Starting phenix.real_space_refine on Thu Mar 5 23:54:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t72_10389/03_2026/6t72_10389.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t72_10389/03_2026/6t72_10389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t72_10389/03_2026/6t72_10389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t72_10389/03_2026/6t72_10389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t72_10389/03_2026/6t72_10389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t72_10389/03_2026/6t72_10389.map" } resolution = 3.7 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= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians Ca 42 9.91 5 S 14 5.16 5 C 16464 2.51 5 N 4046 2.21 5 O 5712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26278 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, Y, 0, D, F, H, J, L, N, P, R, T, V, X, Z, 1 Time building chain proxies: 2.40, per 1000 atoms: 0.09 Number of scatterers: 26278 At special positions: 0 Unit cell: (156.6, 157.68, 157.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 42 19.99 S 14 16.00 O 5712 8.00 N 4046 7.00 C 16464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 ?1-3 " BMA 1 1 " - " MRH 1 2 " " MRH 1 2 " - " MRH 1 3 " " BMA 1 4 " - " MRH 1 5 " " MRH 1 5 " - " MRH 1 6 " " BMA 1 7 " - " MRH 1 8 " " MRH 1 8 " - " MRH 1 9 " " BMA 1 10 " - " MRH 1 11 " " MRH 1 11 " - " MRH 1 12 " " BMA B 1 " - " MRH B 2 " " MRH B 2 " - " MRH B 3 " " BMA B 4 " - " MRH B 5 " " MRH B 5 " - " MRH B 6 " " BMA B 7 " - " MRH B 8 " " MRH B 8 " - " MRH B 9 " " BMA B 10 " - " MRH B 11 " " MRH B 11 " - " MRH B 12 " " BMA D 1 " - " MRH D 2 " " MRH D 2 " - " MRH D 3 " " BMA D 4 " - " MRH D 5 " " MRH D 5 " - " MRH D 6 " " BMA D 7 " - " MRH D 8 " " MRH D 8 " - " MRH D 9 " " BMA D 10 " - " MRH D 11 " " MRH D 11 " - " MRH D 12 " " BMA F 1 " - " MRH F 2 " " MRH F 2 " - " MRH F 3 " " BMA F 4 " - " MRH F 5 " " MRH F 5 " - " MRH F 6 " " BMA F 7 " - " MRH F 8 " " MRH F 8 " - " MRH F 9 " " BMA F 10 " - " MRH F 11 " " MRH F 11 " - " MRH F 12 " " BMA H 1 " - " MRH H 2 " " MRH H 2 " - " MRH H 3 " " BMA H 4 " - " MRH H 5 " " MRH H 5 " - " MRH H 6 " " BMA H 7 " - " MRH H 8 " " MRH H 8 " - " MRH H 9 " " BMA H 10 " - " MRH H 11 " " MRH H 11 " - " MRH H 12 " " BMA J 1 " - " MRH J 2 " " MRH J 2 " - " MRH J 3 " " BMA J 4 " - " MRH J 5 " " MRH J 5 " - " MRH J 6 " " BMA J 7 " - " MRH J 8 " " MRH J 8 " - " MRH J 9 " " BMA J 10 " - " MRH J 11 " " MRH J 11 " - " MRH J 12 " " BMA L 1 " - " MRH L 2 " " MRH L 2 " - " MRH L 3 " " BMA L 4 " - " MRH L 5 " " MRH L 5 " - " MRH L 6 " " BMA L 7 " - " MRH L 8 " " MRH L 8 " - " MRH L 9 " " BMA L 10 " - " MRH L 11 " " MRH L 11 " - " MRH L 12 " " BMA N 1 " - " MRH N 2 " " MRH N 2 " - " MRH N 3 " " BMA N 4 " - " MRH N 5 " " MRH N 5 " - " MRH N 6 " " BMA N 7 " - " MRH N 8 " " MRH N 8 " - " MRH N 9 " " BMA N 10 " - " MRH N 11 " " MRH N 11 " - " MRH N 12 " " BMA P 1 " - " MRH P 2 " " MRH P 2 " - " MRH P 3 " " BMA P 4 " - " MRH P 5 " " MRH P 5 " - " MRH P 6 " " BMA P 7 " - " MRH P 8 " " MRH P 8 " - " MRH P 9 " " BMA P 10 " - " MRH P 11 " " MRH P 11 " - " MRH P 12 " " BMA R 1 " - " MRH R 2 " " MRH R 2 " - " MRH R 3 " " BMA R 4 " - " MRH R 5 " " MRH R 5 " - " MRH R 6 " " BMA R 7 " - " MRH R 8 " " MRH R 8 " - " MRH R 9 " " BMA R 10 " - " MRH R 11 " " MRH R 11 " - " MRH R 12 " " BMA T 1 " - " MRH T 2 " " MRH T 2 " - " MRH T 3 " " BMA T 4 " - " MRH T 5 " " MRH T 5 " - " MRH T 6 " " BMA T 7 " - " MRH T 8 " " MRH T 8 " - " MRH T 9 " " BMA T 10 " - " MRH T 11 " " MRH T 11 " - " MRH T 12 " " BMA V 1 " - " MRH V 2 " " MRH V 2 " - " MRH V 3 " " BMA V 4 " - " MRH V 5 " " MRH V 5 " - " MRH V 6 " " BMA V 7 " - " MRH V 8 " " MRH V 8 " - " MRH V 9 " " BMA V 10 " - " MRH V 11 " " MRH V 11 " - " MRH V 12 " " BMA X 1 " - " MRH X 2 " " MRH X 2 " - " MRH X 3 " " BMA X 4 " - " MRH X 5 " " MRH X 5 " - " MRH X 6 " " BMA X 7 " - " MRH X 8 " " MRH X 8 " - " MRH X 9 " " BMA X 10 " - " MRH X 11 " " MRH X 11 " - " MRH X 12 " " BMA Z 1 " - " MRH Z 2 " " MRH Z 2 " - " MRH Z 3 " " BMA Z 4 " - " MRH Z 5 " " MRH Z 5 " - " MRH Z 6 " " BMA Z 7 " - " MRH Z 8 " " MRH Z 8 " - " MRH Z 9 " " BMA Z 10 " - " MRH Z 11 " " MRH Z 11 " - " MRH Z 12 " BETA1-3 " MRH 1 3 " - " BMA 1 4 " " MRH 1 6 " - " BMA 1 7 " " MRH 1 9 " - " BMA 1 10 " " MRH B 3 " - " BMA B 4 " " MRH B 6 " - " BMA B 7 " " MRH B 9 " - " BMA B 10 " " MRH D 3 " - " BMA D 4 " " MRH D 6 " - " BMA D 7 " " MRH D 9 " - " BMA D 10 " " MRH F 3 " - " BMA F 4 " " MRH F 6 " - " BMA F 7 " " MRH F 9 " - " BMA F 10 " " MRH H 3 " - " BMA H 4 " " MRH H 6 " - " BMA H 7 " " MRH H 9 " - " BMA H 10 " " MRH J 3 " - " BMA J 4 " " MRH J 6 " - " BMA J 7 " " MRH J 9 " - " BMA J 10 " " MRH L 3 " - " BMA L 4 " " MRH L 6 " - " BMA L 7 " " MRH L 9 " - " BMA L 10 " " MRH N 3 " - " BMA N 4 " " MRH N 6 " - " BMA N 7 " " MRH N 9 " - " BMA N 10 " " MRH P 3 " - " BMA P 4 " " MRH P 6 " - " BMA P 7 " " MRH P 9 " - " BMA P 10 " " MRH R 3 " - " BMA R 4 " " MRH R 6 " - " BMA R 7 " " MRH R 9 " - " BMA R 10 " " MRH T 3 " - " BMA T 4 " " MRH T 6 " - " BMA T 7 " " MRH T 9 " - " BMA T 10 " " MRH V 3 " - " BMA V 4 " " MRH V 6 " - " BMA V 7 " " MRH V 9 " - " BMA V 10 " " MRH X 3 " - " BMA X 4 " " MRH X 6 " - " BMA X 7 " " MRH X 9 " - " BMA X 10 " " MRH Z 3 " - " BMA Z 4 " " MRH Z 6 " - " BMA Z 7 " " MRH Z 9 " - " BMA Z 10 " Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 971.5 milliseconds 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6300 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.559A pdb=" N VAL A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 38 removed outlier: 3.569A pdb=" N THR A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.507A pdb=" N LEU A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 removed outlier: 3.591A pdb=" N THR A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.822A pdb=" N GLY A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 180 Processing helix chain 'A' and resid 184 through 206 removed outlier: 3.508A pdb=" N ILE A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 224 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'C' and resid 4 through 16 removed outlier: 3.558A pdb=" N VAL C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 38 removed outlier: 3.569A pdb=" N THR C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 53 removed outlier: 3.506A pdb=" N LEU C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 3.591A pdb=" N THR C 64 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 83 Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 100 through 115 removed outlier: 3.823A pdb=" N GLY C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 180 Processing helix chain 'C' and resid 184 through 206 removed outlier: 3.509A pdb=" N ILE C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 224 Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'E' and resid 4 through 16 removed outlier: 3.559A pdb=" N VAL E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 38 removed outlier: 3.569A pdb=" N THR E 36 " --> pdb=" O TYR E 32 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 53 removed outlier: 3.507A pdb=" N LEU E 53 " --> pdb=" O ASN E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 70 removed outlier: 3.591A pdb=" N THR E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 83 Processing helix chain 'E' and resid 93 through 97 Processing helix chain 'E' and resid 100 through 115 removed outlier: 3.822A pdb=" N GLY E 115 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA E 125 " --> pdb=" O THR E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'E' and resid 155 through 165 removed outlier: 3.607A pdb=" N ALA E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 184 through 206 removed outlier: 3.508A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 193 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 224 Processing helix chain 'E' and resid 237 through 242 Processing helix chain 'G' and resid 4 through 16 removed outlier: 3.559A pdb=" N VAL G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR G 10 " --> pdb=" O ALA G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 38 removed outlier: 3.570A pdb=" N THR G 36 " --> pdb=" O TYR G 32 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR G 38 " --> pdb=" O THR G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 53 removed outlier: 3.506A pdb=" N LEU G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 70 removed outlier: 3.590A pdb=" N THR G 64 " --> pdb=" O VAL G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 83 Processing helix chain 'G' and resid 93 through 97 Processing helix chain 'G' and resid 100 through 115 removed outlier: 3.822A pdb=" N GLY G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA G 125 " --> pdb=" O THR G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 145 Processing helix chain 'G' and resid 146 through 153 Processing helix chain 'G' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 180 Processing helix chain 'G' and resid 184 through 206 removed outlier: 3.508A pdb=" N ILE G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 224 Processing helix chain 'G' and resid 237 through 242 Processing helix chain 'I' and resid 4 through 16 removed outlier: 3.558A pdb=" N VAL I 9 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR I 10 " --> pdb=" O ALA I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 38 removed outlier: 3.569A pdb=" N THR I 36 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR I 38 " --> pdb=" O THR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 53 removed outlier: 3.506A pdb=" N LEU I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 70 removed outlier: 3.591A pdb=" N THR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 Processing helix chain 'I' and resid 93 through 97 Processing helix chain 'I' and resid 100 through 115 removed outlier: 3.822A pdb=" N GLY I 115 " --> pdb=" O ASN I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA I 125 " --> pdb=" O THR I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 145 Processing helix chain 'I' and resid 146 through 153 Processing helix chain 'I' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA I 159 " --> pdb=" O ASP I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 180 Processing helix chain 'I' and resid 184 through 206 removed outlier: 3.508A pdb=" N ILE I 188 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP I 189 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 224 Processing helix chain 'I' and resid 237 through 242 Processing helix chain 'K' and resid 4 through 16 removed outlier: 3.559A pdb=" N VAL K 9 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR K 10 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 38 removed outlier: 3.570A pdb=" N THR K 36 " --> pdb=" O TYR K 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR K 38 " --> pdb=" O THR K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 53 removed outlier: 3.507A pdb=" N LEU K 53 " --> pdb=" O ASN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 70 removed outlier: 3.590A pdb=" N THR K 64 " --> pdb=" O VAL K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 83 Processing helix chain 'K' and resid 93 through 97 Processing helix chain 'K' and resid 100 through 115 removed outlier: 3.823A pdb=" N GLY K 115 " --> pdb=" O ASN K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA K 125 " --> pdb=" O THR K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 145 Processing helix chain 'K' and resid 146 through 153 Processing helix chain 'K' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 180 Processing helix chain 'K' and resid 184 through 206 removed outlier: 3.509A pdb=" N ILE K 188 " --> pdb=" O ALA K 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP K 189 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 193 " --> pdb=" O ASP K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 224 Processing helix chain 'K' and resid 237 through 242 Processing helix chain 'M' and resid 4 through 16 removed outlier: 3.559A pdb=" N VAL M 9 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR M 10 " --> pdb=" O ALA M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 38 removed outlier: 3.569A pdb=" N THR M 36 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR M 38 " --> pdb=" O THR M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 53 removed outlier: 3.506A pdb=" N LEU M 53 " --> pdb=" O ASN M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 70 removed outlier: 3.591A pdb=" N THR M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 83 Processing helix chain 'M' and resid 93 through 97 Processing helix chain 'M' and resid 100 through 115 removed outlier: 3.822A pdb=" N GLY M 115 " --> pdb=" O ASN M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 127 removed outlier: 3.522A pdb=" N ALA M 125 " --> pdb=" O THR M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 145 Processing helix chain 'M' and resid 146 through 153 Processing helix chain 'M' and resid 155 through 165 removed outlier: 3.607A pdb=" N ALA M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 180 Processing helix chain 'M' and resid 184 through 206 removed outlier: 3.509A pdb=" N ILE M 188 " --> pdb=" O ALA M 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP M 189 " --> pdb=" O ALA M 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS M 193 " --> pdb=" O ASP M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 224 Processing helix chain 'M' and resid 237 through 242 Processing helix chain 'O' and resid 4 through 16 removed outlier: 3.558A pdb=" N VAL O 9 " --> pdb=" O THR O 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 38 removed outlier: 3.569A pdb=" N THR O 36 " --> pdb=" O TYR O 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR O 38 " --> pdb=" O THR O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 53 removed outlier: 3.507A pdb=" N LEU O 53 " --> pdb=" O ASN O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 70 removed outlier: 3.591A pdb=" N THR O 64 " --> pdb=" O VAL O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 83 Processing helix chain 'O' and resid 93 through 97 Processing helix chain 'O' and resid 100 through 115 removed outlier: 3.822A pdb=" N GLY O 115 " --> pdb=" O ASN O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA O 125 " --> pdb=" O THR O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 145 Processing helix chain 'O' and resid 146 through 153 Processing helix chain 'O' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA O 159 " --> pdb=" O ASP O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 180 Processing helix chain 'O' and resid 184 through 206 removed outlier: 3.508A pdb=" N ILE O 188 " --> pdb=" O ALA O 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP O 189 " --> pdb=" O ALA O 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS O 193 " --> pdb=" O ASP O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 224 Processing helix chain 'O' and resid 237 through 242 Processing helix chain 'Q' and resid 4 through 16 removed outlier: 3.558A pdb=" N VAL Q 9 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 38 removed outlier: 3.569A pdb=" N THR Q 36 " --> pdb=" O TYR Q 32 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 53 removed outlier: 3.507A pdb=" N LEU Q 53 " --> pdb=" O ASN Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 70 removed outlier: 3.591A pdb=" N THR Q 64 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 83 Processing helix chain 'Q' and resid 93 through 97 Processing helix chain 'Q' and resid 100 through 115 removed outlier: 3.823A pdb=" N GLY Q 115 " --> pdb=" O ASN Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA Q 125 " --> pdb=" O THR Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 145 Processing helix chain 'Q' and resid 146 through 153 Processing helix chain 'Q' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA Q 159 " --> pdb=" O ASP Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 180 Processing helix chain 'Q' and resid 184 through 206 removed outlier: 3.508A pdb=" N ILE Q 188 " --> pdb=" O ALA Q 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP Q 189 " --> pdb=" O ALA Q 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS Q 193 " --> pdb=" O ASP Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 224 Processing helix chain 'Q' and resid 237 through 242 Processing helix chain 'S' and resid 4 through 16 removed outlier: 3.559A pdb=" N VAL S 9 " --> pdb=" O THR S 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR S 10 " --> pdb=" O ALA S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 38 removed outlier: 3.570A pdb=" N THR S 36 " --> pdb=" O TYR S 32 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR S 38 " --> pdb=" O THR S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 53 removed outlier: 3.506A pdb=" N LEU S 53 " --> pdb=" O ASN S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 58 through 70 removed outlier: 3.591A pdb=" N THR S 64 " --> pdb=" O VAL S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 83 Processing helix chain 'S' and resid 93 through 97 Processing helix chain 'S' and resid 100 through 115 removed outlier: 3.823A pdb=" N GLY S 115 " --> pdb=" O ASN S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA S 125 " --> pdb=" O THR S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 145 Processing helix chain 'S' and resid 146 through 153 Processing helix chain 'S' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA S 159 " --> pdb=" O ASP S 155 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 180 Processing helix chain 'S' and resid 184 through 206 removed outlier: 3.509A pdb=" N ILE S 188 " --> pdb=" O ALA S 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP S 189 " --> pdb=" O ALA S 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS S 193 " --> pdb=" O ASP S 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 210 through 224 Processing helix chain 'S' and resid 237 through 242 Processing helix chain 'U' and resid 4 through 16 removed outlier: 3.558A pdb=" N VAL U 9 " --> pdb=" O THR U 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR U 10 " --> pdb=" O ALA U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 38 removed outlier: 3.569A pdb=" N THR U 36 " --> pdb=" O TYR U 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR U 38 " --> pdb=" O THR U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 53 removed outlier: 3.506A pdb=" N LEU U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 70 removed outlier: 3.591A pdb=" N THR U 64 " --> pdb=" O VAL U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 83 Processing helix chain 'U' and resid 93 through 97 Processing helix chain 'U' and resid 100 through 115 removed outlier: 3.822A pdb=" N GLY U 115 " --> pdb=" O ASN U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA U 125 " --> pdb=" O THR U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 131 through 145 Processing helix chain 'U' and resid 146 through 153 Processing helix chain 'U' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA U 159 " --> pdb=" O ASP U 155 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 180 Processing helix chain 'U' and resid 184 through 206 removed outlier: 3.508A pdb=" N ILE U 188 " --> pdb=" O ALA U 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP U 189 " --> pdb=" O ALA U 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS U 193 " --> pdb=" O ASP U 189 " (cutoff:3.500A) Processing helix chain 'U' and resid 210 through 224 Processing helix chain 'U' and resid 237 through 242 Processing helix chain 'W' and resid 4 through 16 removed outlier: 3.558A pdb=" N VAL W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR W 10 " --> pdb=" O ALA W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 38 removed outlier: 3.569A pdb=" N THR W 36 " --> pdb=" O TYR W 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR W 38 " --> pdb=" O THR W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 53 removed outlier: 3.506A pdb=" N LEU W 53 " --> pdb=" O ASN W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 70 removed outlier: 3.590A pdb=" N THR W 64 " --> pdb=" O VAL W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 74 through 83 Processing helix chain 'W' and resid 93 through 97 Processing helix chain 'W' and resid 100 through 115 removed outlier: 3.822A pdb=" N GLY W 115 " --> pdb=" O ASN W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 127 removed outlier: 3.522A pdb=" N ALA W 125 " --> pdb=" O THR W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 145 Processing helix chain 'W' and resid 146 through 153 Processing helix chain 'W' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA W 159 " --> pdb=" O ASP W 155 " (cutoff:3.500A) Processing helix chain 'W' and resid 165 through 180 Processing helix chain 'W' and resid 184 through 206 removed outlier: 3.508A pdb=" N ILE W 188 " --> pdb=" O ALA W 184 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP W 189 " --> pdb=" O ALA W 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS W 193 " --> pdb=" O ASP W 189 " (cutoff:3.500A) Processing helix chain 'W' and resid 210 through 224 Processing helix chain 'W' and resid 237 through 242 Processing helix chain 'Y' and resid 4 through 16 removed outlier: 3.559A pdb=" N VAL Y 9 " --> pdb=" O THR Y 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 38 removed outlier: 3.570A pdb=" N THR Y 36 " --> pdb=" O TYR Y 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR Y 38 " --> pdb=" O THR Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 53 removed outlier: 3.507A pdb=" N LEU Y 53 " --> pdb=" O ASN Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 58 through 70 removed outlier: 3.591A pdb=" N THR Y 64 " --> pdb=" O VAL Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 74 through 83 Processing helix chain 'Y' and resid 93 through 97 Processing helix chain 'Y' and resid 100 through 115 removed outlier: 3.823A pdb=" N GLY Y 115 " --> pdb=" O ASN Y 111 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA Y 125 " --> pdb=" O THR Y 121 " (cutoff:3.500A) Processing helix chain 'Y' and resid 131 through 145 Processing helix chain 'Y' and resid 146 through 153 Processing helix chain 'Y' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA Y 159 " --> pdb=" O ASP Y 155 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 180 Processing helix chain 'Y' and resid 184 through 206 removed outlier: 3.509A pdb=" N ILE Y 188 " --> pdb=" O ALA Y 184 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP Y 189 " --> pdb=" O ALA Y 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS Y 193 " --> pdb=" O ASP Y 189 " (cutoff:3.500A) Processing helix chain 'Y' and resid 210 through 224 Processing helix chain 'Y' and resid 237 through 242 Processing helix chain '0' and resid 4 through 16 removed outlier: 3.559A pdb=" N VAL 0 9 " --> pdb=" O THR 0 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR 0 10 " --> pdb=" O ALA 0 6 " (cutoff:3.500A) Processing helix chain '0' and resid 22 through 38 removed outlier: 3.570A pdb=" N THR 0 36 " --> pdb=" O TYR 0 32 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR 0 38 " --> pdb=" O THR 0 34 " (cutoff:3.500A) Processing helix chain '0' and resid 42 through 53 removed outlier: 3.506A pdb=" N LEU 0 53 " --> pdb=" O ASN 0 49 " (cutoff:3.500A) Processing helix chain '0' and resid 58 through 70 removed outlier: 3.590A pdb=" N THR 0 64 " --> pdb=" O VAL 0 60 " (cutoff:3.500A) Processing helix chain '0' and resid 74 through 83 Processing helix chain '0' and resid 93 through 97 Processing helix chain '0' and resid 100 through 115 removed outlier: 3.822A pdb=" N GLY 0 115 " --> pdb=" O ASN 0 111 " (cutoff:3.500A) Processing helix chain '0' and resid 119 through 127 removed outlier: 3.523A pdb=" N ALA 0 125 " --> pdb=" O THR 0 121 " (cutoff:3.500A) Processing helix chain '0' and resid 131 through 145 Processing helix chain '0' and resid 146 through 153 Processing helix chain '0' and resid 155 through 165 removed outlier: 3.606A pdb=" N ALA 0 159 " --> pdb=" O ASP 0 155 " (cutoff:3.500A) Processing helix chain '0' and resid 165 through 180 Processing helix chain '0' and resid 184 through 206 removed outlier: 3.509A pdb=" N ILE 0 188 " --> pdb=" O ALA 0 184 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP 0 189 " --> pdb=" O ALA 0 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS 0 193 " --> pdb=" O ASP 0 189 " (cutoff:3.500A) Processing helix chain '0' and resid 210 through 224 Processing helix chain '0' and resid 237 through 242 1652 hydrogen bonds defined for protein. 4872 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: 4.34 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6292 1.34 - 1.46: 7641 1.46 - 1.57: 12639 1.57 - 1.69: 0 1.69 - 1.80: 28 Bond restraints: 26600 Sorted by residual: bond pdb=" C ALA O 20 " pdb=" N PRO O 21 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.22e-02 6.72e+03 5.27e+00 bond pdb=" C ALA W 20 " pdb=" N PRO W 21 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.22e-02 6.72e+03 5.21e+00 bond pdb=" C ALA 0 20 " pdb=" N PRO 0 21 " ideal model delta sigma weight residual 1.330 1.357 -0.027 1.22e-02 6.72e+03 5.05e+00 bond pdb=" C ALA A 20 " pdb=" N PRO A 21 " ideal model delta sigma weight residual 1.330 1.357 -0.027 1.22e-02 6.72e+03 5.02e+00 bond pdb=" C ALA U 20 " pdb=" N PRO U 21 " ideal model delta sigma weight residual 1.330 1.357 -0.027 1.22e-02 6.72e+03 5.01e+00 ... (remaining 26595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 25432 1.51 - 3.02: 8869 3.02 - 4.53: 2028 4.53 - 6.04: 198 6.04 - 7.55: 27 Bond angle restraints: 36554 Sorted by residual: angle pdb=" C ASP U 93 " pdb=" N ALA U 94 " pdb=" CA ALA U 94 " ideal model delta sigma weight residual 120.44 125.91 -5.47 1.30e+00 5.92e-01 1.77e+01 angle pdb=" C ASP G 93 " pdb=" N ALA G 94 " pdb=" CA ALA G 94 " ideal model delta sigma weight residual 120.44 125.90 -5.46 1.30e+00 5.92e-01 1.76e+01 angle pdb=" C ASP Y 93 " pdb=" N ALA Y 94 " pdb=" CA ALA Y 94 " ideal model delta sigma weight residual 120.44 125.89 -5.45 1.30e+00 5.92e-01 1.76e+01 angle pdb=" C ASP I 93 " pdb=" N ALA I 94 " pdb=" CA ALA I 94 " ideal model delta sigma weight residual 120.44 125.89 -5.45 1.30e+00 5.92e-01 1.76e+01 angle pdb=" C ASP S 93 " pdb=" N ALA S 94 " pdb=" CA ALA S 94 " ideal model delta sigma weight residual 120.44 125.89 -5.45 1.30e+00 5.92e-01 1.76e+01 ... (remaining 36549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.52: 15512 19.52 - 39.03: 1022 39.03 - 58.55: 280 58.55 - 78.06: 350 78.06 - 97.58: 196 Dihedral angle restraints: 17360 sinusoidal: 7518 harmonic: 9842 Sorted by residual: dihedral pdb=" CA ALA M 113 " pdb=" C ALA M 113 " pdb=" N THR M 114 " pdb=" CA THR M 114 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ALA K 113 " pdb=" C ALA K 113 " pdb=" N THR K 114 " pdb=" CA THR K 114 " ideal model delta harmonic sigma weight residual -180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ALA S 113 " pdb=" C ALA S 113 " pdb=" N THR S 114 " pdb=" CA THR S 114 " ideal model delta harmonic sigma weight residual 180.00 -160.55 -19.45 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 17357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2295 0.063 - 0.127: 1630 0.127 - 0.190: 594 0.190 - 0.253: 314 0.253 - 0.316: 151 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C1 BMA T 10 " pdb=" O3 MRH T 9 " pdb=" C2 BMA T 10 " pdb=" O5 BMA T 10 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.54e+01 chirality pdb=" C1 BMA F 10 " pdb=" O3 MRH F 9 " pdb=" C2 BMA F 10 " pdb=" O5 BMA F 10 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.51e+01 chirality pdb=" C1 BMA 1 10 " pdb=" O3 MRH 1 9 " pdb=" C2 BMA 1 10 " pdb=" O5 BMA 1 10 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.48e+01 ... (remaining 4981 not shown) Planarity restraints: 4480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 MRH X 12 " -0.284 2.00e-02 2.50e+03 2.50e-01 7.79e+02 pdb=" C7 MRH X 12 " 0.041 2.00e-02 2.50e+03 pdb=" C8 MRH X 12 " -0.022 2.00e-02 2.50e+03 pdb=" N4 MRH X 12 " 0.443 2.00e-02 2.50e+03 pdb=" O7 MRH X 12 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 MRH H 12 " -0.284 2.00e-02 2.50e+03 2.50e-01 7.78e+02 pdb=" C7 MRH H 12 " 0.041 2.00e-02 2.50e+03 pdb=" C8 MRH H 12 " -0.022 2.00e-02 2.50e+03 pdb=" N4 MRH H 12 " 0.443 2.00e-02 2.50e+03 pdb=" O7 MRH H 12 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 MRH Z 12 " -0.284 2.00e-02 2.50e+03 2.50e-01 7.78e+02 pdb=" C7 MRH Z 12 " 0.042 2.00e-02 2.50e+03 pdb=" C8 MRH Z 12 " -0.022 2.00e-02 2.50e+03 pdb=" N4 MRH Z 12 " 0.443 2.00e-02 2.50e+03 pdb=" O7 MRH Z 12 " -0.178 2.00e-02 2.50e+03 ... (remaining 4477 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 873 2.71 - 3.26: 27529 3.26 - 3.81: 40949 3.81 - 4.35: 53469 4.35 - 4.90: 85536 Nonbonded interactions: 208356 Sorted by model distance: nonbonded pdb=" O ALA G 124 " pdb=" OG1 THR G 128 " model vdw 2.167 3.040 nonbonded pdb=" O ALA Y 124 " pdb=" OG1 THR Y 128 " model vdw 2.167 3.040 nonbonded pdb=" O ALA W 124 " pdb=" OG1 THR W 128 " model vdw 2.167 3.040 nonbonded pdb=" O ALA Q 124 " pdb=" OG1 THR Q 128 " model vdw 2.167 3.040 nonbonded pdb=" O ALA M 124 " pdb=" OG1 THR M 128 " model vdw 2.167 3.040 ... (remaining 208351 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain '0' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain '1' } 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 group one per residue 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: 1.660 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.590 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.008 0.042 26754 Z= 0.501 Angle : 1.596 7.550 37016 Z= 1.033 Chirality : 0.108 0.316 4984 Planarity : 0.024 0.250 4480 Dihedral : 21.393 97.577 11060 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.12), residues: 3360 helix: -1.41 (0.09), residues: 2408 sheet: None (None), residues: 0 loop : -1.92 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG C 165 TYR 0.014 0.002 TYR E 95 PHE 0.014 0.003 PHE Q 68 Details of bonding type rmsd covalent geometry : bond 0.00820 (26600) covalent geometry : angle 1.55281 (36554) hydrogen bonds : bond 0.26927 ( 1652) hydrogen bonds : angle 8.30767 ( 4872) glycosidic custom : bond 0.01366 ( 112) glycosidic custom : angle 3.86690 ( 336) link_BETA1-3 : bond 0.00841 ( 42) link_BETA1-3 : angle 2.97117 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.815 Fit side-chains REVERT: A 79 ASP cc_start: 0.8537 (t70) cc_final: 0.8295 (t0) REVERT: A 166 GLN cc_start: 0.8605 (tp40) cc_final: 0.7913 (tp40) REVERT: A 170 ASP cc_start: 0.7890 (m-30) cc_final: 0.7682 (m-30) REVERT: C 52 LYS cc_start: 0.8596 (tttt) cc_final: 0.8365 (ttmm) REVERT: C 170 ASP cc_start: 0.8626 (m-30) cc_final: 0.8285 (m-30) REVERT: E 102 GLU cc_start: 0.8473 (tt0) cc_final: 0.8246 (tt0) REVERT: E 166 GLN cc_start: 0.7974 (tp40) cc_final: 0.7616 (tm-30) REVERT: E 212 TYR cc_start: 0.8729 (m-80) cc_final: 0.8520 (m-80) REVERT: G 30 ASP cc_start: 0.8471 (t70) cc_final: 0.8137 (t0) REVERT: G 52 LYS cc_start: 0.8561 (tttt) cc_final: 0.8288 (ttmm) REVERT: G 189 ASP cc_start: 0.8922 (t0) cc_final: 0.7887 (m-30) REVERT: I 95 TYR cc_start: 0.9150 (t80) cc_final: 0.8760 (t80) REVERT: K 162 PHE cc_start: 0.7783 (t80) cc_final: 0.7257 (t80) REVERT: K 171 TYR cc_start: 0.8124 (t80) cc_final: 0.7874 (t80) REVERT: M 155 ASP cc_start: 0.7416 (t70) cc_final: 0.7113 (p0) REVERT: S 114 THR cc_start: 0.9249 (p) cc_final: 0.8966 (t) REVERT: U 87 ASN cc_start: 0.9112 (t0) cc_final: 0.8831 (t0) REVERT: U 93 ASP cc_start: 0.7924 (t70) cc_final: 0.7212 (t0) REVERT: U 134 GLN cc_start: 0.8677 (mt0) cc_final: 0.8352 (mt0) REVERT: U 166 GLN cc_start: 0.8562 (tp40) cc_final: 0.8193 (tp-100) REVERT: U 177 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7783 (ttm-80) REVERT: W 30 ASP cc_start: 0.8039 (t70) cc_final: 0.7756 (t0) REVERT: W 52 LYS cc_start: 0.8784 (tttt) cc_final: 0.8464 (ttmm) REVERT: W 79 ASP cc_start: 0.7906 (t70) cc_final: 0.7570 (t70) REVERT: Y 231 ASP cc_start: 0.8160 (t0) cc_final: 0.7925 (t0) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.1783 time to fit residues: 102.2801 Evaluate side-chains 171 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.0170 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 63 GLN A 89 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN A 111 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN C 49 ASN C 63 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 111 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN E 49 ASN E 63 GLN E 92 ASN E 107 ASN E 111 ASN E 134 GLN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 ASN G 49 ASN G 63 GLN G 89 ASN G 92 ASN G 107 ASN G 111 ASN G 134 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN I 49 ASN I 89 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN I 111 ASN I 134 GLN ** I 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 ASN K 63 GLN K 107 ASN K 111 ASN K 237 ASN M 35 GLN M 49 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 107 ASN M 134 GLN ** M 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 237 ASN O 49 ASN O 63 GLN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 GLN O 107 ASN O 111 ASN ** O 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 ASN Q 49 ASN Q 63 GLN Q 89 ASN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 GLN Q 107 ASN Q 111 ASN Q 134 GLN Q 168 ASN ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 237 ASN S 49 ASN S 63 GLN S 89 ASN S 92 ASN S 107 ASN S 111 ASN S 134 GLN ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 237 ASN U 49 ASN U 63 GLN U 107 ASN U 111 ASN U 134 GLN ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 237 ASN W 49 ASN W 63 GLN W 107 ASN W 111 ASN W 134 GLN ** W 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 237 ASN Y 49 ASN Y 63 GLN Y 87 ASN Y 89 ASN Y 107 ASN Y 111 ASN Y 134 GLN ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 237 ASN 0 49 ASN ** 0 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 101 GLN 0 107 ASN 0 134 GLN ** 0 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 237 ASN Total number of N/Q/H flips: 89 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.083380 restraints weight = 49576.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.084739 restraints weight = 38528.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.085121 restraints weight = 31295.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.085652 restraints weight = 27416.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.085795 restraints weight = 24986.628| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 26754 Z= 0.136 Angle : 0.699 9.172 37016 Z= 0.335 Chirality : 0.046 0.249 4984 Planarity : 0.003 0.041 4480 Dihedral : 14.633 63.884 6776 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.27 % Allowed : 10.80 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3360 helix: 0.69 (0.10), residues: 2366 sheet: None (None), residues: 0 loop : -1.19 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 165 TYR 0.018 0.001 TYR G 171 PHE 0.013 0.002 PHE A 175 Details of bonding type rmsd covalent geometry : bond 0.00268 (26600) covalent geometry : angle 0.66566 (36554) hydrogen bonds : bond 0.04863 ( 1652) hydrogen bonds : angle 5.37435 ( 4872) glycosidic custom : bond 0.00201 ( 112) glycosidic custom : angle 1.66442 ( 336) link_BETA1-3 : bond 0.00376 ( 42) link_BETA1-3 : angle 2.78049 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 219 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.8238 (t70) cc_final: 0.7854 (t0) REVERT: A 89 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8054 (p0) REVERT: C 30 ASP cc_start: 0.8418 (t70) cc_final: 0.7931 (t0) REVERT: C 52 LYS cc_start: 0.8578 (tttt) cc_final: 0.8338 (ttmm) REVERT: C 93 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7675 (t0) REVERT: E 165 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7306 (ptp90) REVERT: E 170 ASP cc_start: 0.6435 (m-30) cc_final: 0.5629 (m-30) REVERT: G 30 ASP cc_start: 0.8363 (t70) cc_final: 0.8034 (t0) REVERT: G 52 LYS cc_start: 0.8679 (tttt) cc_final: 0.8372 (ttmm) REVERT: G 93 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7726 (t0) REVERT: G 189 ASP cc_start: 0.8339 (t0) cc_final: 0.7793 (m-30) REVERT: I 89 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7649 (p0) REVERT: I 93 ASP cc_start: 0.6371 (OUTLIER) cc_final: 0.6165 (t0) REVERT: K 162 PHE cc_start: 0.7884 (t80) cc_final: 0.6077 (t80) REVERT: K 165 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.5806 (ptp90) REVERT: K 171 TYR cc_start: 0.8235 (t80) cc_final: 0.7959 (t80) REVERT: M 111 ASN cc_start: 0.7740 (m-40) cc_final: 0.7496 (m-40) REVERT: M 202 ASN cc_start: 0.8787 (t0) cc_final: 0.8551 (t0) REVERT: Q 91 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8892 (mt) REVERT: Q 93 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7276 (t0) REVERT: S 98 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8288 (mtpp) REVERT: S 165 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7274 (ttp80) REVERT: U 93 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6872 (t0) REVERT: U 162 PHE cc_start: 0.8406 (t80) cc_final: 0.8093 (t80) REVERT: U 172 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8175 (mm) REVERT: W 93 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7605 (t0) REVERT: W 189 ASP cc_start: 0.7524 (t0) cc_final: 0.7232 (t0) REVERT: Y 93 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6790 (t0) REVERT: 0 35 GLN cc_start: 0.8651 (mm-40) cc_final: 0.7600 (tm-30) REVERT: 0 89 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.7014 (p0) outliers start: 77 outliers final: 27 residues processed: 289 average time/residue: 0.1887 time to fit residues: 83.4499 Evaluate side-chains 181 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 165 ARG Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain Q residue 89 ASN Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 165 ARG Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 165 ARG Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Y residue 93 ASP Chi-restraints excluded: chain 0 residue 89 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 145 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 209 optimal weight: 0.5980 chunk 230 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 92 ASN C 134 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 101 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN I 92 ASN ** K 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN Q 92 ASN ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 ASN ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 89 ASN ** W 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 7 GLN 0 66 GLN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.098203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.080928 restraints weight = 50531.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.081759 restraints weight = 42216.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.081945 restraints weight = 35313.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.082278 restraints weight = 33317.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.082540 restraints weight = 30279.357| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26754 Z= 0.162 Angle : 0.644 9.635 37016 Z= 0.306 Chirality : 0.042 0.251 4984 Planarity : 0.003 0.041 4480 Dihedral : 11.206 56.104 6776 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.06 % Allowed : 13.31 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.14), residues: 3360 helix: 1.27 (0.11), residues: 2380 sheet: None (None), residues: 0 loop : -1.10 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 165 TYR 0.018 0.001 TYR Y 171 PHE 0.024 0.002 PHE C 162 Details of bonding type rmsd covalent geometry : bond 0.00370 (26600) covalent geometry : angle 0.61570 (36554) hydrogen bonds : bond 0.04255 ( 1652) hydrogen bonds : angle 4.98800 ( 4872) glycosidic custom : bond 0.00175 ( 112) glycosidic custom : angle 1.37919 ( 336) link_BETA1-3 : bond 0.00619 ( 42) link_BETA1-3 : angle 2.58396 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 79 ASP cc_start: 0.8264 (t70) cc_final: 0.7960 (t0) REVERT: A 89 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8187 (p0) REVERT: C 30 ASP cc_start: 0.8422 (t70) cc_final: 0.8051 (t0) REVERT: C 52 LYS cc_start: 0.8674 (tttt) cc_final: 0.8452 (ttmm) REVERT: E 166 GLN cc_start: 0.7506 (tm-30) cc_final: 0.6603 (tm-30) REVERT: E 170 ASP cc_start: 0.6569 (m-30) cc_final: 0.6037 (m-30) REVERT: E 207 SER cc_start: 0.9167 (p) cc_final: 0.8955 (m) REVERT: G 30 ASP cc_start: 0.8307 (t70) cc_final: 0.7928 (t0) REVERT: G 52 LYS cc_start: 0.8814 (tttt) cc_final: 0.8497 (ttmm) REVERT: G 91 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8397 (mt) REVERT: G 93 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7989 (t0) REVERT: I 93 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6385 (t0) REVERT: K 62 ILE cc_start: 0.9150 (mm) cc_final: 0.8858 (mt) REVERT: K 79 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7718 (t70) REVERT: K 162 PHE cc_start: 0.7950 (t80) cc_final: 0.7641 (t80) REVERT: M 177 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7632 (ttm-80) REVERT: M 202 ASN cc_start: 0.8911 (t0) cc_final: 0.8650 (t0) REVERT: S 89 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8383 (p0) REVERT: S 165 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7391 (ttp80) REVERT: U 111 ASN cc_start: 0.8219 (m-40) cc_final: 0.8007 (m110) REVERT: U 162 PHE cc_start: 0.8396 (t80) cc_final: 0.8143 (t80) REVERT: U 166 GLN cc_start: 0.8300 (tp-100) cc_final: 0.8086 (tp-100) REVERT: W 93 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7933 (t0) REVERT: 0 35 GLN cc_start: 0.8704 (mm-40) cc_final: 0.7602 (tm-30) outliers start: 72 outliers final: 44 residues processed: 233 average time/residue: 0.1725 time to fit residues: 63.9155 Evaluate side-chains 196 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 165 ARG Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Y residue 200 ILE Chi-restraints excluded: chain 0 residue 60 VAL Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 0 residue 91 LEU Chi-restraints excluded: chain 0 residue 114 THR Chi-restraints excluded: chain 0 residue 189 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 224 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 236 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 287 optimal weight: 0.2980 chunk 175 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 134 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN M 63 GLN M 89 ASN ** Q 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 89 ASN ** W 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.083717 restraints weight = 49926.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.084269 restraints weight = 40695.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.084623 restraints weight = 34021.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085065 restraints weight = 31635.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.085149 restraints weight = 29180.928| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26754 Z= 0.100 Angle : 0.567 9.721 37016 Z= 0.268 Chirality : 0.040 0.245 4984 Planarity : 0.002 0.023 4480 Dihedral : 8.692 52.350 6776 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.38 % Allowed : 14.75 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3360 helix: 1.63 (0.11), residues: 2366 sheet: None (None), residues: 0 loop : -0.86 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 177 TYR 0.019 0.001 TYR K 171 PHE 0.014 0.001 PHE A 175 Details of bonding type rmsd covalent geometry : bond 0.00202 (26600) covalent geometry : angle 0.53592 (36554) hydrogen bonds : bond 0.03030 ( 1652) hydrogen bonds : angle 4.69311 ( 4872) glycosidic custom : bond 0.00155 ( 112) glycosidic custom : angle 1.48994 ( 336) link_BETA1-3 : bond 0.00505 ( 42) link_BETA1-3 : angle 2.28531 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 79 ASP cc_start: 0.8243 (t70) cc_final: 0.7959 (t0) REVERT: A 89 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8051 (p0) REVERT: A 93 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6957 (t0) REVERT: C 30 ASP cc_start: 0.8435 (t70) cc_final: 0.8049 (t0) REVERT: C 52 LYS cc_start: 0.8705 (tttt) cc_final: 0.8479 (ttmm) REVERT: E 166 GLN cc_start: 0.7468 (tm-30) cc_final: 0.6499 (tm-30) REVERT: E 170 ASP cc_start: 0.6582 (m-30) cc_final: 0.5977 (m-30) REVERT: G 30 ASP cc_start: 0.8350 (t70) cc_final: 0.7923 (t0) REVERT: G 52 LYS cc_start: 0.8842 (tttt) cc_final: 0.8516 (ttmm) REVERT: G 91 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8301 (mt) REVERT: G 93 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7895 (t0) REVERT: K 62 ILE cc_start: 0.9084 (mm) cc_final: 0.8833 (mt) REVERT: K 79 ASP cc_start: 0.8045 (t0) cc_final: 0.7735 (t70) REVERT: K 93 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8520 (m-30) REVERT: K 162 PHE cc_start: 0.7827 (t80) cc_final: 0.7550 (t80) REVERT: M 35 GLN cc_start: 0.9031 (mm110) cc_final: 0.8465 (mm110) REVERT: M 177 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7710 (ttm-80) REVERT: M 202 ASN cc_start: 0.8882 (t0) cc_final: 0.8527 (t0) REVERT: Q 93 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6995 (t0) REVERT: U 111 ASN cc_start: 0.8250 (m-40) cc_final: 0.8005 (m110) REVERT: U 166 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7970 (tp-100) REVERT: W 162 PHE cc_start: 0.8392 (t80) cc_final: 0.8159 (t80) REVERT: W 189 ASP cc_start: 0.7328 (t0) cc_final: 0.6944 (t0) REVERT: Y 93 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.6993 (t0) REVERT: 0 35 GLN cc_start: 0.8710 (mm-40) cc_final: 0.7644 (tm-30) outliers start: 56 outliers final: 30 residues processed: 238 average time/residue: 0.1659 time to fit residues: 62.7661 Evaluate side-chains 187 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 93 ASP Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 24 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 ASN A 179 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN C 92 ASN C 134 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 ASN G 92 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 237 ASN S 89 ASN S 111 ASN ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 237 ASN ** W 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 237 ASN 0 92 ASN 0 237 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.079833 restraints weight = 50488.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.079468 restraints weight = 43746.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.079681 restraints weight = 40973.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.079873 restraints weight = 38099.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.079974 restraints weight = 36261.500| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26754 Z= 0.187 Angle : 0.627 9.864 37016 Z= 0.299 Chirality : 0.042 0.259 4984 Planarity : 0.003 0.034 4480 Dihedral : 8.084 53.590 6776 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.53 % Allowed : 14.75 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.14), residues: 3360 helix: 1.55 (0.11), residues: 2380 sheet: None (None), residues: 0 loop : -0.81 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 165 TYR 0.016 0.001 TYR Y 171 PHE 0.016 0.002 PHE A 175 Details of bonding type rmsd covalent geometry : bond 0.00451 (26600) covalent geometry : angle 0.59675 (36554) hydrogen bonds : bond 0.04046 ( 1652) hydrogen bonds : angle 4.73257 ( 4872) glycosidic custom : bond 0.00162 ( 112) glycosidic custom : angle 1.57558 ( 336) link_BETA1-3 : bond 0.00540 ( 42) link_BETA1-3 : angle 2.38427 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 149 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 89 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.7993 (p0) REVERT: A 93 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7126 (t0) REVERT: C 30 ASP cc_start: 0.8565 (t70) cc_final: 0.8231 (t0) REVERT: C 52 LYS cc_start: 0.8798 (tttt) cc_final: 0.8559 (ttmm) REVERT: E 166 GLN cc_start: 0.7578 (tm-30) cc_final: 0.6532 (tm-30) REVERT: E 170 ASP cc_start: 0.6736 (m-30) cc_final: 0.6104 (m-30) REVERT: G 30 ASP cc_start: 0.8380 (t70) cc_final: 0.7946 (t0) REVERT: G 52 LYS cc_start: 0.8862 (tttt) cc_final: 0.8525 (ttmm) REVERT: G 91 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8446 (mt) REVERT: K 62 ILE cc_start: 0.9111 (mm) cc_final: 0.8839 (mt) REVERT: K 79 ASP cc_start: 0.8134 (t0) cc_final: 0.7848 (t70) REVERT: K 93 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8703 (m-30) REVERT: K 162 PHE cc_start: 0.7897 (t80) cc_final: 0.7554 (t80) REVERT: M 35 GLN cc_start: 0.9146 (mm110) cc_final: 0.8622 (mm110) REVERT: M 177 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7851 (ttm-80) REVERT: M 202 ASN cc_start: 0.8896 (t0) cc_final: 0.8639 (t0) REVERT: S 89 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8364 (p0) REVERT: U 111 ASN cc_start: 0.8189 (m-40) cc_final: 0.7949 (m110) REVERT: U 166 GLN cc_start: 0.8290 (tp-100) cc_final: 0.7985 (tp-100) REVERT: W 93 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8014 (t0) REVERT: Y 93 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7066 (t0) REVERT: 0 35 GLN cc_start: 0.8727 (mm-40) cc_final: 0.7712 (tm-30) REVERT: 0 89 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.7241 (p0) outliers start: 83 outliers final: 63 residues processed: 226 average time/residue: 0.1668 time to fit residues: 60.4000 Evaluate side-chains 209 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 138 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 205 THR Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 93 ASP Chi-restraints excluded: chain Y residue 220 ILE Chi-restraints excluded: chain 0 residue 51 LEU Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 0 residue 89 ASN Chi-restraints excluded: chain 0 residue 91 LEU Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 254 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 222 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 92 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 134 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN O 237 ASN ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 89 ASN W 92 ASN Y 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.083728 restraints weight = 49973.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.083854 restraints weight = 44706.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.084233 restraints weight = 40528.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.084325 restraints weight = 36300.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.085124 restraints weight = 34116.141| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26754 Z= 0.095 Angle : 0.542 9.722 37016 Z= 0.257 Chirality : 0.038 0.245 4984 Planarity : 0.002 0.029 4480 Dihedral : 7.264 52.269 6776 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.47 % Allowed : 15.77 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.15), residues: 3360 helix: 1.78 (0.11), residues: 2380 sheet: None (None), residues: 0 loop : -0.65 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 165 TYR 0.016 0.001 TYR Y 171 PHE 0.012 0.001 PHE A 175 Details of bonding type rmsd covalent geometry : bond 0.00188 (26600) covalent geometry : angle 0.51373 (36554) hydrogen bonds : bond 0.02868 ( 1652) hydrogen bonds : angle 4.51578 ( 4872) glycosidic custom : bond 0.00151 ( 112) glycosidic custom : angle 1.41106 ( 336) link_BETA1-3 : bond 0.00510 ( 42) link_BETA1-3 : angle 2.12257 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 164 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 93 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6895 (t0) REVERT: C 30 ASP cc_start: 0.8498 (t70) cc_final: 0.8154 (t0) REVERT: C 52 LYS cc_start: 0.8812 (tttt) cc_final: 0.8582 (ttmm) REVERT: C 65 TYR cc_start: 0.9226 (OUTLIER) cc_final: 0.8052 (t80) REVERT: C 146 ASN cc_start: 0.7975 (m-40) cc_final: 0.7742 (m-40) REVERT: E 166 GLN cc_start: 0.7492 (tm-30) cc_final: 0.6440 (tm-30) REVERT: E 170 ASP cc_start: 0.6776 (m-30) cc_final: 0.6169 (m-30) REVERT: G 30 ASP cc_start: 0.8369 (t70) cc_final: 0.7853 (t0) REVERT: G 52 LYS cc_start: 0.8853 (tttt) cc_final: 0.8518 (ttmm) REVERT: G 162 PHE cc_start: 0.8731 (t80) cc_final: 0.8444 (t80) REVERT: K 62 ILE cc_start: 0.9090 (mm) cc_final: 0.8847 (mt) REVERT: K 79 ASP cc_start: 0.8074 (t0) cc_final: 0.7808 (t70) REVERT: K 162 PHE cc_start: 0.7817 (t80) cc_final: 0.7539 (t80) REVERT: K 171 TYR cc_start: 0.8214 (t80) cc_final: 0.7929 (t80) REVERT: M 35 GLN cc_start: 0.9098 (mm110) cc_final: 0.8534 (mm110) REVERT: M 177 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7812 (ttm-80) REVERT: M 202 ASN cc_start: 0.8795 (t0) cc_final: 0.8548 (t0) REVERT: S 65 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.7203 (t80) REVERT: S 111 ASN cc_start: 0.8255 (m-40) cc_final: 0.8036 (m110) REVERT: U 111 ASN cc_start: 0.8167 (m-40) cc_final: 0.7934 (m110) REVERT: U 166 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7905 (tp-100) REVERT: W 93 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7880 (t0) REVERT: Y 93 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7222 (t70) REVERT: 0 35 GLN cc_start: 0.8664 (mm-40) cc_final: 0.7673 (tm-30) outliers start: 58 outliers final: 40 residues processed: 217 average time/residue: 0.1791 time to fit residues: 60.9709 Evaluate side-chains 185 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain C residue 65 TYR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 93 ASP Chi-restraints excluded: chain 0 residue 51 LEU Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 307 optimal weight: 0.6980 chunk 214 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 283 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 ASN C 92 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 ASN M 89 ASN S 89 ASN ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 89 ASN Y 37 GLN 0 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.082726 restraints weight = 49872.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.082792 restraints weight = 43077.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.082901 restraints weight = 40260.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.083113 restraints weight = 37290.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.083212 restraints weight = 35509.028| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26754 Z= 0.120 Angle : 0.553 9.769 37016 Z= 0.262 Chirality : 0.038 0.250 4984 Planarity : 0.002 0.045 4480 Dihedral : 6.900 52.628 6776 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.81 % Allowed : 15.73 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.15), residues: 3360 helix: 1.79 (0.11), residues: 2394 sheet: None (None), residues: 0 loop : -0.53 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 165 TYR 0.016 0.001 TYR 0 171 PHE 0.014 0.001 PHE A 175 Details of bonding type rmsd covalent geometry : bond 0.00271 (26600) covalent geometry : angle 0.52504 (36554) hydrogen bonds : bond 0.03132 ( 1652) hydrogen bonds : angle 4.49153 ( 4872) glycosidic custom : bond 0.00140 ( 112) glycosidic custom : angle 1.42787 ( 336) link_BETA1-3 : bond 0.00482 ( 42) link_BETA1-3 : angle 2.11462 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 151 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 89 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8084 (p0) REVERT: A 93 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6818 (t70) REVERT: C 30 ASP cc_start: 0.8446 (t70) cc_final: 0.8116 (t0) REVERT: C 52 LYS cc_start: 0.8801 (tttt) cc_final: 0.8591 (ttmm) REVERT: C 65 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.8010 (t80) REVERT: C 146 ASN cc_start: 0.7981 (m-40) cc_final: 0.7745 (m-40) REVERT: E 51 LEU cc_start: 0.8790 (mm) cc_final: 0.8561 (mm) REVERT: E 166 GLN cc_start: 0.7547 (tm-30) cc_final: 0.6528 (tm-30) REVERT: E 170 ASP cc_start: 0.6716 (m-30) cc_final: 0.6113 (m-30) REVERT: G 30 ASP cc_start: 0.8305 (t70) cc_final: 0.7769 (t0) REVERT: G 52 LYS cc_start: 0.8877 (tttt) cc_final: 0.8539 (ttmm) REVERT: K 62 ILE cc_start: 0.9144 (mm) cc_final: 0.8892 (mt) REVERT: K 79 ASP cc_start: 0.8077 (t0) cc_final: 0.7825 (t70) REVERT: K 162 PHE cc_start: 0.7802 (t80) cc_final: 0.7531 (t80) REVERT: K 171 TYR cc_start: 0.8165 (t80) cc_final: 0.7947 (t80) REVERT: M 35 GLN cc_start: 0.9096 (mm110) cc_final: 0.8496 (mm110) REVERT: M 202 ASN cc_start: 0.8832 (t0) cc_final: 0.8578 (t0) REVERT: S 65 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.7301 (t80) REVERT: W 88 THR cc_start: 0.8846 (p) cc_final: 0.8611 (p) REVERT: W 93 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7946 (t0) REVERT: W 162 PHE cc_start: 0.8381 (t80) cc_final: 0.8113 (t80) REVERT: Y 93 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7316 (t70) REVERT: 0 35 GLN cc_start: 0.8636 (mm-40) cc_final: 0.7726 (tm-30) outliers start: 66 outliers final: 51 residues processed: 212 average time/residue: 0.1775 time to fit residues: 59.5513 Evaluate side-chains 196 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain C residue 65 TYR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 93 ASP Chi-restraints excluded: chain 0 residue 51 LEU Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 78 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 258 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 ASN C 92 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN M 63 GLN M 89 ASN M 237 ASN S 111 ASN ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 89 ASN Y 37 GLN Y 89 ASN 0 89 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.082468 restraints weight = 50307.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.082268 restraints weight = 42179.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.082432 restraints weight = 40883.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.082508 restraints weight = 39037.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.082988 restraints weight = 36425.394| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26754 Z= 0.140 Angle : 0.568 9.807 37016 Z= 0.271 Chirality : 0.039 0.253 4984 Planarity : 0.002 0.042 4480 Dihedral : 6.791 52.946 6776 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.02 % Allowed : 15.86 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.15), residues: 3360 helix: 1.80 (0.11), residues: 2380 sheet: None (None), residues: 0 loop : -0.54 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 165 TYR 0.021 0.001 TYR Y 171 PHE 0.014 0.001 PHE M 175 Details of bonding type rmsd covalent geometry : bond 0.00327 (26600) covalent geometry : angle 0.54111 (36554) hydrogen bonds : bond 0.03346 ( 1652) hydrogen bonds : angle 4.49644 ( 4872) glycosidic custom : bond 0.00144 ( 112) glycosidic custom : angle 1.42918 ( 336) link_BETA1-3 : bond 0.00461 ( 42) link_BETA1-3 : angle 2.10192 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 151 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 89 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8258 (p0) REVERT: C 30 ASP cc_start: 0.8487 (t70) cc_final: 0.8164 (t0) REVERT: C 65 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8069 (t80) REVERT: C 146 ASN cc_start: 0.8013 (m-40) cc_final: 0.7762 (m-40) REVERT: E 51 LEU cc_start: 0.8804 (mm) cc_final: 0.8576 (mm) REVERT: E 166 GLN cc_start: 0.7597 (tm-30) cc_final: 0.6562 (tm-30) REVERT: E 170 ASP cc_start: 0.6720 (m-30) cc_final: 0.6126 (m-30) REVERT: G 30 ASP cc_start: 0.8347 (t70) cc_final: 0.7820 (t0) REVERT: G 52 LYS cc_start: 0.8896 (tttt) cc_final: 0.8566 (ttmm) REVERT: K 62 ILE cc_start: 0.9149 (mm) cc_final: 0.8897 (mt) REVERT: K 79 ASP cc_start: 0.8111 (t0) cc_final: 0.7846 (t70) REVERT: K 162 PHE cc_start: 0.7906 (t80) cc_final: 0.7633 (t80) REVERT: K 171 TYR cc_start: 0.8202 (t80) cc_final: 0.7982 (t80) REVERT: M 35 GLN cc_start: 0.9083 (mm110) cc_final: 0.8569 (mm110) REVERT: M 202 ASN cc_start: 0.8846 (t0) cc_final: 0.8608 (t0) REVERT: S 89 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8278 (p0) REVERT: W 162 PHE cc_start: 0.8352 (t80) cc_final: 0.8092 (t80) REVERT: Y 93 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7447 (t70) REVERT: 0 35 GLN cc_start: 0.8665 (mm-40) cc_final: 0.7745 (tm-30) outliers start: 71 outliers final: 57 residues processed: 218 average time/residue: 0.1673 time to fit residues: 58.7944 Evaluate side-chains 199 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 138 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain C residue 65 TYR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 93 ASP Chi-restraints excluded: chain Y residue 220 ILE Chi-restraints excluded: chain 0 residue 51 LEU Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 53 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 255 optimal weight: 0.2980 chunk 143 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 267 optimal weight: 5.9990 chunk 332 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 92 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN S 89 ASN ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN 0 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.082949 restraints weight = 50289.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.083155 restraints weight = 43334.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.083250 restraints weight = 39845.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.083555 restraints weight = 37830.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.083703 restraints weight = 33919.525| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26754 Z= 0.108 Angle : 0.545 9.746 37016 Z= 0.260 Chirality : 0.038 0.277 4984 Planarity : 0.002 0.032 4480 Dihedral : 6.571 52.463 6776 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.47 % Allowed : 16.62 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.15), residues: 3360 helix: 1.85 (0.11), residues: 2394 sheet: None (None), residues: 0 loop : -0.44 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 165 TYR 0.018 0.001 TYR 0 171 PHE 0.019 0.001 PHE K 175 Details of bonding type rmsd covalent geometry : bond 0.00239 (26600) covalent geometry : angle 0.51869 (36554) hydrogen bonds : bond 0.03026 ( 1652) hydrogen bonds : angle 4.43469 ( 4872) glycosidic custom : bond 0.00138 ( 112) glycosidic custom : angle 1.36493 ( 336) link_BETA1-3 : bond 0.00482 ( 42) link_BETA1-3 : angle 2.03432 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: C 30 ASP cc_start: 0.8541 (t70) cc_final: 0.8232 (t0) REVERT: C 65 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8037 (t80) REVERT: C 146 ASN cc_start: 0.7950 (m-40) cc_final: 0.7732 (m-40) REVERT: E 51 LEU cc_start: 0.8680 (mm) cc_final: 0.8424 (mm) REVERT: E 166 GLN cc_start: 0.7594 (tm-30) cc_final: 0.6509 (tm-30) REVERT: E 170 ASP cc_start: 0.6859 (m-30) cc_final: 0.6213 (m-30) REVERT: G 30 ASP cc_start: 0.8350 (t70) cc_final: 0.7758 (t0) REVERT: G 52 LYS cc_start: 0.8882 (tttt) cc_final: 0.8524 (ttmm) REVERT: G 166 GLN cc_start: 0.7945 (tp40) cc_final: 0.7726 (tp40) REVERT: K 62 ILE cc_start: 0.9098 (mm) cc_final: 0.8868 (mt) REVERT: K 79 ASP cc_start: 0.8126 (t0) cc_final: 0.7835 (t70) REVERT: K 162 PHE cc_start: 0.7915 (t80) cc_final: 0.7630 (t80) REVERT: K 171 TYR cc_start: 0.8247 (t80) cc_final: 0.8012 (t80) REVERT: M 35 GLN cc_start: 0.9059 (mm110) cc_final: 0.8540 (mm110) REVERT: M 202 ASN cc_start: 0.8807 (t0) cc_final: 0.8572 (t0) REVERT: S 65 TYR cc_start: 0.9176 (OUTLIER) cc_final: 0.7280 (t80) REVERT: W 162 PHE cc_start: 0.8361 (t80) cc_final: 0.8061 (t80) REVERT: Y 93 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7474 (t70) REVERT: 0 35 GLN cc_start: 0.8725 (mm-40) cc_final: 0.7755 (tm-30) outliers start: 58 outliers final: 50 residues processed: 204 average time/residue: 0.1726 time to fit residues: 56.0828 Evaluate side-chains 192 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain C residue 65 TYR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 93 ASP Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 146 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 323 optimal weight: 5.9990 chunk 237 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 ASN C 92 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN K 237 ASN S 89 ASN ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 89 ASN Y 37 GLN 0 89 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.082844 restraints weight = 49915.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.082860 restraints weight = 42159.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.083139 restraints weight = 38556.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.083208 restraints weight = 36088.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.083292 restraints weight = 34524.020| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26754 Z= 0.121 Angle : 0.553 9.773 37016 Z= 0.264 Chirality : 0.038 0.262 4984 Planarity : 0.002 0.034 4480 Dihedral : 6.457 52.669 6776 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.42 % Allowed : 16.67 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.15), residues: 3360 helix: 1.86 (0.11), residues: 2394 sheet: None (None), residues: 0 loop : -0.44 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 177 TYR 0.024 0.001 TYR Y 171 PHE 0.014 0.001 PHE M 175 Details of bonding type rmsd covalent geometry : bond 0.00278 (26600) covalent geometry : angle 0.52735 (36554) hydrogen bonds : bond 0.03098 ( 1652) hydrogen bonds : angle 4.43526 ( 4872) glycosidic custom : bond 0.00137 ( 112) glycosidic custom : angle 1.36892 ( 336) link_BETA1-3 : bond 0.00471 ( 42) link_BETA1-3 : angle 2.02359 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 89 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.7986 (p0) REVERT: C 30 ASP cc_start: 0.8473 (t70) cc_final: 0.8177 (t0) REVERT: C 65 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8036 (t80) REVERT: E 51 LEU cc_start: 0.8685 (mm) cc_final: 0.8434 (mm) REVERT: E 166 GLN cc_start: 0.7650 (tm-30) cc_final: 0.6622 (tm-30) REVERT: E 170 ASP cc_start: 0.6734 (m-30) cc_final: 0.6133 (m-30) REVERT: G 30 ASP cc_start: 0.8319 (t70) cc_final: 0.7875 (t0) REVERT: G 52 LYS cc_start: 0.8886 (tttt) cc_final: 0.8556 (ttmm) REVERT: K 62 ILE cc_start: 0.9143 (mm) cc_final: 0.8896 (mt) REVERT: K 79 ASP cc_start: 0.8110 (t0) cc_final: 0.7839 (t70) REVERT: K 162 PHE cc_start: 0.7862 (t80) cc_final: 0.7608 (t80) REVERT: K 171 TYR cc_start: 0.8158 (t80) cc_final: 0.7952 (t80) REVERT: M 202 ASN cc_start: 0.8823 (t0) cc_final: 0.8577 (t0) REVERT: S 65 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.7334 (t80) REVERT: U 35 GLN cc_start: 0.9056 (mm110) cc_final: 0.8774 (mm110) REVERT: W 162 PHE cc_start: 0.8305 (t80) cc_final: 0.8071 (t80) REVERT: Y 93 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7473 (t70) REVERT: 0 35 GLN cc_start: 0.8697 (mm-40) cc_final: 0.7797 (tm-30) outliers start: 57 outliers final: 46 residues processed: 195 average time/residue: 0.1650 time to fit residues: 51.7183 Evaluate side-chains 183 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain C residue 65 TYR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 93 ASP Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 242 optimal weight: 0.7980 chunk 265 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 281 optimal weight: 0.1980 chunk 142 optimal weight: 6.9990 chunk 303 optimal weight: 0.7980 chunk 301 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 89 ASN Y 37 GLN 0 89 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.084213 restraints weight = 49653.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.084007 restraints weight = 43617.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.084271 restraints weight = 39673.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.084448 restraints weight = 36851.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.084615 restraints weight = 34660.328| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26754 Z= 0.095 Angle : 0.527 9.727 37016 Z= 0.253 Chirality : 0.037 0.245 4984 Planarity : 0.002 0.048 4480 Dihedral : 6.185 52.081 6776 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.04 % Allowed : 16.92 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.15), residues: 3360 helix: 1.97 (0.11), residues: 2394 sheet: None (None), residues: 0 loop : -0.38 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 165 TYR 0.021 0.001 TYR 0 171 PHE 0.017 0.001 PHE K 175 Details of bonding type rmsd covalent geometry : bond 0.00196 (26600) covalent geometry : angle 0.50374 (36554) hydrogen bonds : bond 0.02627 ( 1652) hydrogen bonds : angle 4.36537 ( 4872) glycosidic custom : bond 0.00139 ( 112) glycosidic custom : angle 1.28325 ( 336) link_BETA1-3 : bond 0.00503 ( 42) link_BETA1-3 : angle 1.93062 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3185.00 seconds wall clock time: 56 minutes 30.30 seconds (3390.30 seconds total)