Starting phenix.real_space_refine on Sun Jul 5 07:53:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7peo_13355/07_2026/7peo_13355.cif Found real_map, /net/cci-nas-00/data/ceres_data/7peo_13355/07_2026/7peo_13355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7peo_13355/07_2026/7peo_13355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7peo_13355/07_2026/7peo_13355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7peo_13355/07_2026/7peo_13355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7peo_13355/07_2026/7peo_13355.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7peo_13355/07_2026/7peo_13355.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7peo_13355/07_2026/7peo_13355.cif" } resolution = 4.37 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= 0.002 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: 6 Type Number sf(0) Gaussians Ho 14 14.37 5 Ca 28 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 chiralities: 12 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} 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: 2.92, per 1000 atoms: 0.11 Number of scatterers: 26278 At special positions: 0 Unit cell: (159.84, 159.84, 165.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ho 14 66.95 Ca 28 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: 3.26 Conformation dependent library (CDL) restraints added in 979.9 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: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.566A pdb=" N VAL A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 38 removed outlier: 3.515A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.542A pdb=" N LEU A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 removed outlier: 3.551A 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: 3.841A pdb=" N GLY A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.525A 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 removed outlier: 3.503A pdb=" N THR A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.612A 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: 3.560A pdb=" N ASP A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.566A pdb=" N VAL C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 38 removed outlier: 3.516A pdb=" N LEU C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 53 removed outlier: 3.543A pdb=" N LEU C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 3.551A 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: 3.842A pdb=" N GLY C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.525A 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 removed outlier: 3.504A pdb=" N THR C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 165 removed outlier: 3.612A 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: 3.559A pdb=" N ASP C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.533A 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: 3.566A pdb=" N VAL E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 38 removed outlier: 3.515A pdb=" N LEU E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR E 36 " --> pdb=" O TYR E 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 53 removed outlier: 3.543A pdb=" N LEU E 53 " --> pdb=" O ASN E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 70 removed outlier: 3.551A 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: 3.841A pdb=" N GLY E 115 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 127 removed outlier: 3.525A 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 removed outlier: 3.503A pdb=" N THR E 150 " --> pdb=" O ASN E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 165 removed outlier: 3.612A 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: 3.560A pdb=" N ASP E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 3.533A 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: 3.566A pdb=" N VAL G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR G 10 " --> pdb=" O ALA G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 38 removed outlier: 3.515A pdb=" N LEU G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR G 36 " --> pdb=" O TYR G 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR G 38 " --> pdb=" O THR G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 53 removed outlier: 3.542A pdb=" N LEU G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 70 removed outlier: 3.551A 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: 3.841A pdb=" N GLY G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 127 removed outlier: 3.525A 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 removed outlier: 3.503A pdb=" N THR G 150 " --> pdb=" O ASN G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 165 removed outlier: 3.612A 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: 3.560A pdb=" N ASP G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.566A pdb=" N VAL I 9 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR I 10 " --> pdb=" O ALA I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 38 removed outlier: 3.515A pdb=" N LEU I 27 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR I 36 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR I 38 " --> pdb=" O THR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 53 removed outlier: 3.542A pdb=" N LEU I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 70 removed outlier: 3.551A 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: 3.841A pdb=" N GLY I 115 " --> pdb=" O ASN I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 127 removed outlier: 3.524A 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 removed outlier: 3.503A pdb=" N THR I 150 " --> pdb=" O ASN I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 165 removed outlier: 3.612A 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: 3.560A pdb=" N ASP I 189 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.567A pdb=" N VAL K 9 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR K 10 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 38 removed outlier: 3.516A pdb=" N LEU K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR K 36 " --> pdb=" O TYR K 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR K 38 " --> pdb=" O THR K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 53 removed outlier: 3.542A pdb=" N LEU K 53 " --> pdb=" O ASN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 70 removed outlier: 3.551A 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: 3.842A pdb=" N GLY K 115 " --> pdb=" O ASN K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 127 removed outlier: 3.525A 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 removed outlier: 3.503A pdb=" N THR K 150 " --> pdb=" O ASN K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 165 removed outlier: 3.613A 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: 3.560A pdb=" N ASP K 189 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 3.533A 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: 3.566A pdb=" N VAL M 9 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR M 10 " --> pdb=" O ALA M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 38 removed outlier: 3.516A pdb=" N LEU M 27 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR M 36 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR M 38 " --> pdb=" O THR M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 53 removed outlier: 3.543A pdb=" N LEU M 53 " --> pdb=" O ASN M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 70 removed outlier: 3.551A 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: 3.842A pdb=" N GLY M 115 " --> pdb=" O ASN M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 127 removed outlier: 3.525A 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 removed outlier: 3.503A pdb=" N THR M 150 " --> pdb=" O ASN M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 165 removed outlier: 3.612A 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: 3.559A pdb=" N ASP M 189 " --> pdb=" O ALA M 185 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.566A pdb=" N VAL O 9 " --> pdb=" O THR O 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 38 removed outlier: 3.515A pdb=" N LEU O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR O 36 " --> pdb=" O TYR O 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR O 38 " --> pdb=" O THR O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 53 removed outlier: 3.542A pdb=" N LEU O 53 " --> pdb=" O ASN O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 70 removed outlier: 3.551A 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: 3.841A pdb=" N GLY O 115 " --> pdb=" O ASN O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 127 removed outlier: 3.524A 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 removed outlier: 3.504A pdb=" N THR O 150 " --> pdb=" O ASN O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 165 removed outlier: 3.612A 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: 3.559A pdb=" N ASP O 189 " --> pdb=" O ALA O 185 " (cutoff:3.500A) removed outlier: 3.533A 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: 3.565A pdb=" N VAL Q 9 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 38 removed outlier: 3.516A pdb=" N LEU Q 27 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR Q 36 " --> pdb=" O TYR Q 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 53 removed outlier: 3.543A pdb=" N LEU Q 53 " --> pdb=" O ASN Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 70 removed outlier: 3.551A 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: 3.841A pdb=" N GLY Q 115 " --> pdb=" O ASN Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 127 removed outlier: 3.525A 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 removed outlier: 3.504A pdb=" N THR Q 150 " --> pdb=" O ASN Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 165 removed outlier: 3.612A 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: 3.559A pdb=" N ASP Q 189 " --> pdb=" O ALA Q 185 " (cutoff:3.500A) removed outlier: 3.533A 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: 3.566A pdb=" N VAL S 9 " --> pdb=" O THR S 5 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR S 10 " --> pdb=" O ALA S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 38 removed outlier: 3.515A pdb=" N LEU S 27 " --> pdb=" O ALA S 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR S 36 " --> pdb=" O TYR S 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR S 38 " --> pdb=" O THR S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 53 removed outlier: 3.542A pdb=" N LEU S 53 " --> pdb=" O ASN S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 58 through 70 removed outlier: 3.550A 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: 3.841A pdb=" N GLY S 115 " --> pdb=" O ASN S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 127 removed outlier: 3.525A 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 removed outlier: 3.503A pdb=" N THR S 150 " --> pdb=" O ASN S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 155 through 165 removed outlier: 3.612A 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: 3.560A pdb=" N ASP S 189 " --> pdb=" O ALA S 185 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.566A pdb=" N VAL U 9 " --> pdb=" O THR U 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR U 10 " --> pdb=" O ALA U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 38 removed outlier: 3.516A pdb=" N LEU U 27 " --> pdb=" O ALA U 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR U 36 " --> pdb=" O TYR U 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR U 38 " --> pdb=" O THR U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 53 removed outlier: 3.542A pdb=" N LEU U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 70 removed outlier: 3.551A 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: 3.841A pdb=" N GLY U 115 " --> pdb=" O ASN U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 119 through 127 removed outlier: 3.525A 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 removed outlier: 3.503A pdb=" N THR U 150 " --> pdb=" O ASN U 146 " (cutoff:3.500A) Processing helix chain 'U' and resid 155 through 165 removed outlier: 3.612A 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: 3.559A pdb=" N ASP U 189 " --> pdb=" O ALA U 185 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.566A pdb=" N VAL W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR W 10 " --> pdb=" O ALA W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 38 removed outlier: 3.516A pdb=" N LEU W 27 " --> pdb=" O ALA W 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR W 36 " --> pdb=" O TYR W 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR W 38 " --> pdb=" O THR W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 53 removed outlier: 3.542A pdb=" N LEU W 53 " --> pdb=" O ASN W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 70 removed outlier: 3.551A 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: 3.841A pdb=" N GLY W 115 " --> pdb=" O ASN W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 127 removed outlier: 3.525A 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 removed outlier: 3.503A pdb=" N THR W 150 " --> pdb=" O ASN W 146 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 165 removed outlier: 3.612A 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: 3.559A pdb=" N ASP W 189 " --> pdb=" O ALA W 185 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.566A pdb=" N VAL Y 9 " --> pdb=" O THR Y 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 38 removed outlier: 3.515A pdb=" N LEU Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR Y 36 " --> pdb=" O TYR Y 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR Y 38 " --> pdb=" O THR Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 53 removed outlier: 3.542A pdb=" N LEU Y 53 " --> pdb=" O ASN Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 58 through 70 removed outlier: 3.551A 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: 3.842A pdb=" N GLY Y 115 " --> pdb=" O ASN Y 111 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 127 removed outlier: 3.525A 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 removed outlier: 3.503A pdb=" N THR Y 150 " --> pdb=" O ASN Y 146 " (cutoff:3.500A) Processing helix chain 'Y' and resid 155 through 165 removed outlier: 3.612A 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: 3.560A pdb=" N ASP Y 189 " --> pdb=" O ALA Y 185 " (cutoff:3.500A) removed outlier: 3.533A 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: 3.566A pdb=" N VAL 0 9 " --> pdb=" O THR 0 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR 0 10 " --> pdb=" O ALA 0 6 " (cutoff:3.500A) Processing helix chain '0' and resid 22 through 38 removed outlier: 3.515A pdb=" N LEU 0 27 " --> pdb=" O ALA 0 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR 0 36 " --> pdb=" O TYR 0 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR 0 38 " --> pdb=" O THR 0 34 " (cutoff:3.500A) Processing helix chain '0' and resid 42 through 53 removed outlier: 3.542A pdb=" N LEU 0 53 " --> pdb=" O ASN 0 49 " (cutoff:3.500A) Processing helix chain '0' and resid 58 through 70 removed outlier: 3.551A 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: 3.842A pdb=" N GLY 0 115 " --> pdb=" O ASN 0 111 " (cutoff:3.500A) Processing helix chain '0' and resid 119 through 127 removed outlier: 3.524A 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 removed outlier: 3.504A pdb=" N THR 0 150 " --> pdb=" O ASN 0 146 " (cutoff:3.500A) Processing helix chain '0' and resid 155 through 165 removed outlier: 3.612A 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: 3.560A pdb=" N ASP 0 189 " --> pdb=" O ALA 0 185 " (cutoff:3.500A) removed outlier: 3.533A 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 1638 hydrogen bonds defined for protein. 4830 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: 4.67 Time building geometry restraints manager: 3.96 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: 6929 1.34 - 1.46: 7670 1.46 - 1.57: 11973 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 26600 Sorted by residual: bond pdb=" C ASP S 83 " pdb=" O ASP S 83 " ideal model delta sigma weight residual 1.233 1.278 -0.045 1.12e-02 7.97e+03 1.64e+01 bond pdb=" C ASP M 83 " pdb=" O ASP M 83 " ideal model delta sigma weight residual 1.233 1.278 -0.045 1.12e-02 7.97e+03 1.63e+01 bond pdb=" C ASP K 83 " pdb=" O ASP K 83 " ideal model delta sigma weight residual 1.233 1.278 -0.045 1.12e-02 7.97e+03 1.61e+01 bond pdb=" C ASP 0 83 " pdb=" O ASP 0 83 " ideal model delta sigma weight residual 1.233 1.278 -0.045 1.12e-02 7.97e+03 1.61e+01 bond pdb=" C ASP E 83 " pdb=" O ASP E 83 " ideal model delta sigma weight residual 1.233 1.278 -0.045 1.12e-02 7.97e+03 1.61e+01 ... (remaining 26595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 29747 2.01 - 4.01: 5885 4.01 - 6.02: 838 6.02 - 8.02: 56 8.02 - 10.03: 28 Bond angle restraints: 36554 Sorted by residual: angle pdb=" CA ASP G 93 " pdb=" CB ASP G 93 " pdb=" CG ASP G 93 " ideal model delta sigma weight residual 112.60 118.04 -5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" CA ASP U 93 " pdb=" CB ASP U 93 " pdb=" CG ASP U 93 " ideal model delta sigma weight residual 112.60 118.03 -5.43 1.00e+00 1.00e+00 2.95e+01 angle pdb=" CA ASP M 93 " pdb=" CB ASP M 93 " pdb=" CG ASP M 93 " ideal model delta sigma weight residual 112.60 118.02 -5.42 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA ASP K 93 " pdb=" CB ASP K 93 " pdb=" CG ASP K 93 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA ASP W 93 " pdb=" CB ASP W 93 " pdb=" CG ASP W 93 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.00e+00 1.00e+00 2.93e+01 ... (remaining 36549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 12852 17.46 - 34.92: 994 34.92 - 52.37: 252 52.37 - 69.83: 28 69.83 - 87.29: 42 Dihedral angle restraints: 14168 sinusoidal: 4326 harmonic: 9842 Sorted by residual: dihedral pdb=" CA ASP W 93 " pdb=" C ASP W 93 " pdb=" N ALA W 94 " pdb=" CA ALA W 94 " ideal model delta harmonic sigma weight residual 180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP K 93 " pdb=" C ASP K 93 " pdb=" N ALA K 94 " pdb=" CA ALA K 94 " ideal model delta harmonic sigma weight residual 180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP U 93 " pdb=" C ASP U 93 " pdb=" N ALA U 94 " pdb=" CA ALA U 94 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 14165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 4239 0.164 - 0.327: 680 0.327 - 0.491: 32 0.491 - 0.655: 5 0.655 - 0.818: 28 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C1 BMA D 4 " pdb=" O3 MRH D 3 " pdb=" C2 BMA D 4 " pdb=" O5 BMA D 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.67e+03 chirality pdb=" C1 BMA F 4 " pdb=" O3 MRH F 3 " pdb=" C2 BMA F 4 " pdb=" O5 BMA F 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.67e+03 chirality pdb=" C1 BMA B 4 " pdb=" O3 MRH B 3 " pdb=" C2 BMA B 4 " pdb=" O5 BMA B 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.66e+03 ... (remaining 4981 not shown) Planarity restraints: 4480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 MRH V 12 " -0.268 2.00e-02 2.50e+03 2.34e-01 6.86e+02 pdb=" C7 MRH V 12 " 0.040 2.00e-02 2.50e+03 pdb=" C8 MRH V 12 " -0.002 2.00e-02 2.50e+03 pdb=" N4 MRH V 12 " 0.411 2.00e-02 2.50e+03 pdb=" O7 MRH V 12 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 MRH F 12 " -0.268 2.00e-02 2.50e+03 2.34e-01 6.86e+02 pdb=" C7 MRH F 12 " 0.040 2.00e-02 2.50e+03 pdb=" C8 MRH F 12 " -0.002 2.00e-02 2.50e+03 pdb=" N4 MRH F 12 " 0.411 2.00e-02 2.50e+03 pdb=" O7 MRH F 12 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 MRH N 12 " -0.268 2.00e-02 2.50e+03 2.34e-01 6.86e+02 pdb=" C7 MRH N 12 " 0.040 2.00e-02 2.50e+03 pdb=" C8 MRH N 12 " -0.002 2.00e-02 2.50e+03 pdb=" N4 MRH N 12 " 0.411 2.00e-02 2.50e+03 pdb=" O7 MRH N 12 " -0.180 2.00e-02 2.50e+03 ... (remaining 4477 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1507 2.74 - 3.28: 27942 3.28 - 3.82: 42544 3.82 - 4.36: 50862 4.36 - 4.90: 84831 Nonbonded interactions: 207686 Sorted by model distance: nonbonded pdb=" O ALA W 124 " pdb=" OG1 THR W 128 " model vdw 2.206 3.040 nonbonded pdb=" O ALA S 124 " pdb=" OG1 THR S 128 " model vdw 2.206 3.040 nonbonded pdb=" O ALA 0 124 " pdb=" OG1 THR 0 128 " model vdw 2.206 3.040 nonbonded pdb=" O ALA I 124 " pdb=" OG1 THR I 128 " model vdw 2.206 3.040 nonbonded pdb=" O ALA K 124 " pdb=" OG1 THR K 128 " model vdw 2.206 3.040 ... (remaining 207681 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: 0.13 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: 2.060 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.400 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.009 0.053 26754 Z= 0.543 Angle : 2.016 33.754 37016 Z= 1.137 Chirality : 0.129 0.818 4984 Planarity : 0.018 0.234 4480 Dihedral : 14.800 87.291 7868 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.60 % Allowed : 10.71 % Favored : 88.69 % 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: -2.52 (0.12), residues: 3360 helix: -1.38 (0.09), residues: 2394 sheet: None (None), residues: 0 loop : -2.02 (0.17), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.002 ARG K 165 TYR 0.014 0.004 TYR G 171 PHE 0.012 0.003 PHE U 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00891 / 0.54 (26600) covalent geometry : angle 1.63401 / 1.07 (36554) hydrogen bonds : bond 0.27098 / 18.20 ( 1638) hydrogen bonds : angle 8.28969 / 5.88 ( 4830) glycosidic custom : bond 0.00385 / 0.24 ( 112) glycosidic custom : angle 10.71750 / 7.77 ( 336) link_BETA1-3 : bond 0.00681 / 0.43 ( 42) link_BETA1-3 : angle 10.65908 / 7.18 ( 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 343 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 329 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ARG cc_start: 0.9710 (OUTLIER) cc_final: 0.9170 (ptt90) REVERT: C 62 ILE cc_start: 0.9770 (mt) cc_final: 0.9474 (mp) REVERT: C 143 ILE cc_start: 0.9569 (mt) cc_final: 0.9219 (tt) REVERT: C 165 ARG cc_start: 0.9504 (OUTLIER) cc_final: 0.9182 (ptt90) REVERT: E 63 GLN cc_start: 0.9592 (mt0) cc_final: 0.9368 (mm-40) REVERT: E 165 ARG cc_start: 0.9700 (OUTLIER) cc_final: 0.9119 (ptt90) REVERT: E 166 GLN cc_start: 0.9734 (tp40) cc_final: 0.9406 (tp-100) REVERT: G 62 ILE cc_start: 0.9809 (mt) cc_final: 0.9454 (tt) REVERT: G 165 ARG cc_start: 0.9510 (OUTLIER) cc_final: 0.9029 (ptt90) REVERT: G 166 GLN cc_start: 0.9652 (tp40) cc_final: 0.9141 (tp-100) REVERT: G 220 ILE cc_start: 0.9524 (mt) cc_final: 0.9242 (mt) REVERT: G 223 LEU cc_start: 0.9761 (tp) cc_final: 0.9489 (tt) REVERT: I 127 TYR cc_start: 0.9190 (m-80) cc_final: 0.8752 (m-80) REVERT: I 166 GLN cc_start: 0.9571 (tp40) cc_final: 0.8961 (tp-100) REVERT: I 170 ASP cc_start: 0.9641 (m-30) cc_final: 0.9399 (m-30) REVERT: I 223 LEU cc_start: 0.9698 (tp) cc_final: 0.9425 (tt) REVERT: K 63 GLN cc_start: 0.9437 (mt0) cc_final: 0.9194 (mt0) REVERT: K 127 TYR cc_start: 0.8867 (m-80) cc_final: 0.8598 (m-80) REVERT: K 177 ARG cc_start: 0.9663 (ttm110) cc_final: 0.9404 (tpm170) REVERT: K 197 ILE cc_start: 0.9764 (mt) cc_final: 0.9545 (tp) REVERT: K 223 LEU cc_start: 0.9734 (tp) cc_final: 0.9335 (tt) REVERT: M 78 LEU cc_start: 0.9595 (mt) cc_final: 0.9373 (mt) REVERT: M 223 LEU cc_start: 0.9793 (tp) cc_final: 0.9554 (tt) REVERT: O 200 ILE cc_start: 0.9561 (mt) cc_final: 0.9260 (tt) REVERT: Q 62 ILE cc_start: 0.9826 (mt) cc_final: 0.9599 (mp) REVERT: S 166 GLN cc_start: 0.9644 (tp40) cc_final: 0.9224 (tp-100) REVERT: U 63 GLN cc_start: 0.9795 (mt0) cc_final: 0.9221 (mm-40) REVERT: U 78 LEU cc_start: 0.9867 (mt) cc_final: 0.9659 (mt) REVERT: U 143 ILE cc_start: 0.9755 (mt) cc_final: 0.9464 (tt) REVERT: U 165 ARG cc_start: 0.9744 (OUTLIER) cc_final: 0.9270 (ptt90) REVERT: U 200 ILE cc_start: 0.9865 (mt) cc_final: 0.9619 (tt) REVERT: U 219 MET cc_start: 0.9635 (ttt) cc_final: 0.9181 (tpp) REVERT: U 223 LEU cc_start: 0.9608 (tp) cc_final: 0.9392 (tp) REVERT: W 63 GLN cc_start: 0.9742 (mt0) cc_final: 0.9236 (mm110) REVERT: W 78 LEU cc_start: 0.9871 (mt) cc_final: 0.9623 (mt) REVERT: W 165 ARG cc_start: 0.9657 (OUTLIER) cc_final: 0.9219 (ptt90) REVERT: W 177 ARG cc_start: 0.9788 (ttm110) cc_final: 0.9429 (tpm170) REVERT: Y 196 LEU cc_start: 0.9510 (mt) cc_final: 0.9293 (mt) REVERT: 0 165 ARG cc_start: 0.9498 (OUTLIER) cc_final: 0.9273 (ptt90) REVERT: 0 166 GLN cc_start: 0.9187 (tp40) cc_final: 0.8515 (tp40) outliers start: 14 outliers final: 0 residues processed: 343 average time/residue: 0.1983 time to fit residues: 101.5221 Evaluate side-chains 143 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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: 0.0570 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 6.9990 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN A 63 GLN A 92 ASN A 111 ASN A 237 ASN C 49 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 111 ASN C 237 ASN E 49 ASN E 63 GLN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN E 134 GLN E 237 ASN G 49 ASN G 63 GLN G 107 ASN G 111 ASN G 134 GLN G 179 ASN G 237 ASN I 49 ASN I 92 ASN I 107 ASN I 111 ASN I 134 GLN I 237 ASN K 49 ASN K 63 GLN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 ASN K 134 GLN K 179 ASN K 237 ASN M 49 ASN M 63 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN M 134 GLN M 237 ASN O 49 ASN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 ASN O 134 GLN O 237 ASN Q 49 ASN Q 63 GLN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 ASN Q 134 GLN Q 237 ASN S 49 ASN S 63 GLN S 92 ASN S 111 ASN S 134 GLN S 237 ASN U 49 ASN ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 111 ASN U 237 ASN W 49 ASN W 63 GLN ** W 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 111 ASN ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 179 ASN W 237 ASN Y 49 ASN Y 63 GLN ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 107 ASN Y 111 ASN Y 134 GLN Y 179 ASN Y 237 ASN 0 49 ASN 0 63 GLN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 107 ASN 0 111 ASN 0 134 GLN 0 179 ASN 0 237 ASN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.024274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2200 r_free = 0.2200 target = 0.016783 restraints weight = 290708.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2220 r_free = 0.2220 target = 0.017216 restraints weight = 220938.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2235 r_free = 0.2235 target = 0.017569 restraints weight = 180653.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2247 r_free = 0.2247 target = 0.017852 restraints weight = 154241.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2256 r_free = 0.2256 target = 0.018049 restraints weight = 136117.744| |-----------------------------------------------------------------------------| r_work (final): 0.2245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26754 Z= 0.155 Angle : 0.723 9.248 37016 Z= 0.352 Chirality : 0.042 0.257 4984 Planarity : 0.003 0.048 4480 Dihedral : 5.042 18.573 3584 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.17 % Allowed : 0.98 % Favored : 98.85 % 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: -0.04 (0.14), residues: 3360 helix: 0.50 (0.10), residues: 2394 sheet: None (None), residues: 0 loop : -1.18 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 165 TYR 0.030 0.002 TYR Y 65 PHE 0.019 0.002 PHE O 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (26600) covalent geometry : angle 0.70504 / 0.35 (36554) hydrogen bonds : bond 0.04994 / 3.41 ( 1638) hydrogen bonds : angle 5.55373 / 3.96 ( 4830) glycosidic custom : bond 0.00274 / 0.19 ( 112) glycosidic custom : angle 1.19026 / 0.85 ( 336) link_BETA1-3 : bond 0.00439 / 0.27 ( 42) link_BETA1-3 : angle 2.32440 / 1.58 ( 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 207 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 203 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.9779 (tt) cc_final: 0.9536 (pp) REVERT: C 223 LEU cc_start: 0.9841 (tt) cc_final: 0.9619 (pp) REVERT: E 166 GLN cc_start: 0.9440 (tp40) cc_final: 0.8943 (tp-100) REVERT: E 170 ASP cc_start: 0.9851 (m-30) cc_final: 0.9537 (m-30) REVERT: E 196 LEU cc_start: 0.9690 (mt) cc_final: 0.9481 (mt) REVERT: G 219 MET cc_start: 0.9186 (tmm) cc_final: 0.8672 (ppp) REVERT: I 127 TYR cc_start: 0.8739 (m-80) cc_final: 0.8513 (m-80) REVERT: I 171 TYR cc_start: 0.9687 (t80) cc_final: 0.9409 (t80) REVERT: I 223 LEU cc_start: 0.9726 (tp) cc_final: 0.9454 (tt) REVERT: K 63 GLN cc_start: 0.9662 (mt0) cc_final: 0.9440 (mt0) REVERT: K 212 TYR cc_start: 0.9326 (m-80) cc_final: 0.9041 (m-10) REVERT: K 223 LEU cc_start: 0.9633 (tp) cc_final: 0.9397 (tt) REVERT: O 134 GLN cc_start: 0.9543 (mt0) cc_final: 0.9299 (mp10) REVERT: O 197 ILE cc_start: 0.9028 (tp) cc_final: 0.8813 (tp) REVERT: Q 134 GLN cc_start: 0.9628 (mt0) cc_final: 0.9331 (mt0) REVERT: Q 219 MET cc_start: 0.9460 (ppp) cc_final: 0.9201 (ppp) REVERT: Q 231 ASP cc_start: 0.9346 (t0) cc_final: 0.8603 (p0) REVERT: S 127 TYR cc_start: 0.8471 (m-10) cc_final: 0.8271 (m-80) REVERT: U 219 MET cc_start: 0.9783 (ttt) cc_final: 0.9452 (tpp) REVERT: U 223 LEU cc_start: 0.9459 (tp) cc_final: 0.8980 (tt) REVERT: W 63 GLN cc_start: 0.9821 (mt0) cc_final: 0.9378 (mm110) REVERT: W 223 LEU cc_start: 0.9578 (tp) cc_final: 0.9235 (tt) REVERT: Y 63 GLN cc_start: 0.9510 (mt0) cc_final: 0.9087 (mm110) REVERT: Y 196 LEU cc_start: 0.9625 (mt) cc_final: 0.9325 (mt) REVERT: Y 219 MET cc_start: 0.9693 (ttm) cc_final: 0.9480 (ttm) REVERT: Y 223 LEU cc_start: 0.9399 (tt) cc_final: 0.8978 (pp) REVERT: 0 219 MET cc_start: 0.9517 (ttm) cc_final: 0.9202 (ttm) REVERT: 0 223 LEU cc_start: 0.8950 (tt) cc_final: 0.8431 (pp) outliers start: 4 outliers final: 1 residues processed: 206 average time/residue: 0.2222 time to fit residues: 67.3145 Evaluate side-chains 104 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 145 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 239 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 7 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 ASN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 237 ASN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 237 ASN ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 237 ASN W 7 GLN ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 237 ASN Y 7 GLN ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 107 ASN 0 202 ASN 0 237 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.022119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2131 r_free = 0.2131 target = 0.015375 restraints weight = 303405.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2149 r_free = 0.2149 target = 0.015764 restraints weight = 232065.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2164 r_free = 0.2164 target = 0.016082 restraints weight = 189877.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2175 r_free = 0.2175 target = 0.016316 restraints weight = 162651.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2183 r_free = 0.2183 target = 0.016468 restraints weight = 144686.377| |-----------------------------------------------------------------------------| r_work (final): 0.2175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26754 Z= 0.192 Angle : 0.658 9.349 37016 Z= 0.327 Chirality : 0.037 0.244 4984 Planarity : 0.003 0.035 4480 Dihedral : 4.565 18.102 3584 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % 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: 1.22 (0.14), residues: 3360 helix: 1.36 (0.10), residues: 2478 sheet: None (None), residues: 0 loop : -0.67 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 177 TYR 0.021 0.002 TYR Y 65 PHE 0.020 0.002 PHE M 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (26600) covalent geometry : angle 0.64443 / 0.33 (36554) hydrogen bonds : bond 0.03379 / 2.30 ( 1638) hydrogen bonds : angle 5.17021 / 3.69 ( 4830) glycosidic custom : bond 0.00477 / 0.30 ( 112) glycosidic custom : angle 1.11208 / 0.79 ( 336) link_BETA1-3 : bond 0.00299 / 0.18 ( 42) link_BETA1-3 : angle 1.83711 / 1.24 ( 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 141 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9710 (ttp) cc_final: 0.9172 (ppp) REVERT: A 223 LEU cc_start: 0.9846 (tt) cc_final: 0.9621 (pp) REVERT: C 142 LYS cc_start: 0.9794 (tttt) cc_final: 0.9578 (ttmm) REVERT: G 30 ASP cc_start: 0.9494 (m-30) cc_final: 0.9266 (m-30) REVERT: G 99 PHE cc_start: 0.9477 (m-80) cc_final: 0.9128 (m-80) REVERT: G 219 MET cc_start: 0.9403 (tmm) cc_final: 0.8813 (ppp) REVERT: G 223 LEU cc_start: 0.9764 (tt) cc_final: 0.9520 (pp) REVERT: I 127 TYR cc_start: 0.8864 (m-80) cc_final: 0.8397 (m-80) REVERT: I 223 LEU cc_start: 0.9807 (tp) cc_final: 0.9532 (pp) REVERT: K 63 GLN cc_start: 0.9723 (mt0) cc_final: 0.9355 (mt0) REVERT: K 223 LEU cc_start: 0.9797 (tp) cc_final: 0.9527 (tt) REVERT: M 63 GLN cc_start: 0.9647 (mt0) cc_final: 0.9419 (mt0) REVERT: M 96 TYR cc_start: 0.9213 (m-80) cc_final: 0.8854 (m-80) REVERT: O 134 GLN cc_start: 0.9595 (mt0) cc_final: 0.9277 (mt0) REVERT: Q 134 GLN cc_start: 0.9672 (mt0) cc_final: 0.9443 (mt0) REVERT: Q 219 MET cc_start: 0.9458 (ppp) cc_final: 0.9178 (ppp) REVERT: Q 231 ASP cc_start: 0.9343 (t0) cc_final: 0.8598 (p0) REVERT: U 142 LYS cc_start: 0.9718 (tttt) cc_final: 0.9512 (ttmm) REVERT: U 219 MET cc_start: 0.9781 (ttt) cc_final: 0.9386 (tpp) REVERT: U 223 LEU cc_start: 0.9669 (tp) cc_final: 0.9051 (pp) REVERT: W 63 GLN cc_start: 0.9821 (mt0) cc_final: 0.9388 (mm110) REVERT: W 219 MET cc_start: 0.9464 (ppp) cc_final: 0.8944 (ppp) REVERT: W 223 LEU cc_start: 0.9698 (tp) cc_final: 0.9494 (tt) REVERT: Y 63 GLN cc_start: 0.9542 (mt0) cc_final: 0.9112 (mm110) REVERT: Y 196 LEU cc_start: 0.9646 (mt) cc_final: 0.9346 (mt) REVERT: 0 219 MET cc_start: 0.9579 (ttm) cc_final: 0.9327 (ttm) REVERT: 0 223 LEU cc_start: 0.9204 (tt) cc_final: 0.8651 (pp) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.2327 time to fit residues: 47.5761 Evaluate side-chains 81 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 224 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 236 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 287 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 237 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 237 ASN 0 202 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.022215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2143 r_free = 0.2143 target = 0.015505 restraints weight = 304685.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2163 r_free = 0.2163 target = 0.015906 restraints weight = 227929.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2179 r_free = 0.2179 target = 0.016239 restraints weight = 184500.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2190 r_free = 0.2190 target = 0.016489 restraints weight = 156433.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2199 r_free = 0.2199 target = 0.016677 restraints weight = 138068.317| |-----------------------------------------------------------------------------| r_work (final): 0.2191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26754 Z= 0.110 Angle : 0.553 9.521 37016 Z= 0.275 Chirality : 0.036 0.245 4984 Planarity : 0.002 0.032 4480 Dihedral : 4.264 18.557 3584 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: 1.64 (0.15), residues: 3360 helix: 1.69 (0.11), residues: 2478 sheet: None (None), residues: 0 loop : -0.57 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG S 177 TYR 0.023 0.001 TYR Y 212 PHE 0.019 0.001 PHE E 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (26600) covalent geometry : angle 0.54170 / 0.27 (36554) hydrogen bonds : bond 0.02876 / 1.96 ( 1638) hydrogen bonds : angle 4.87381 / 3.47 ( 4830) glycosidic custom : bond 0.00174 / 0.11 ( 112) glycosidic custom : angle 0.73942 / 0.52 ( 336) link_BETA1-3 : bond 0.00306 / 0.19 ( 42) link_BETA1-3 : angle 1.84492 / 1.25 ( 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 138 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9715 (ttp) cc_final: 0.9164 (ppp) REVERT: A 223 LEU cc_start: 0.9831 (tt) cc_final: 0.9618 (pp) REVERT: E 134 GLN cc_start: 0.9733 (mt0) cc_final: 0.9374 (mt0) REVERT: E 196 LEU cc_start: 0.9707 (mt) cc_final: 0.9499 (mt) REVERT: E 219 MET cc_start: 0.9476 (ppp) cc_final: 0.9105 (ppp) REVERT: G 30 ASP cc_start: 0.9485 (m-30) cc_final: 0.9244 (m-30) REVERT: G 99 PHE cc_start: 0.9473 (m-80) cc_final: 0.9132 (m-80) REVERT: G 219 MET cc_start: 0.9424 (tmm) cc_final: 0.8728 (ppp) REVERT: G 223 LEU cc_start: 0.9755 (tt) cc_final: 0.9539 (pp) REVERT: I 127 TYR cc_start: 0.8923 (m-80) cc_final: 0.8494 (m-80) REVERT: I 223 LEU cc_start: 0.9793 (tp) cc_final: 0.9493 (pp) REVERT: K 30 ASP cc_start: 0.9349 (m-30) cc_final: 0.8993 (m-30) REVERT: K 63 GLN cc_start: 0.9732 (mt0) cc_final: 0.9301 (mt0) REVERT: K 127 TYR cc_start: 0.8743 (m-80) cc_final: 0.8168 (m-80) REVERT: K 221 ASN cc_start: 0.9461 (m110) cc_final: 0.9224 (m-40) REVERT: K 223 LEU cc_start: 0.9757 (tp) cc_final: 0.9462 (tt) REVERT: M 63 GLN cc_start: 0.9648 (mt0) cc_final: 0.9443 (mt0) REVERT: M 96 TYR cc_start: 0.8965 (m-80) cc_final: 0.8662 (m-80) REVERT: O 134 GLN cc_start: 0.9633 (mt0) cc_final: 0.9294 (mt0) REVERT: Q 134 GLN cc_start: 0.9699 (mt0) cc_final: 0.9385 (mt0) REVERT: Q 219 MET cc_start: 0.9439 (ppp) cc_final: 0.9134 (ppp) REVERT: Q 231 ASP cc_start: 0.9346 (t0) cc_final: 0.8641 (p0) REVERT: U 142 LYS cc_start: 0.9729 (tttt) cc_final: 0.9512 (ttmm) REVERT: U 219 MET cc_start: 0.9780 (ttt) cc_final: 0.9331 (tpp) REVERT: U 223 LEU cc_start: 0.9663 (tp) cc_final: 0.9002 (pp) REVERT: W 63 GLN cc_start: 0.9814 (mt0) cc_final: 0.9380 (mm110) REVERT: W 219 MET cc_start: 0.9187 (ppp) cc_final: 0.8828 (ppp) REVERT: W 223 LEU cc_start: 0.9672 (tp) cc_final: 0.9426 (tt) REVERT: Y 63 GLN cc_start: 0.9488 (mt0) cc_final: 0.9128 (mm110) REVERT: Y 196 LEU cc_start: 0.9667 (mt) cc_final: 0.9382 (mt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2179 time to fit residues: 44.7211 Evaluate side-chains 84 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 24 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 0.0170 chunk 178 optimal weight: 10.0000 chunk 218 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 overall best weight: 6.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 237 ASN C 107 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 ASN G 202 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN O 237 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 107 ASN ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 7 GLN 0 202 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.020448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2068 r_free = 0.2068 target = 0.014285 restraints weight = 328909.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2088 r_free = 0.2088 target = 0.014654 restraints weight = 243237.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2103 r_free = 0.2103 target = 0.014956 restraints weight = 196047.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2114 r_free = 0.2114 target = 0.015183 restraints weight = 166493.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2122 r_free = 0.2122 target = 0.015330 restraints weight = 146972.975| |-----------------------------------------------------------------------------| r_work (final): 0.2114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26754 Z= 0.254 Angle : 0.740 10.293 37016 Z= 0.359 Chirality : 0.039 0.260 4984 Planarity : 0.003 0.032 4480 Dihedral : 4.477 19.385 3584 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % 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: 1.57 (0.14), residues: 3360 helix: 1.69 (0.10), residues: 2492 sheet: None (None), residues: 0 loop : -0.81 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 165 TYR 0.019 0.002 TYR M 140 PHE 0.029 0.002 PHE I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.25 (26600) covalent geometry : angle 0.71854 / 0.36 (36554) hydrogen bonds : bond 0.02999 / 2.02 ( 1638) hydrogen bonds : angle 5.05309 / 3.60 ( 4830) glycosidic custom : bond 0.00717 / 0.45 ( 112) glycosidic custom : angle 1.65350 / 1.17 ( 336) link_BETA1-3 : bond 0.00462 / 0.29 ( 42) link_BETA1-3 : angle 1.96179 / 1.31 ( 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 118 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 LYS cc_start: 0.9792 (tttt) cc_final: 0.9541 (ttmm) REVERT: E 134 GLN cc_start: 0.9721 (mt0) cc_final: 0.9440 (mt0) REVERT: E 196 LEU cc_start: 0.9721 (mt) cc_final: 0.9503 (mt) REVERT: G 30 ASP cc_start: 0.9484 (m-30) cc_final: 0.9243 (m-30) REVERT: G 99 PHE cc_start: 0.9556 (m-80) cc_final: 0.9240 (m-10) REVERT: G 202 ASN cc_start: 0.9283 (OUTLIER) cc_final: 0.8790 (t0) REVERT: G 219 MET cc_start: 0.9632 (tmm) cc_final: 0.9394 (ppp) REVERT: I 127 TYR cc_start: 0.9108 (m-80) cc_final: 0.8606 (m-80) REVERT: I 201 LEU cc_start: 0.9814 (mt) cc_final: 0.9496 (tp) REVERT: I 223 LEU cc_start: 0.9834 (tp) cc_final: 0.9578 (pp) REVERT: K 30 ASP cc_start: 0.9367 (m-30) cc_final: 0.9014 (m-30) REVERT: K 140 TYR cc_start: 0.9702 (t80) cc_final: 0.9468 (t80) REVERT: K 223 LEU cc_start: 0.9816 (tp) cc_final: 0.9553 (tt) REVERT: M 63 GLN cc_start: 0.9677 (mt0) cc_final: 0.9406 (mt0) REVERT: M 96 TYR cc_start: 0.9165 (m-10) cc_final: 0.8859 (m-80) REVERT: O 134 GLN cc_start: 0.9671 (mt0) cc_final: 0.9337 (mt0) REVERT: Q 134 GLN cc_start: 0.9703 (mt0) cc_final: 0.9396 (mt0) REVERT: Q 219 MET cc_start: 0.9489 (ppp) cc_final: 0.9142 (ppp) REVERT: Q 231 ASP cc_start: 0.9231 (t0) cc_final: 0.8409 (p0) REVERT: U 30 ASP cc_start: 0.9658 (m-30) cc_final: 0.9442 (m-30) REVERT: U 142 LYS cc_start: 0.9727 (tttt) cc_final: 0.9481 (ttmm) REVERT: U 219 MET cc_start: 0.9783 (ttt) cc_final: 0.9329 (tpp) REVERT: U 223 LEU cc_start: 0.9786 (tp) cc_final: 0.9266 (pp) REVERT: W 63 GLN cc_start: 0.9815 (mt0) cc_final: 0.9394 (mm110) REVERT: W 219 MET cc_start: 0.9382 (ppp) cc_final: 0.9007 (ppp) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.2059 time to fit residues: 36.4388 Evaluate side-chains 71 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 293 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 GLN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 GLN S 237 ASN ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.021019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2091 r_free = 0.2091 target = 0.014635 restraints weight = 316474.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2112 r_free = 0.2112 target = 0.015028 restraints weight = 234585.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2127 r_free = 0.2127 target = 0.015337 restraints weight = 188273.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2138 r_free = 0.2138 target = 0.015539 restraints weight = 159429.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2148 r_free = 0.2148 target = 0.015742 restraints weight = 141479.502| |-----------------------------------------------------------------------------| r_work (final): 0.2139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 26754 Z= 0.106 Angle : 0.561 9.562 37016 Z= 0.274 Chirality : 0.036 0.276 4984 Planarity : 0.002 0.031 4480 Dihedral : 4.213 17.007 3584 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.04 % Allowed : 1.96 % Favored : 98.00 % 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: 1.99 (0.11), residues: 2478 sheet: None (None), residues: 0 loop : -0.70 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 177 TYR 0.015 0.001 TYR K 140 PHE 0.021 0.002 PHE I 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (26600) covalent geometry : angle 0.55086 / 0.27 (36554) hydrogen bonds : bond 0.02663 / 1.80 ( 1638) hydrogen bonds : angle 4.77843 / 3.41 ( 4830) glycosidic custom : bond 0.00165 / 0.10 ( 112) glycosidic custom : angle 0.67040 / 0.48 ( 336) link_BETA1-3 : bond 0.00298 / 0.19 ( 42) link_BETA1-3 : angle 1.75381 / 1.19 ( 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 123 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.9825 (tt) cc_final: 0.9574 (pp) REVERT: C 142 LYS cc_start: 0.9781 (tttt) cc_final: 0.9430 (tmtt) REVERT: E 134 GLN cc_start: 0.9724 (mt0) cc_final: 0.9371 (mt0) REVERT: E 196 LEU cc_start: 0.9729 (mt) cc_final: 0.9521 (mt) REVERT: E 219 MET cc_start: 0.9431 (ppp) cc_final: 0.9181 (ppp) REVERT: G 30 ASP cc_start: 0.9521 (m-30) cc_final: 0.9280 (m-30) REVERT: G 219 MET cc_start: 0.9603 (tmm) cc_final: 0.9394 (ppp) REVERT: I 127 TYR cc_start: 0.9034 (m-80) cc_final: 0.8570 (m-80) REVERT: I 201 LEU cc_start: 0.9804 (mt) cc_final: 0.9485 (tp) REVERT: I 223 LEU cc_start: 0.9821 (tp) cc_final: 0.9503 (pp) REVERT: K 30 ASP cc_start: 0.9393 (m-30) cc_final: 0.9046 (m-30) REVERT: K 63 GLN cc_start: 0.9645 (mt0) cc_final: 0.9255 (mt0) REVERT: K 127 TYR cc_start: 0.8995 (m-80) cc_final: 0.8495 (m-80) REVERT: K 223 LEU cc_start: 0.9786 (tp) cc_final: 0.9447 (pp) REVERT: M 63 GLN cc_start: 0.9643 (mt0) cc_final: 0.9398 (mt0) REVERT: M 96 TYR cc_start: 0.9042 (m-10) cc_final: 0.8816 (m-80) REVERT: M 196 LEU cc_start: 0.9435 (mt) cc_final: 0.9228 (mt) REVERT: O 134 GLN cc_start: 0.9686 (mt0) cc_final: 0.9339 (mt0) REVERT: Q 134 GLN cc_start: 0.9717 (mt0) cc_final: 0.9401 (mt0) REVERT: Q 219 MET cc_start: 0.9460 (ppp) cc_final: 0.9127 (ppp) REVERT: Q 231 ASP cc_start: 0.9280 (t0) cc_final: 0.8485 (p0) REVERT: U 30 ASP cc_start: 0.9674 (m-30) cc_final: 0.9452 (m-30) REVERT: U 63 GLN cc_start: 0.9688 (mt0) cc_final: 0.9130 (mm110) REVERT: U 142 LYS cc_start: 0.9720 (tttt) cc_final: 0.9473 (ttmm) REVERT: U 219 MET cc_start: 0.9779 (ttt) cc_final: 0.9395 (tpp) REVERT: W 63 GLN cc_start: 0.9783 (mt0) cc_final: 0.9365 (mm110) REVERT: W 219 MET cc_start: 0.9408 (ppp) cc_final: 0.9131 (ppp) REVERT: W 223 LEU cc_start: 0.9673 (tp) cc_final: 0.9426 (tt) REVERT: Y 196 LEU cc_start: 0.9655 (mt) cc_final: 0.9386 (mt) REVERT: 0 102 GLU cc_start: 0.9781 (pm20) cc_final: 0.9548 (pm20) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1999 time to fit residues: 36.9926 Evaluate side-chains 77 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 307 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 283 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 311 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN M 92 ASN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 GLN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.020007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2050 r_free = 0.2050 target = 0.013929 restraints weight = 342190.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2071 r_free = 0.2071 target = 0.014316 restraints weight = 248573.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2086 r_free = 0.2086 target = 0.014591 restraints weight = 197656.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2099 r_free = 0.2099 target = 0.014845 restraints weight = 166779.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2108 r_free = 0.2108 target = 0.015001 restraints weight = 146152.476| |-----------------------------------------------------------------------------| r_work (final): 0.2100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26754 Z= 0.214 Angle : 0.673 10.927 37016 Z= 0.327 Chirality : 0.038 0.255 4984 Planarity : 0.003 0.052 4480 Dihedral : 4.339 17.446 3584 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.04 % Allowed : 0.85 % Favored : 99.11 % 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: 1.83 (0.15), residues: 3360 helix: 1.91 (0.10), residues: 2492 sheet: None (None), residues: 0 loop : -0.86 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 177 TYR 0.016 0.002 TYR M 140 PHE 0.028 0.002 PHE Y 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 (26600) covalent geometry : angle 0.65547 / 0.32 (36554) hydrogen bonds : bond 0.02774 / 1.87 ( 1638) hydrogen bonds : angle 4.92612 / 3.50 ( 4830) glycosidic custom : bond 0.00608 / 0.39 ( 112) glycosidic custom : angle 1.37101 / 0.98 ( 336) link_BETA1-3 : bond 0.00322 / 0.20 ( 42) link_BETA1-3 : angle 1.85086 / 1.25 ( 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 112 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 134 GLN cc_start: 0.9732 (mt0) cc_final: 0.9438 (mt0) REVERT: E 196 LEU cc_start: 0.9729 (mt) cc_final: 0.9510 (mt) REVERT: E 219 MET cc_start: 0.9506 (ppp) cc_final: 0.9258 (ppp) REVERT: G 30 ASP cc_start: 0.9508 (m-30) cc_final: 0.9268 (m-30) REVERT: G 99 PHE cc_start: 0.9584 (m-80) cc_final: 0.9174 (m-80) REVERT: I 127 TYR cc_start: 0.9125 (m-80) cc_final: 0.8614 (m-80) REVERT: I 201 LEU cc_start: 0.9814 (mt) cc_final: 0.9506 (tp) REVERT: I 223 LEU cc_start: 0.9843 (tp) cc_final: 0.9560 (pp) REVERT: K 30 ASP cc_start: 0.9342 (m-30) cc_final: 0.8982 (m-30) REVERT: K 63 GLN cc_start: 0.9668 (mt0) cc_final: 0.9239 (mt0) REVERT: K 127 TYR cc_start: 0.9190 (m-80) cc_final: 0.8804 (m-80) REVERT: K 223 LEU cc_start: 0.9815 (tp) cc_final: 0.9552 (tt) REVERT: M 63 GLN cc_start: 0.9675 (mt0) cc_final: 0.9392 (mt0) REVERT: M 196 LEU cc_start: 0.9495 (mt) cc_final: 0.9249 (mt) REVERT: O 134 GLN cc_start: 0.9690 (mt0) cc_final: 0.9356 (mt0) REVERT: Q 134 GLN cc_start: 0.9707 (mt0) cc_final: 0.9402 (mt0) REVERT: Q 219 MET cc_start: 0.9517 (ppp) cc_final: 0.9215 (ppp) REVERT: Q 231 ASP cc_start: 0.9235 (t0) cc_final: 0.8357 (p0) REVERT: U 30 ASP cc_start: 0.9670 (m-30) cc_final: 0.9456 (m-30) REVERT: U 63 GLN cc_start: 0.9727 (mt0) cc_final: 0.9173 (pt0) REVERT: U 142 LYS cc_start: 0.9733 (tttt) cc_final: 0.9481 (ttmm) REVERT: U 219 MET cc_start: 0.9793 (ttt) cc_final: 0.9394 (tpp) REVERT: W 63 GLN cc_start: 0.9812 (mt0) cc_final: 0.9399 (mm110) REVERT: W 219 MET cc_start: 0.9504 (ppp) cc_final: 0.9202 (ppp) REVERT: Y 196 LEU cc_start: 0.9673 (mt) cc_final: 0.9386 (mt) REVERT: 0 102 GLU cc_start: 0.9791 (pm20) cc_final: 0.9575 (pm20) REVERT: 0 134 GLN cc_start: 0.9690 (tp-100) cc_final: 0.9444 (tp-100) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.2150 time to fit residues: 36.2232 Evaluate side-chains 74 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 78 optimal weight: 0.9980 chunk 254 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 229 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 63 GLN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN W 134 GLN Y 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.020533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2079 r_free = 0.2079 target = 0.014316 restraints weight = 331983.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2100 r_free = 0.2100 target = 0.014716 restraints weight = 240616.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2117 r_free = 0.2117 target = 0.015039 restraints weight = 190761.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2128 r_free = 0.2128 target = 0.015236 restraints weight = 159930.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2138 r_free = 0.2138 target = 0.015450 restraints weight = 141364.028| |-----------------------------------------------------------------------------| r_work (final): 0.2129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 26754 Z= 0.097 Angle : 0.545 10.018 37016 Z= 0.266 Chirality : 0.036 0.249 4984 Planarity : 0.002 0.030 4480 Dihedral : 4.086 15.653 3584 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.04 % Allowed : 0.89 % Favored : 99.06 % 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: 2.11 (0.15), residues: 3360 helix: 2.13 (0.11), residues: 2478 sheet: None (None), residues: 0 loop : -0.74 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 0 177 TYR 0.012 0.001 TYR Q 3 PHE 0.015 0.001 PHE Y 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (26600) covalent geometry : angle 0.53620 / 0.27 (36554) hydrogen bonds : bond 0.02537 / 1.71 ( 1638) hydrogen bonds : angle 4.68265 / 3.34 ( 4830) glycosidic custom : bond 0.00130 / 0.08 ( 112) glycosidic custom : angle 0.65064 / 0.46 ( 336) link_BETA1-3 : bond 0.00353 / 0.23 ( 42) link_BETA1-3 : angle 1.68721 / 1.15 ( 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 119 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.9840 (tt) cc_final: 0.9593 (pp) REVERT: E 134 GLN cc_start: 0.9740 (mt0) cc_final: 0.9456 (mt0) REVERT: E 196 LEU cc_start: 0.9741 (mt) cc_final: 0.9522 (mt) REVERT: E 219 MET cc_start: 0.9518 (ppp) cc_final: 0.9256 (ppp) REVERT: G 30 ASP cc_start: 0.9529 (m-30) cc_final: 0.9270 (m-30) REVERT: G 201 LEU cc_start: 0.9681 (mt) cc_final: 0.9441 (tp) REVERT: I 127 TYR cc_start: 0.9091 (m-80) cc_final: 0.8617 (m-80) REVERT: I 201 LEU cc_start: 0.9802 (mt) cc_final: 0.9488 (tp) REVERT: I 223 LEU cc_start: 0.9833 (tp) cc_final: 0.9522 (pp) REVERT: K 30 ASP cc_start: 0.9381 (m-30) cc_final: 0.9027 (m-30) REVERT: K 63 GLN cc_start: 0.9664 (mt0) cc_final: 0.9271 (mt0) REVERT: K 127 TYR cc_start: 0.9120 (m-80) cc_final: 0.8752 (m-80) REVERT: K 223 LEU cc_start: 0.9772 (tp) cc_final: 0.9474 (pp) REVERT: M 63 GLN cc_start: 0.9617 (mt0) cc_final: 0.9374 (mt0) REVERT: M 96 TYR cc_start: 0.9119 (m-80) cc_final: 0.8888 (m-10) REVERT: M 196 LEU cc_start: 0.9450 (mt) cc_final: 0.9206 (mt) REVERT: Q 134 GLN cc_start: 0.9721 (mt0) cc_final: 0.9405 (mt0) REVERT: Q 142 LYS cc_start: 0.9517 (ttmm) cc_final: 0.9129 (mmtp) REVERT: Q 219 MET cc_start: 0.9465 (ppp) cc_final: 0.9158 (ppp) REVERT: Q 231 ASP cc_start: 0.9279 (t0) cc_final: 0.8480 (p0) REVERT: S 219 MET cc_start: 0.9406 (ppp) cc_final: 0.9157 (ppp) REVERT: U 30 ASP cc_start: 0.9664 (m-30) cc_final: 0.9435 (m-30) REVERT: U 63 GLN cc_start: 0.9679 (mt0) cc_final: 0.9094 (pt0) REVERT: U 142 LYS cc_start: 0.9723 (tttt) cc_final: 0.9473 (ttmm) REVERT: U 219 MET cc_start: 0.9786 (ttt) cc_final: 0.9444 (tpp) REVERT: W 63 GLN cc_start: 0.9774 (mt0) cc_final: 0.9359 (mm110) REVERT: W 219 MET cc_start: 0.9466 (ppp) cc_final: 0.9068 (ppp) REVERT: W 223 LEU cc_start: 0.9678 (tp) cc_final: 0.9276 (pp) REVERT: Y 63 GLN cc_start: 0.9514 (mt0) cc_final: 0.9194 (mm110) REVERT: Y 219 MET cc_start: 0.9383 (ppp) cc_final: 0.9150 (ppp) REVERT: 0 102 GLU cc_start: 0.9800 (pm20) cc_final: 0.9576 (pm20) REVERT: 0 134 GLN cc_start: 0.9659 (tp-100) cc_final: 0.9404 (tp-100) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.2014 time to fit residues: 36.1636 Evaluate side-chains 79 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 53 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 275 optimal weight: 30.0000 chunk 237 optimal weight: 6.9990 chunk 274 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 332 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 179 ASN E 7 GLN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2369 r_free = 0.2369 target = 0.020362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2072 r_free = 0.2072 target = 0.014153 restraints weight = 330886.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2093 r_free = 0.2093 target = 0.014538 restraints weight = 242251.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2108 r_free = 0.2108 target = 0.014820 restraints weight = 193090.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2121 r_free = 0.2121 target = 0.015076 restraints weight = 162977.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2129 r_free = 0.2129 target = 0.015234 restraints weight = 142977.333| |-----------------------------------------------------------------------------| r_work (final): 0.2123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 26754 Z= 0.117 Angle : 0.554 9.696 37016 Z= 0.273 Chirality : 0.036 0.282 4984 Planarity : 0.002 0.030 4480 Dihedral : 3.991 16.164 3584 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 2.13 (0.15), residues: 3360 helix: 2.11 (0.11), residues: 2492 sheet: None (None), residues: 0 loop : -0.68 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 165 TYR 0.018 0.001 TYR K 171 PHE 0.015 0.001 PHE E 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (26600) covalent geometry : angle 0.54377 / 0.27 (36554) hydrogen bonds : bond 0.02491 / 1.67 ( 1638) hydrogen bonds : angle 4.69607 / 3.36 ( 4830) glycosidic custom : bond 0.00280 / 0.18 ( 112) glycosidic custom : angle 0.78019 / 0.56 ( 336) link_BETA1-3 : bond 0.00248 / 0.15 ( 42) link_BETA1-3 : angle 1.68840 / 1.15 ( 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 117 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.9828 (tt) cc_final: 0.9606 (pp) REVERT: E 134 GLN cc_start: 0.9745 (mt0) cc_final: 0.9399 (mt0) REVERT: E 196 LEU cc_start: 0.9738 (mt) cc_final: 0.9520 (mt) REVERT: E 219 MET cc_start: 0.9546 (ppp) cc_final: 0.9287 (ppp) REVERT: G 30 ASP cc_start: 0.9506 (m-30) cc_final: 0.9273 (m-30) REVERT: G 99 PHE cc_start: 0.9540 (m-80) cc_final: 0.9217 (m-80) REVERT: G 201 LEU cc_start: 0.9670 (mt) cc_final: 0.9425 (tp) REVERT: I 127 TYR cc_start: 0.9077 (m-80) cc_final: 0.8585 (m-80) REVERT: I 201 LEU cc_start: 0.9787 (mt) cc_final: 0.9483 (tp) REVERT: I 223 LEU cc_start: 0.9842 (tp) cc_final: 0.9555 (pp) REVERT: K 30 ASP cc_start: 0.9366 (m-30) cc_final: 0.9014 (m-30) REVERT: K 63 GLN cc_start: 0.9658 (mt0) cc_final: 0.9234 (mt0) REVERT: K 127 TYR cc_start: 0.9195 (m-80) cc_final: 0.8875 (m-80) REVERT: K 223 LEU cc_start: 0.9802 (tp) cc_final: 0.9483 (pp) REVERT: M 63 GLN cc_start: 0.9610 (mt0) cc_final: 0.9360 (mt0) REVERT: M 96 TYR cc_start: 0.9187 (m-80) cc_final: 0.8951 (m-80) REVERT: M 196 LEU cc_start: 0.9467 (mt) cc_final: 0.9209 (mt) REVERT: Q 134 GLN cc_start: 0.9719 (mt0) cc_final: 0.9398 (mt0) REVERT: Q 142 LYS cc_start: 0.9515 (ttmm) cc_final: 0.9147 (mmtp) REVERT: Q 219 MET cc_start: 0.9463 (ppp) cc_final: 0.9148 (ppp) REVERT: Q 231 ASP cc_start: 0.9282 (t0) cc_final: 0.8465 (p0) REVERT: S 219 MET cc_start: 0.9404 (ppp) cc_final: 0.9169 (ppp) REVERT: U 30 ASP cc_start: 0.9667 (m-30) cc_final: 0.9442 (m-30) REVERT: U 63 GLN cc_start: 0.9683 (mt0) cc_final: 0.9111 (pt0) REVERT: U 142 LYS cc_start: 0.9724 (tttt) cc_final: 0.9476 (ttmm) REVERT: U 219 MET cc_start: 0.9811 (ttt) cc_final: 0.9435 (tpp) REVERT: U 223 LEU cc_start: 0.9679 (mt) cc_final: 0.9325 (tt) REVERT: W 63 GLN cc_start: 0.9773 (mt0) cc_final: 0.9371 (mm110) REVERT: W 219 MET cc_start: 0.9496 (ppp) cc_final: 0.9147 (ppp) REVERT: W 223 LEU cc_start: 0.9698 (tp) cc_final: 0.9448 (tt) REVERT: Y 63 GLN cc_start: 0.9527 (mt0) cc_final: 0.9203 (mm-40) REVERT: Y 219 MET cc_start: 0.9412 (ppp) cc_final: 0.9207 (ppp) REVERT: 0 102 GLU cc_start: 0.9809 (pm20) cc_final: 0.9588 (pm20) REVERT: 0 134 GLN cc_start: 0.9683 (tp-100) cc_final: 0.9422 (tp-100) REVERT: 0 166 GLN cc_start: 0.9594 (mm-40) cc_final: 0.8809 (tp40) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2089 time to fit residues: 36.6575 Evaluate side-chains 79 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 146 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 227 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 323 optimal weight: 30.0000 chunk 237 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 237 ASN Y 134 GLN 0 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.019743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2047 r_free = 0.2047 target = 0.013757 restraints weight = 341373.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2067 r_free = 0.2067 target = 0.014134 restraints weight = 248690.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2083 r_free = 0.2083 target = 0.014435 restraints weight = 198349.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2094 r_free = 0.2094 target = 0.014652 restraints weight = 167589.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2102 r_free = 0.2102 target = 0.014788 restraints weight = 147582.931| |-----------------------------------------------------------------------------| r_work (final): 0.2095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26754 Z= 0.186 Angle : 0.638 11.206 37016 Z= 0.310 Chirality : 0.037 0.295 4984 Planarity : 0.003 0.036 4480 Dihedral : 4.152 17.206 3584 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 2.06 (0.15), residues: 3360 helix: 2.11 (0.11), residues: 2478 sheet: None (None), residues: 0 loop : -0.82 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Y 165 TYR 0.014 0.002 TYR E 65 PHE 0.021 0.002 PHE K 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (26600) covalent geometry : angle 0.62152 / 0.31 (36554) hydrogen bonds : bond 0.02623 / 1.76 ( 1638) hydrogen bonds : angle 4.79999 / 3.42 ( 4830) glycosidic custom : bond 0.00554 / 0.35 ( 112) glycosidic custom : angle 1.25340 / 0.90 ( 336) link_BETA1-3 : bond 0.00233 / 0.14 ( 42) link_BETA1-3 : angle 1.79201 / 1.22 ( 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 106 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 134 GLN cc_start: 0.9746 (mt0) cc_final: 0.9451 (mt0) REVERT: E 196 LEU cc_start: 0.9743 (mt) cc_final: 0.9537 (mt) REVERT: E 219 MET cc_start: 0.9556 (ppp) cc_final: 0.9293 (ppp) REVERT: G 30 ASP cc_start: 0.9550 (m-30) cc_final: 0.9280 (m-30) REVERT: G 201 LEU cc_start: 0.9718 (mt) cc_final: 0.9468 (tp) REVERT: I 127 TYR cc_start: 0.9085 (m-80) cc_final: 0.8562 (m-80) REVERT: I 201 LEU cc_start: 0.9806 (mt) cc_final: 0.9494 (tp) REVERT: I 223 LEU cc_start: 0.9843 (tp) cc_final: 0.9556 (pp) REVERT: K 30 ASP cc_start: 0.9381 (m-30) cc_final: 0.9028 (m-30) REVERT: K 63 GLN cc_start: 0.9581 (mt0) cc_final: 0.9226 (mt0) REVERT: K 223 LEU cc_start: 0.9792 (tp) cc_final: 0.9485 (pp) REVERT: M 63 GLN cc_start: 0.9641 (mt0) cc_final: 0.9333 (mt0) REVERT: M 96 TYR cc_start: 0.9176 (m-80) cc_final: 0.8954 (m-80) REVERT: M 196 LEU cc_start: 0.9529 (mt) cc_final: 0.9255 (mt) REVERT: O 134 GLN cc_start: 0.9721 (mt0) cc_final: 0.9385 (mt0) REVERT: Q 134 GLN cc_start: 0.9722 (mt0) cc_final: 0.9383 (mt0) REVERT: Q 142 LYS cc_start: 0.9489 (ttmm) cc_final: 0.9135 (mmtp) REVERT: Q 219 MET cc_start: 0.9463 (ppp) cc_final: 0.9162 (ppp) REVERT: Q 231 ASP cc_start: 0.9194 (t0) cc_final: 0.8252 (p0) REVERT: S 219 MET cc_start: 0.9384 (ppp) cc_final: 0.9162 (ppp) REVERT: U 30 ASP cc_start: 0.9669 (m-30) cc_final: 0.9444 (m-30) REVERT: U 63 GLN cc_start: 0.9702 (mt0) cc_final: 0.9175 (pt0) REVERT: U 142 LYS cc_start: 0.9704 (tttt) cc_final: 0.9480 (ttmm) REVERT: U 219 MET cc_start: 0.9789 (ttt) cc_final: 0.9398 (tpp) REVERT: W 63 GLN cc_start: 0.9767 (mt0) cc_final: 0.9350 (mm110) REVERT: W 219 MET cc_start: 0.9509 (ppp) cc_final: 0.9175 (ppp) REVERT: W 223 LEU cc_start: 0.9721 (tp) cc_final: 0.9478 (tt) REVERT: Y 219 MET cc_start: 0.9414 (ppp) cc_final: 0.9213 (ppp) REVERT: 0 134 GLN cc_start: 0.9658 (tp-100) cc_final: 0.9412 (tp-100) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2239 time to fit residues: 35.0699 Evaluate side-chains 70 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 242 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 236 optimal weight: 0.3980 chunk 148 optimal weight: 8.9990 chunk 252 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 303 optimal weight: 20.0000 chunk 301 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.019730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2048 r_free = 0.2048 target = 0.013734 restraints weight = 340121.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2068 r_free = 0.2068 target = 0.014118 restraints weight = 245716.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2084 r_free = 0.2084 target = 0.014423 restraints weight = 195026.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2096 r_free = 0.2096 target = 0.014651 restraints weight = 164326.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2104 r_free = 0.2104 target = 0.014796 restraints weight = 144206.844| |-----------------------------------------------------------------------------| r_work (final): 0.2098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26754 Z= 0.143 Angle : 0.575 9.617 37016 Z= 0.282 Chirality : 0.036 0.255 4984 Planarity : 0.002 0.032 4480 Dihedral : 4.052 18.336 3584 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 2.14 (0.15), residues: 3360 helix: 2.15 (0.10), residues: 2478 sheet: None (None), residues: 0 loop : -0.75 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 165 TYR 0.019 0.001 TYR K 171 PHE 0.019 0.002 PHE E 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (26600) covalent geometry : angle 0.56305 / 0.28 (36554) hydrogen bonds : bond 0.02515 / 1.68 ( 1638) hydrogen bonds : angle 4.71853 / 3.37 ( 4830) glycosidic custom : bond 0.00386 / 0.25 ( 112) glycosidic custom : angle 0.88718 / 0.64 ( 336) link_BETA1-3 : bond 0.00258 / 0.15 ( 42) link_BETA1-3 : angle 1.73246 / 1.19 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.80 seconds wall clock time: 64 minutes 45.73 seconds (3885.73 seconds total)