT: C 150 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: C 151 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8475 (mmp) REVERT: C 190 GLU cc_start: 0.7193 (tp30) cc_final: 0.6971 (tt0) REVERT: C 243 VAL cc_start: 0.6817 (OUTLIER) cc_final: 0.6462 (t) REVERT: C 273 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: G 208 ASN cc_start: 0.7891 (t0) cc_final: 0.7621 (t160) outliers start: 48 outliers final: 17 residues processed: 242 average time/residue: 0.6287 time to fit residues: 169.8569 Evaluate side-chains 221 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain 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: chunk 205 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 203 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 H 6 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN C 208 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.086751 restraints weight = 23649.969| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.04 r_work: 0.2861 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2517 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= 0.145 Angle : 0.544 7.079 23532 Z= 0.286 Chirality : 0.044 0.188 2556 Planarity : 0.004 0.054 3060 Dihedral : 4.335 18.886 2376 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.17 % Allowed : 13.66 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2151 helix: 0.49 (0.29), residues: 333 sheet: -0.90 (0.19), residues: 717 loop : -1.82 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 24 TYR 0.018 0.002 TYR E 49 PHE 0.010 0.001 PHE A 251 TRP 0.011 0.001 TRP D 92 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.14 (17352) covalent geometry : angle 0.53595 / 0.28 (23457) SS BOND : bond 0.00393 / 0.22 ( 24) SS BOND : angle 1.84846 / 1.09 ( 48) hydrogen bonds : bond 0.04102 / 2.85 ( 603) hydrogen bonds : angle 4.96748 / 3.44 ( 1728) link_NAG-ASN : bond 0.00135 / 0.09 ( 9) link_NAG-ASN : angle 1.50693 / 0.92 ( 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 263 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8272 (tt0) cc_final: 0.7898 (mp0) REVERT: A 273 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8277 (pt0) REVERT: B 123 LYS cc_start: 0.8191 (tttt) cc_final: 0.7719 (ttmt) REVERT: L 24 ARG cc_start: 0.8233 (ptm160) cc_final: 0.7903 (mtp85) REVERT: L 74 LYS cc_start: 0.7558 (ttmm) cc_final: 0.7295 (mmmt) REVERT: H 69 MET cc_start: 0.8954 (mtt) cc_final: 0.8306 (mtm) REVERT: D 74 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: D 171 ILE cc_start: 0.8227 (pt) cc_final: 0.7688 (mp) REVERT: E 34 ASP cc_start: 0.8162 (m-30) cc_final: 0.7445 (m-30) REVERT: E 74 LYS cc_start: 0.7775 (ttmm) cc_final: 0.6714 (tptt) REVERT: F 80 MET cc_start: 0.8688 (tmm) cc_final: 0.8375 (tmm) REVERT: I 123 LYS cc_start: 0.8219 (tttt) cc_final: 0.7959 (ttmm) REVERT: I 144 CYS cc_start: 0.6577 (t) cc_final: 0.6318 (t) REVERT: I 149 MET cc_start: 0.7526 (mmt) cc_final: 0.7238 (mmm) REVERT: J 34 ASP cc_start: 0.8150 (m-30) cc_final: 0.7684 (m-30) REVERT: J 74 LYS cc_start: 0.7810 (ttmm) cc_final: 0.6751 (tptt) REVERT: K 3 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6458 (pp30) REVERT: K 43 GLN cc_start: 0.8346 (mt0) cc_final: 0.8079 (mm110) REVERT: C 114 GLU cc_start: 0.7943 (tt0) cc_final: 0.7404 (pt0) REVERT: C 123 MET cc_start: 0.8403 (mtt) cc_final: 0.8200 (mtt) REVERT: C 140 ARG cc_start: 0.7906 (mmm160) cc_final: 0.7564 (mmm160) REVERT: C 150 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: C 243 VAL cc_start: 0.6810 (OUTLIER) cc_final: 0.6486 (t) REVERT: C 273 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: G 208 ASN cc_start: 0.7893 (t0) cc_final: 0.7604 (t160) REVERT: G 307 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.6559 (mmt180) outliers start: 58 outliers final: 23 residues processed: 242 average time/residue: 0.6296 time to fit residues: 169.9846 Evaluate side-chains 221 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain H residue 66 ARG 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 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 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 237 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 307 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 71 optimal weight: 0.0070 chunk 132 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 95 optimal weight: 0.0870 chunk 90 optimal weight: 0.8980 overall best weight: 0.5776 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.107684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.087460 restraints weight = 23706.626| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.06 r_work: 0.2885 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17385 Z= 0.098 Angle : 0.491 7.113 23532 Z= 0.260 Chirality : 0.042 0.175 2556 Planarity : 0.004 0.049 3060 Dihedral : 4.078 18.186 2376 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.13 % Allowed : 15.30 % Favored : 82.57 % 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: -1.35 (0.17), residues: 2151 helix: 1.09 (0.29), residues: 333 sheet: -0.71 (0.19), residues: 717 loop : -1.66 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 24 TYR 0.013 0.001 TYR E 49 PHE 0.007 0.001 PHE A 245 TRP 0.009 0.001 TRP D 83 HIS 0.002 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (17352) covalent geometry : angle 0.48397 / 0.26 (23457) SS BOND : bond 0.00298 / 0.16 ( 24) SS BOND : angle 1.65237 / 0.95 ( 48) hydrogen bonds : bond 0.03515 / 2.44 ( 603) hydrogen bonds : angle 4.68097 / 3.23 ( 1728) link_NAG-ASN : bond 0.00177 / 0.10 ( 9) link_NAG-ASN : angle 1.30191 / 0.78 ( 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 250 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8168 (tt0) cc_final: 0.7709 (pt0) REVERT: A 241 ASP cc_start: 0.8379 (m-30) cc_final: 0.8156 (t0) REVERT: A 255 ASP cc_start: 0.8590 (t0) cc_final: 0.8291 (t0) REVERT: A 320 MET cc_start: 0.8610 (ptp) cc_final: 0.8334 (ptp) REVERT: B 102 MET cc_start: 0.8113 (ttp) cc_final: 0.7882 (ttp) REVERT: B 123 LYS cc_start: 0.8182 (tttt) cc_final: 0.7753 (ttmt) REVERT: L 24 ARG cc_start: 0.8193 (ptm160) cc_final: 0.7899 (mtp-110) REVERT: L 74 LYS cc_start: 0.7537 (ttmm) cc_final: 0.7305 (mmmt) REVERT: H 69 MET cc_start: 0.8935 (mtt) cc_final: 0.8436 (mtt) REVERT: D 171 ILE cc_start: 0.8086 (pt) cc_final: 0.7603 (mp) REVERT: E 34 ASP cc_start: 0.8109 (m-30) cc_final: 0.7455 (m-30) REVERT: E 74 LYS cc_start: 0.7784 (ttmm) cc_final: 0.6739 (tptt) REVERT: F 80 MET cc_start: 0.8653 (tmm) cc_final: 0.8354 (tmm) REVERT: J 34 ASP cc_start: 0.7956 (m-30) cc_final: 0.7505 (m-30) REVERT: J 74 LYS cc_start: 0.7764 (ttmm) cc_final: 0.6713 (tptt) REVERT: K 3 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6580 (pp30) REVERT: K 43 GLN cc_start: 0.8333 (mt0) cc_final: 0.8058 (mm110) REVERT: C 114 GLU cc_start: 0.7880 (tt0) cc_final: 0.7470 (pt0) REVERT: C 123 MET cc_start: 0.8376 (mtt) cc_final: 0.8155 (mtt) REVERT: C 150 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: C 243 VAL cc_start: 0.6860 (p) cc_final: 0.6632 (t) REVERT: G 208 ASN cc_start: 0.7790 (t0) cc_final: 0.7476 (t160) REVERT: G 273 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8009 (pt0) outliers start: 39 outliers final: 17 residues processed: 238 average time/residue: 0.6431 time to fit residues: 170.0730 Evaluate side-chains 206 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 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 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 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 273 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 92 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 140 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.699 > 50:) chunk 172 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A 224 ASN B 60 ASN B 125 GLN L 27 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN C 211 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.085242 restraints weight = 23750.267| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.03 r_work: 0.2851 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17385 Z= 0.213 Angle : 0.619 9.261 23532 Z= 0.322 Chirality : 0.047 0.213 2556 Planarity : 0.004 0.055 3060 Dihedral : 4.474 19.741 2376 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.28 % Allowed : 14.64 % Favored : 82.08 % 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: 0.71 (0.29), residues: 327 sheet: -0.74 (0.19), residues: 723 loop : -1.71 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 54 TYR 0.023 0.002 TYR L 49 PHE 0.012 0.002 PHE A 251 TRP 0.014 0.002 TRP D 92 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.21 (17352) covalent geometry : angle 0.60847 / 0.32 (23457) SS BOND : bond 0.00449 / 0.26 ( 24) SS BOND : angle 2.34818 / 1.41 ( 48) hydrogen bonds : bond 0.04461 / 3.10 ( 603) hydrogen bonds : angle 4.97402 / 3.44 ( 1728) link_NAG-ASN : bond 0.00189 / 0.13 ( 9) link_NAG-ASN : angle 1.70739 / 1.11 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 196 time to evaluate : 0.716 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: 0.8273 (tt0) cc_final: 0.7882 (pt0) REVERT: A 273 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: B 123 LYS cc_start: 0.8185 (tttt) cc_final: 0.7781 (ttmp) REVERT: L 24 ARG cc_start: 0.8195 (ptm160) cc_final: 0.7978 (mtp85) REVERT: L 74 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7318 (mmmt) REVERT: H 69 MET cc_start: 0.8912 (mtt) cc_final: 0.8262 (mtt) REVERT: D 102 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7224 (ttt) REVERT: D 171 ILE cc_start: 0.8126 (pt) cc_final: 0.7600 (mp) REVERT: E 34 ASP cc_start: 0.8135 (m-30) cc_final: 0.7425 (m-30) REVERT: F 45 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7659 (mt) REVERT: F 80 MET cc_start: 0.8500 (tmm) cc_final: 0.8285 (tmm) REVERT: I 144 CYS cc_start: 0.6658 (t) cc_final: 0.6378 (t) REVERT: I 149 MET cc_start: 0.7600 (mmt) cc_final: 0.7347 (mmm) REVERT: I 162 TYR cc_start: 0.8671 (m-80) cc_final: 0.8459 (m-80) REVERT: I 168 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: J 34 ASP cc_start: 0.8157 (m-30) cc_final: 0.7543 (m-30) REVERT: J 74 LYS cc_start: 0.7831 (ttmm) cc_final: 0.6806 (tttp) REVERT: K 3 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6563 (pp30) REVERT: K 43 GLN cc_start: 0.8312 (mt0) cc_final: 0.8057 (mm110) REVERT: C 114 GLU cc_start: 0.8105 (tt0) cc_final: 0.7649 (pt0) REVERT: C 123 MET cc_start: 0.8441 (mtt) cc_final: 0.8224 (mtt) REVERT: C 140 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7584 (mmm160) REVERT: C 150 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: G 208 ASN cc_start: 0.7968 (t0) cc_final: 0.7628 (t160) REVERT: G 273 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: G 307 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.6612 (mmt180) outliers start: 60 outliers final: 35 residues processed: 237 average time/residue: 0.6505 time to fit residues: 171.6013 Evaluate side-chains 233 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 168 GLN Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 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: chunk 160 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 170 optimal weight: 8.9990 chunk 2 optimal weight: 0.0980 chunk 166 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 91 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.113086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.095049 restraints weight = 23267.906| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.66 r_work: 0.3000 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2908 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= 0.099 Angle : 0.497 6.088 23532 Z= 0.263 Chirality : 0.042 0.172 2556 Planarity : 0.004 0.049 3060 Dihedral : 4.091 17.821 2376 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.24 % Allowed : 16.12 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.17), residues: 2151 helix: 1.41 (0.30), residues: 324 sheet: -0.61 (0.20), residues: 708 loop : -1.52 (0.16), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 24 TYR 0.035 0.001 TYR C 195 PHE 0.008 0.001 PHE C 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 0.00227 / 0.10 (17352) covalent geometry : angle 0.48980 / 0.26 (23457) SS BOND : bond 0.00276 / 0.16 ( 24) SS BOND : angle 1.67118 / 0.97 ( 48) hydrogen bonds : bond 0.03493 / 2.42 ( 603) hydrogen bonds : angle 4.63161 / 3.20 ( 1728) link_NAG-ASN : bond 0.00139 / 0.08 ( 9) link_NAG-ASN : angle 1.37747 / 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 240 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 0.691 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: 0.8523 (OUTLIER) cc_final: 0.8249 (pt0) REVERT: B 123 LYS cc_start: 0.8237 (tttt) cc_final: 0.7964 (ttmt) REVERT: H 69 MET cc_start: 0.8913 (mtt) cc_final: 0.8305 (mtt) REVERT: D 74 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: D 124 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7432 (mtp180) REVERT: D 171 ILE cc_start: 0.8305 (pt) cc_final: 0.7831 (mp) REVERT: E 34 ASP cc_start: 0.7947 (m-30) cc_final: 0.7295 (m-30) REVERT: F 80 MET cc_start: 0.8575 (tmm) cc_final: 0.8213 (tmm) REVERT: J 34 ASP cc_start: 0.7778 (m-30) cc_final: 0.7474 (m-30) REVERT: J 60 ASP cc_start: 0.7974 (m-30) cc_final: 0.7458 (t0) REVERT: J 74 LYS cc_start: 0.7909 (ttmm) cc_final: 0.7052 (tttp) REVERT: K 3 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6668 (pp30) REVERT: C 114 GLU cc_start: 0.8002 (tt0) cc_final: 0.7714 (pt0) REVERT: C 123 MET cc_start: 0.8445 (mtt) cc_final: 0.8232 (mtt) REVERT: C 140 ARG cc_start: 0.7908 (mmm160) cc_final: 0.7604 (mmm160) REVERT: C 150 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: G 208 ASN cc_start: 0.7709 (t0) cc_final: 0.7412 (t160) outliers start: 41 outliers final: 19 residues processed: 227 average time/residue: 0.6255 time to fit residues: 157.9450 Evaluate side-chains 211 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 K residue 3 GLN 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 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: chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 224 ASN B 60 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092227 restraints weight = 23379.990| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.66 r_work: 0.2968 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17385 Z= 0.218 Angle : 0.629 7.807 23532 Z= 0.327 Chirality : 0.047 0.219 2556 Planarity : 0.005 0.061 3060 Dihedral : 4.485 19.869 2376 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.35 % Allowed : 16.56 % 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: -1.41 (0.17), residues: 2151 helix: 0.84 (0.29), residues: 333 sheet: -0.68 (0.19), residues: 726 loop : -1.68 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 24 TYR 0.034 0.002 TYR C 195 PHE 0.014 0.002 PHE C 294 TRP 0.015 0.002 TRP K 47 HIS 0.005 0.001 HIS G 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.22 (17352) covalent geometry : angle 0.61978 / 0.32 (23457) SS BOND : bond 0.00456 / 0.27 ( 24) SS BOND : angle 2.19801 / 1.33 ( 48) hydrogen bonds : bond 0.04482 / 3.11 ( 603) hydrogen bonds : angle 4.95096 / 3.42 ( 1728) link_NAG-ASN : bond 0.00200 / 0.14 ( 9) link_NAG-ASN : angle 1.67881 / 1.04 ( 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 232 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.725 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: 0.8509 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: B 123 LYS cc_start: 0.8279 (tttt) cc_final: 0.8002 (ttmp) REVERT: L 24 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7710 (mtp85) REVERT: H 69 MET cc_start: 0.8874 (mtt) cc_final: 0.8341 (mtt) REVERT: D 171 ILE cc_start: 0.8373 (pt) cc_final: 0.7849 (mp) REVERT: E 34 ASP cc_start: 0.7992 (m-30) cc_final: 0.7325 (m-30) REVERT: F 80 MET cc_start: 0.8408 (tmm) cc_final: 0.8033 (tmm) REVERT: I 168 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: J 34 ASP cc_start: 0.7994 (m-30) cc_final: 0.7518 (m-30) REVERT: J 74 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7014 (tttp) REVERT: K 3 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6670 (pp30) REVERT: C 114 GLU cc_start: 0.8057 (tt0) cc_final: 0.7758 (pt0) REVERT: C 123 MET cc_start: 0.8503 (mtt) cc_final: 0.8276 (mtt) REVERT: C 150 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: C 295 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7608 (pp30) REVERT: G 208 ASN cc_start: 0.7921 (t0) cc_final: 0.7612 (t160) outliers start: 43 outliers final: 28 residues processed: 219 average time/residue: 0.6834 time to fit residues: 165.6492 Evaluate side-chains 219 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain L residue 9 LEU 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 147 ASP Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 168 GLN 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 K residue 100 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain G residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 14 optimal weight: 0.8980 chunk 187 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 124 optimal weight: 0.0040 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 104 optimal weight: 0.0010 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 B 125 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095258 restraints weight = 23315.561| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.66 r_work: 0.3026 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3029 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= 0.095 Angle : 0.497 6.675 23532 Z= 0.263 Chirality : 0.042 0.175 2556 Planarity : 0.004 0.059 3060 Dihedral : 4.072 17.286 2376 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.69 % Allowed : 17.27 % 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: -1.04 (0.17), residues: 2151 helix: 1.47 (0.30), residues: 327 sheet: -0.53 (0.20), residues: 705 loop : -1.46 (0.16), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 24 TYR 0.032 0.001 TYR C 195 PHE 0.009 0.001 PHE C 245 TRP 0.009 0.001 TRP D 83 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (17352) covalent geometry : angle 0.49103 / 0.26 (23457) SS BOND : bond 0.00284 / 0.16 ( 24) SS BOND : angle 1.55690 / 0.91 ( 48) hydrogen bonds : bond 0.03408 / 2.36 ( 603) hydrogen bonds : angle 4.60075 / 3.18 ( 1728) link_NAG-ASN : bond 0.00150 / 0.08 ( 9) link_NAG-ASN : angle 1.30731 / 0.77 ( 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 227 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.704 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: 0.8528 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: A 277 CYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6613 (p) REVERT: B 123 LYS cc_start: 0.8236 (tttt) cc_final: 0.7985 (ttmp) REVERT: H 69 MET cc_start: 0.8843 (mtt) cc_final: 0.8252 (mtt) REVERT: D 124 ARG cc_start: 0.7936 (mtt90) cc_final: 0.7494 (mtp180) REVERT: D 149 MET cc_start: 0.7271 (mmm) cc_final: 0.6972 (mtm) REVERT: D 171 ILE cc_start: 0.8308 (pt) cc_final: 0.7848 (mp) REVERT: E 34 ASP cc_start: 0.7972 (m-30) cc_final: 0.7316 (m-30) REVERT: F 66 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7771 (ptm160) REVERT: F 69 MET cc_start: 0.8800 (mtt) cc_final: 0.8308 (mtm) REVERT: F 80 MET cc_start: 0.8562 (tmm) cc_final: 0.8192 (tmm) REVERT: J 34 ASP cc_start: 0.7724 (m-30) cc_final: 0.7378 (m-30) REVERT: J 60 ASP cc_start: 0.7911 (m-30) cc_final: 0.7497 (t0) REVERT: J 74 LYS cc_start: 0.7918 (ttmm) cc_final: 0.7090 (tttp) REVERT: K 3 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6717 (pp30) REVERT: C 114 GLU cc_start: 0.8040 (tt0) cc_final: 0.7789 (pt0) REVERT: C 123 MET cc_start: 0.8481 (mtt) cc_final: 0.8274 (mtt) REVERT: C 140 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7593 (mmm160) REVERT: C 150 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: G 208 ASN cc_start: 0.7749 (t0) cc_final: 0.7443 (t160) outliers start: 31 outliers final: 19 residues processed: 217 average time/residue: 0.6676 time to fit residues: 160.5088 Evaluate side-chains 208 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 D residue 156 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 66 ARG 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 J residue 33 LEU Chi-restraints excluded: chain K residue 3 GLN 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 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 277 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 137 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 179 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.094637 restraints weight = 23255.583| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.66 r_work: 0.3016 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17385 Z= 0.115 Angle : 0.520 6.802 23532 Z= 0.272 Chirality : 0.043 0.171 2556 Planarity : 0.004 0.065 3060 Dihedral : 4.071 17.413 2376 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.37 % Allowed : 17.98 % Favored : 80.66 % 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: -0.99 (0.17), residues: 2151 helix: 1.51 (0.29), residues: 333 sheet: -0.52 (0.20), residues: 708 loop : -1.44 (0.16), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 24 TYR 0.025 0.001 TYR C 195 PHE 0.007 0.001 PHE C 245 TRP 0.010 0.001 TRP B 92 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 (17352) covalent geometry : angle 0.51304 / 0.27 (23457) SS BOND : bond 0.00310 / 0.18 ( 24) SS BOND : angle 1.65536 / 0.98 ( 48) hydrogen bonds : bond 0.03583 / 2.47 ( 603) hydrogen bonds : angle 4.59785 / 3.18 ( 1728) link_NAG-ASN : bond 0.00107 / 0.07 ( 9) link_NAG-ASN : angle 1.34242 / 0.80 ( 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 213 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.714 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: 0.8490 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: A 277 CYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6636 (p) REVERT: B 123 LYS cc_start: 0.8241 (tttt) cc_final: 0.7987 (ttmp) REVERT: H 69 MET cc_start: 0.8866 (mtt) cc_final: 0.8346 (mtt) REVERT: D 124 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7482 (mtp180) REVERT: D 149 MET cc_start: 0.7458 (mmm) cc_final: 0.7008 (mtm) REVERT: D 171 ILE cc_start: 0.8320 (pt) cc_final: 0.7842 (mp) REVERT: E 34 ASP cc_start: 0.7963 (m-30) cc_final: 0.7280 (m-30) REVERT: F 66 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7754 (ptm160) REVERT: F 69 MET cc_start: 0.8783 (mtt) cc_final: 0.8279 (mtm) REVERT: F 80 MET cc_start: 0.8472 (tmm) cc_final: 0.8101 (tmm) REVERT: J 34 ASP cc_start: 0.7889 (m-30) cc_final: 0.7466 (m-30) REVERT: J 60 ASP cc_start: 0.7891 (m-30) cc_final: 0.7481 (t0) REVERT: J 74 LYS cc_start: 0.7917 (ttmm) cc_final: 0.7093 (tttp) REVERT: K 3 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6780 (pp30) REVERT: C 114 GLU cc_start: 0.8056 (tt0) cc_final: 0.7837 (pt0) REVERT: C 123 MET cc_start: 0.8463 (mtt) cc_final: 0.8246 (mtt) REVERT: C 140 ARG cc_start: 0.7910 (mmm160) cc_final: 0.7590 (mmm160) REVERT: C 150 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: G 208 ASN cc_start: 0.7694 (t0) cc_final: 0.7422 (t160) outliers start: 25 outliers final: 18 residues processed: 206 average time/residue: 0.6840 time to fit residues: 155.9249 Evaluate side-chains 209 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 D residue 156 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 3 GLN 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 214 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 277 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 78 optimal weight: 0.6980 chunk 180 optimal weight: 0.0670 chunk 99 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 61 optimal weight: 0.2980 chunk 90 optimal weight: 0.0770 chunk 170 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.113423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095456 restraints weight = 23358.722| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.66 r_work: 0.3029 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17385 Z= 0.100 Angle : 0.496 6.766 23532 Z= 0.261 Chirality : 0.042 0.176 2556 Planarity : 0.004 0.064 3060 Dihedral : 3.977 16.776 2376 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.64 % Allowed : 17.65 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2151 helix: 1.70 (0.29), residues: 333 sheet: -0.47 (0.20), residues: 708 loop : -1.38 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 24 TYR 0.024 0.001 TYR C 195 PHE 0.009 0.001 PHE L 98 TRP 0.009 0.001 TRP D 83 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (17352) covalent geometry : angle 0.48951 / 0.26 (23457) SS BOND : bond 0.00299 / 0.16 ( 24) SS BOND : angle 1.53313 / 0.90 ( 48) hydrogen bonds : bond 0.03395 / 2.35 ( 603) hydrogen bonds : angle 4.49846 / 3.11 ( 1728) link_NAG-ASN : bond 0.00112 / 0.06 ( 9) link_NAG-ASN : angle 1.27798 / 0.75 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6476.11 seconds wall clock time: 111 minutes 4.21 seconds (6664.21 seconds total)