Starting phenix.real_space_refine on Mon Aug 25 08:21:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7peo_13355/08_2025/7peo_13355.cif Found real_map, /net/cci-nas-00/data/ceres_data/7peo_13355/08_2025/7peo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7peo_13355/08_2025/7peo_13355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7peo_13355/08_2025/7peo_13355.map" model { file = "/net/cci-nas-00/data/ceres_data/7peo_13355/08_2025/7peo_13355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7peo_13355/08_2025/7peo_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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26278 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 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: 2.78, 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: 3.98 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.82 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: 4.52 Time building geometry restraints manager: 4.71 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 - 20.88: 15610 20.88 - 41.76: 994 41.76 - 62.64: 230 62.64 - 83.53: 316 83.53 - 104.41: 210 Dihedral angle restraints: 17360 sinusoidal: 7518 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 17357 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain '0' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain '1' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.100 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 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 : 22.193 104.407 11060 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 aren 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 covalent geometry : bond 0.00891 (26600) covalent geometry : angle 1.63401 (36554) hydrogen bonds : bond 0.27098 ( 1638) hydrogen bonds : angle 8.28969 ( 4830) glycosidic custom : bond 0.00385 ( 112) glycosidic custom : angle 10.71750 ( 336) link_BETA1-3 : bond 0.00681 ( 42) link_BETA1-3 : angle 10.65908 ( 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 : 0.723 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: 0.9407 (tp-100) REVERT: G 62 ILE cc_start: 0.9808 (mt) cc_final: 0.9455 (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: 0.9488 (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: 0.9544 (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: 0.9792 (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: 0.9220 (ptt90) REVERT: W 177 ARG cc_start: 0.9788 (ttm110) cc_final: 0.9428 (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: 0.2055 time to fit residues: 104.5341 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 : 0.691 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 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 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: 76 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.024248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2200 r_free = 0.2200 target = 0.016783 restraints weight = 289763.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2220 r_free = 0.2220 target = 0.017212 restraints weight = 221156.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2235 r_free = 0.2235 target = 0.017550 restraints weight = 179971.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2247 r_free = 0.2247 target = 0.017832 restraints weight = 153785.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2256 r_free = 0.2256 target = 0.018031 restraints weight = 135609.726| |-----------------------------------------------------------------------------| r_work (final): 0.2246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26754 Z= 0.161 Angle : 0.804 8.972 37016 Z= 0.374 Chirality : 0.050 0.249 4984 Planarity : 0.004 0.052 4480 Dihedral : 13.353 58.261 6776 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.26 % Allowed : 1.19 % Favored : 98.55 % 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 aren not related in a simple way. whole: -0.09 (0.13), residues: 3360 helix: 0.44 (0.10), residues: 2394 sheet: None (None), residues: 0 loop : -1.13 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 165 TYR 0.029 0.002 TYR Y 65 PHE 0.019 0.002 PHE O 108 Details of bonding type rmsd covalent geometry : bond 0.00331 (26600) covalent geometry : angle 0.76435 (36554) hydrogen bonds : bond 0.04880 ( 1638) hydrogen bonds : angle 5.58114 ( 4830) glycosidic custom : bond 0.00330 ( 112) glycosidic custom : angle 1.92824 ( 336) link_BETA1-3 : bond 0.00464 ( 42) link_BETA1-3 : angle 3.20941 ( 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 209 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 203 time to evaluate : 0.652 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: A 223 LEU cc_start: 0.9782 (tt) cc_final: 0.9514 (pp) REVERT: C 223 LEU cc_start: 0.9845 (tt) cc_final: 0.9621 (pp) REVERT: E 166 GLN cc_start: 0.9434 (tp40) cc_final: 0.8946 (tp-100) REVERT: E 170 ASP cc_start: 0.9853 (m-30) cc_final: 0.9542 (m-30) REVERT: E 196 LEU cc_start: 0.9692 (mt) cc_final: 0.9491 (mt) REVERT: G 219 MET cc_start: 0.9206 (tmm) cc_final: 0.8695 (ppp) REVERT: I 127 TYR cc_start: 0.8748 (m-80) cc_final: 0.8532 (m-80) REVERT: I 171 TYR cc_start: 0.9692 (t80) cc_final: 0.9416 (t80) REVERT: I 223 LEU cc_start: 0.9731 (tp) cc_final: 0.9460 (tt) REVERT: K 63 GLN cc_start: 0.9669 (mt0) cc_final: 0.9442 (mt0) REVERT: K 127 TYR cc_start: 0.8855 (m-80) cc_final: 0.8596 (m-80) REVERT: K 212 TYR cc_start: 0.9318 (m-80) cc_final: 0.9040 (m-10) REVERT: K 223 LEU cc_start: 0.9638 (tp) cc_final: 0.9404 (tt) REVERT: O 197 ILE cc_start: 0.9018 (tp) cc_final: 0.8801 (tp) REVERT: Q 134 GLN cc_start: 0.9627 (mt0) cc_final: 0.9332 (mt0) REVERT: Q 219 MET cc_start: 0.9478 (ppp) cc_final: 0.9232 (ppp) REVERT: Q 231 ASP cc_start: 0.9367 (t0) cc_final: 0.8630 (p0) REVERT: S 127 TYR cc_start: 0.8462 (m-10) cc_final: 0.8259 (m-80) REVERT: U 219 MET cc_start: 0.9787 (ttt) cc_final: 0.9459 (tpp) REVERT: U 223 LEU cc_start: 0.9471 (tp) cc_final: 0.8994 (tt) REVERT: W 63 GLN cc_start: 0.9817 (mt0) cc_final: 0.9358 (mm110) REVERT: W 223 LEU cc_start: 0.9589 (tp) cc_final: 0.9245 (tt) REVERT: Y 63 GLN cc_start: 0.9507 (mt0) cc_final: 0.9110 (mm110) REVERT: Y 196 LEU cc_start: 0.9625 (mt) cc_final: 0.9324 (mt) REVERT: 0 219 MET cc_start: 0.9524 (ttm) cc_final: 0.9233 (ttm) REVERT: 0 223 LEU cc_start: 0.8960 (tt) cc_final: 0.8440 (pp) outliers start: 6 outliers final: 1 residues processed: 208 average time/residue: 0.2168 time to fit residues: 66.1710 Evaluate side-chains 105 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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: 2.9990 chunk 29 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 239 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 199 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 107 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN M 63 GLN M 92 ASN M 237 ASN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 237 ASN ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 237 ASN 0 237 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.022902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2160 r_free = 0.2160 target = 0.015904 restraints weight = 302580.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2182 r_free = 0.2182 target = 0.016311 restraints weight = 228664.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2196 r_free = 0.2196 target = 0.016603 restraints weight = 184930.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2206 r_free = 0.2206 target = 0.016801 restraints weight = 157979.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2215 r_free = 0.2215 target = 0.017011 restraints weight = 141632.399| |-----------------------------------------------------------------------------| r_work (final): 0.2205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26754 Z= 0.149 Angle : 0.666 9.475 37016 Z= 0.315 Chirality : 0.041 0.242 4984 Planarity : 0.003 0.041 4480 Dihedral : 9.977 51.748 6776 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.13 % Allowed : 2.98 % Favored : 96.90 % 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 aren not related in a simple way. whole: 1.15 (0.14), residues: 3360 helix: 1.46 (0.11), residues: 2394 sheet: None (None), residues: 0 loop : -0.96 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 177 TYR 0.019 0.001 TYR Y 65 PHE 0.016 0.002 PHE M 239 Details of bonding type rmsd covalent geometry : bond 0.00298 (26600) covalent geometry : angle 0.62988 (36554) hydrogen bonds : bond 0.03481 ( 1638) hydrogen bonds : angle 5.11856 ( 4830) glycosidic custom : bond 0.00301 ( 112) glycosidic custom : angle 1.62891 ( 336) link_BETA1-3 : bond 0.00346 ( 42) link_BETA1-3 : angle 2.83501 ( 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 144 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.846 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: A 219 MET cc_start: 0.9729 (ttp) cc_final: 0.9165 (ppp) REVERT: E 166 GLN cc_start: 0.9381 (tp40) cc_final: 0.8872 (tp-100) REVERT: E 170 ASP cc_start: 0.9829 (m-30) cc_final: 0.9538 (m-30) REVERT: G 30 ASP cc_start: 0.9481 (m-30) cc_final: 0.9233 (m-30) REVERT: G 99 PHE cc_start: 0.9443 (m-80) cc_final: 0.9089 (m-80) REVERT: G 219 MET cc_start: 0.9333 (tmm) cc_final: 0.8731 (ppp) REVERT: G 223 LEU cc_start: 0.9723 (tt) cc_final: 0.9473 (pp) REVERT: I 223 LEU cc_start: 0.9773 (tp) cc_final: 0.9512 (tt) REVERT: K 63 GLN cc_start: 0.9711 (mt0) cc_final: 0.9426 (mt0) REVERT: K 221 ASN cc_start: 0.9458 (m110) cc_final: 0.9186 (m-40) REVERT: K 223 LEU cc_start: 0.9769 (tp) cc_final: 0.9469 (tt) REVERT: M 62 ILE cc_start: 0.9534 (OUTLIER) cc_final: 0.9267 (tp) REVERT: M 63 GLN cc_start: 0.9654 (mt0) cc_final: 0.9447 (mt0) REVERT: M 78 LEU cc_start: 0.9685 (mt) cc_final: 0.9478 (mt) REVERT: M 96 TYR cc_start: 0.9083 (m-80) cc_final: 0.8672 (m-80) REVERT: O 134 GLN cc_start: 0.9575 (mt0) cc_final: 0.9255 (mt0) REVERT: Q 134 GLN cc_start: 0.9658 (mt0) cc_final: 0.9368 (mt0) REVERT: Q 219 MET cc_start: 0.9457 (ppp) cc_final: 0.9158 (ppp) REVERT: Q 231 ASP cc_start: 0.9369 (t0) cc_final: 0.8645 (p0) REVERT: U 219 MET cc_start: 0.9772 (ttt) cc_final: 0.9337 (tpp) REVERT: U 223 LEU cc_start: 0.9637 (tp) cc_final: 0.8980 (pp) REVERT: W 63 GLN cc_start: 0.9814 (mt0) cc_final: 0.9380 (mm110) REVERT: W 219 MET cc_start: 0.9381 (ppp) cc_final: 0.8879 (ppp) REVERT: Y 63 GLN cc_start: 0.9524 (mt0) cc_final: 0.9095 (mm110) REVERT: Y 196 LEU cc_start: 0.9635 (mt) cc_final: 0.9325 (mt) REVERT: 0 219 MET cc_start: 0.9546 (ttm) cc_final: 0.9289 (ttm) REVERT: 0 223 LEU cc_start: 0.9047 (tt) cc_final: 0.8515 (pp) outliers start: 3 outliers final: 0 residues processed: 144 average time/residue: 0.2469 time to fit residues: 51.7636 Evaluate side-chains 89 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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: 8.9990 chunk 65 optimal weight: 0.8980 chunk 236 optimal weight: 30.0000 chunk 134 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 287 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** K 237 ASN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 GLN Y 237 ASN 0 7 GLN ** 0 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.022277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2147 r_free = 0.2147 target = 0.015671 restraints weight = 307285.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2170 r_free = 0.2170 target = 0.016086 restraints weight = 229991.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2185 r_free = 0.2185 target = 0.016375 restraints weight = 182164.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2196 r_free = 0.2196 target = 0.016589 restraints weight = 155571.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2206 r_free = 0.2206 target = 0.016801 restraints weight = 136178.506| |-----------------------------------------------------------------------------| r_work (final): 0.2193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26754 Z= 0.136 Angle : 0.611 9.599 37016 Z= 0.290 Chirality : 0.040 0.239 4984 Planarity : 0.003 0.031 4480 Dihedral : 7.386 52.258 6776 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.04 % Allowed : 2.51 % Favored : 97.45 % 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 aren not related in a simple way. whole: 1.72 (0.15), residues: 3360 helix: 1.75 (0.11), residues: 2478 sheet: None (None), residues: 0 loop : -0.54 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 177 TYR 0.024 0.001 TYR Q 3 PHE 0.020 0.002 PHE G 105 Details of bonding type rmsd covalent geometry : bond 0.00275 (26600) covalent geometry : angle 0.57385 (36554) hydrogen bonds : bond 0.02698 ( 1638) hydrogen bonds : angle 4.80093 ( 4830) glycosidic custom : bond 0.00269 ( 112) glycosidic custom : angle 1.81522 ( 336) link_BETA1-3 : bond 0.00368 ( 42) link_BETA1-3 : angle 2.30595 ( 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 143 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.809 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: A 223 LEU cc_start: 0.9826 (tt) cc_final: 0.9595 (pp) REVERT: E 134 GLN cc_start: 0.9736 (mt0) cc_final: 0.9373 (mt0) REVERT: E 142 LYS cc_start: 0.9451 (tttt) cc_final: 0.9248 (tmtt) REVERT: E 196 LEU cc_start: 0.9703 (mt) cc_final: 0.9502 (mt) REVERT: E 223 LEU cc_start: 0.9823 (tt) cc_final: 0.9559 (pp) REVERT: G 30 ASP cc_start: 0.9511 (m-30) cc_final: 0.9223 (m-30) REVERT: G 99 PHE cc_start: 0.9447 (m-80) cc_final: 0.9044 (m-80) REVERT: G 219 MET cc_start: 0.9429 (tmm) cc_final: 0.8713 (ppp) REVERT: G 223 LEU cc_start: 0.9754 (tt) cc_final: 0.9552 (pp) REVERT: I 223 LEU cc_start: 0.9778 (tp) cc_final: 0.9476 (pp) REVERT: K 63 GLN cc_start: 0.9732 (mt0) cc_final: 0.9300 (mt0) REVERT: K 127 TYR cc_start: 0.8891 (m-80) cc_final: 0.8410 (m-80) REVERT: K 221 ASN cc_start: 0.9458 (m110) cc_final: 0.9219 (m-40) REVERT: K 223 LEU cc_start: 0.9749 (tp) cc_final: 0.9461 (tt) REVERT: M 62 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9270 (tp) REVERT: M 63 GLN cc_start: 0.9638 (mt0) cc_final: 0.9418 (mt0) REVERT: M 78 LEU cc_start: 0.9701 (mt) cc_final: 0.9456 (mt) REVERT: M 96 TYR cc_start: 0.8948 (m-80) cc_final: 0.8571 (m-80) REVERT: M 127 TYR cc_start: 0.8997 (m-80) cc_final: 0.8669 (m-80) REVERT: O 134 GLN cc_start: 0.9643 (mt0) cc_final: 0.9298 (mt0) REVERT: Q 134 GLN cc_start: 0.9691 (mt0) cc_final: 0.9370 (mt0) REVERT: Q 219 MET cc_start: 0.9438 (ppp) cc_final: 0.9108 (ppp) REVERT: Q 231 ASP cc_start: 0.9313 (t0) cc_final: 0.8581 (p0) REVERT: U 142 LYS cc_start: 0.9703 (tttt) cc_final: 0.9498 (ttmm) REVERT: U 219 MET cc_start: 0.9750 (ttt) cc_final: 0.9322 (tpp) REVERT: U 223 LEU cc_start: 0.9659 (tp) cc_final: 0.9056 (pp) REVERT: W 63 GLN cc_start: 0.9805 (mt0) cc_final: 0.9386 (mm110) REVERT: W 219 MET cc_start: 0.9214 (ppp) cc_final: 0.8870 (ppp) REVERT: W 223 LEU cc_start: 0.9652 (tt) cc_final: 0.9323 (pp) REVERT: Y 63 GLN cc_start: 0.9505 (mt0) cc_final: 0.9076 (mm110) REVERT: Y 196 LEU cc_start: 0.9661 (mt) cc_final: 0.9368 (mt) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.2252 time to fit residues: 46.9120 Evaluate side-chains 89 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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: 10.0000 chunk 39 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 218 optimal weight: 40.0000 chunk 68 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 overall best weight: 7.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 202 ASN 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 202 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN O 101 GLN O 237 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 GLN Q 237 ASN S 237 ASN W 7 GLN ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.019910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2042 r_free = 0.2042 target = 0.013859 restraints weight = 341814.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2062 r_free = 0.2062 target = 0.014230 restraints weight = 252904.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2077 r_free = 0.2077 target = 0.014516 restraints weight = 203675.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2088 r_free = 0.2088 target = 0.014738 restraints weight = 173040.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2097 r_free = 0.2097 target = 0.014895 restraints weight = 152846.964| |-----------------------------------------------------------------------------| r_work (final): 0.2086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 26754 Z= 0.331 Angle : 0.891 11.452 37016 Z= 0.424 Chirality : 0.044 0.253 4984 Planarity : 0.004 0.032 4480 Dihedral : 7.710 54.672 6776 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % 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 aren not related in a simple way. whole: 1.26 (0.14), residues: 3360 helix: 1.47 (0.10), residues: 2492 sheet: None (None), residues: 0 loop : -0.97 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 165 TYR 0.025 0.002 TYR M 140 PHE 0.030 0.003 PHE I 105 Details of bonding type rmsd covalent geometry : bond 0.00624 (26600) covalent geometry : angle 0.84618 (36554) hydrogen bonds : bond 0.03303 ( 1638) hydrogen bonds : angle 5.25624 ( 4830) glycosidic custom : bond 0.00931 ( 112) glycosidic custom : angle 2.69579 ( 336) link_BETA1-3 : bond 0.00768 ( 42) link_BETA1-3 : angle 2.46880 ( 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 115 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.911 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: A 202 ASN cc_start: 0.9608 (OUTLIER) cc_final: 0.9323 (t0) REVERT: C 142 LYS cc_start: 0.9795 (tttt) cc_final: 0.9544 (ttmm) REVERT: G 30 ASP cc_start: 0.9532 (m-30) cc_final: 0.9282 (m-30) REVERT: G 99 PHE cc_start: 0.9546 (m-80) cc_final: 0.9106 (m-80) REVERT: G 219 MET cc_start: 0.9647 (tmm) cc_final: 0.9383 (ppp) REVERT: I 201 LEU cc_start: 0.9822 (mt) cc_final: 0.9519 (tp) REVERT: K 63 GLN cc_start: 0.9664 (mt0) cc_final: 0.9301 (mt0) REVERT: K 127 TYR cc_start: 0.9195 (m-80) cc_final: 0.8819 (m-80) REVERT: M 62 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9208 (tp) REVERT: M 63 GLN cc_start: 0.9686 (mt0) cc_final: 0.9418 (mt0) REVERT: M 78 LEU cc_start: 0.9716 (mt) cc_final: 0.9494 (mt) REVERT: M 96 TYR cc_start: 0.9231 (m-80) cc_final: 0.8981 (m-80) REVERT: O 134 GLN cc_start: 0.9681 (mt0) cc_final: 0.9358 (mt0) REVERT: Q 134 GLN cc_start: 0.9683 (mt0) cc_final: 0.9401 (mt0) REVERT: Q 219 MET cc_start: 0.9516 (ppp) cc_final: 0.9180 (ppp) REVERT: Q 231 ASP cc_start: 0.9173 (t0) cc_final: 0.8285 (p0) REVERT: U 30 ASP cc_start: 0.9716 (m-30) cc_final: 0.9499 (m-30) REVERT: U 142 LYS cc_start: 0.9728 (tttt) cc_final: 0.9476 (ttmm) REVERT: U 219 MET cc_start: 0.9777 (ttt) cc_final: 0.9405 (tpp) REVERT: W 63 GLN cc_start: 0.9822 (mt0) cc_final: 0.9399 (mm110) REVERT: W 219 MET cc_start: 0.9430 (ppp) cc_final: 0.9129 (ppp) outliers start: 3 outliers final: 0 residues processed: 115 average time/residue: 0.2269 time to fit residues: 38.1600 Evaluate side-chains 62 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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: 2.9990 chunk 14 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 293 optimal weight: 0.0670 chunk 106 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN C 107 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 GLN ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.020608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2075 r_free = 0.2075 target = 0.014319 restraints weight = 318550.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2095 r_free = 0.2095 target = 0.014704 restraints weight = 235046.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2110 r_free = 0.2110 target = 0.015015 restraints weight = 188465.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2121 r_free = 0.2121 target = 0.015221 restraints weight = 159549.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2131 r_free = 0.2131 target = 0.015417 restraints weight = 141035.519| |-----------------------------------------------------------------------------| r_work (final): 0.2122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 26754 Z= 0.118 Angle : 0.618 10.929 37016 Z= 0.292 Chirality : 0.039 0.240 4984 Planarity : 0.003 0.032 4480 Dihedral : 7.067 55.225 6776 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.09 % Allowed : 1.91 % 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 aren not related in a simple way. whole: 1.88 (0.15), residues: 3360 helix: 1.94 (0.10), residues: 2478 sheet: None (None), residues: 0 loop : -0.75 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 0 177 TYR 0.021 0.001 TYR Y 212 PHE 0.021 0.002 PHE K 239 Details of bonding type rmsd covalent geometry : bond 0.00248 (26600) covalent geometry : angle 0.59167 (36554) hydrogen bonds : bond 0.02760 ( 1638) hydrogen bonds : angle 4.84443 ( 4830) glycosidic custom : bond 0.00212 ( 112) glycosidic custom : angle 1.51943 ( 336) link_BETA1-3 : bond 0.00324 ( 42) link_BETA1-3 : angle 2.11796 ( 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 114 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.836 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 223 LEU cc_start: 0.9829 (tt) cc_final: 0.9588 (pp) REVERT: C 142 LYS cc_start: 0.9778 (tttt) cc_final: 0.9425 (tmtt) REVERT: E 134 GLN cc_start: 0.9726 (mt0) cc_final: 0.9414 (mt0) REVERT: E 219 MET cc_start: 0.9611 (tmm) cc_final: 0.9366 (tmm) REVERT: E 223 LEU cc_start: 0.9753 (tt) cc_final: 0.9525 (pp) REVERT: G 30 ASP cc_start: 0.9513 (m-30) cc_final: 0.9212 (m-30) REVERT: G 219 MET cc_start: 0.9611 (tmm) cc_final: 0.9407 (ppp) REVERT: I 201 LEU cc_start: 0.9812 (mt) cc_final: 0.9491 (tp) REVERT: I 223 LEU cc_start: 0.9816 (tp) cc_final: 0.9495 (pp) REVERT: K 63 GLN cc_start: 0.9625 (mt0) cc_final: 0.9257 (mt0) REVERT: K 127 TYR cc_start: 0.9022 (m-80) cc_final: 0.8702 (m-80) REVERT: K 221 ASN cc_start: 0.9460 (m110) cc_final: 0.9131 (m110) REVERT: K 223 LEU cc_start: 0.9791 (tp) cc_final: 0.9486 (tt) REVERT: M 63 GLN cc_start: 0.9621 (mt0) cc_final: 0.9403 (mt0) REVERT: M 196 LEU cc_start: 0.9459 (mt) cc_final: 0.9239 (mt) REVERT: Q 134 GLN cc_start: 0.9726 (mt0) cc_final: 0.9397 (mt0) REVERT: Q 219 MET cc_start: 0.9462 (ppp) cc_final: 0.9165 (ppp) REVERT: Q 231 ASP cc_start: 0.9220 (t0) cc_final: 0.8393 (p0) REVERT: U 30 ASP cc_start: 0.9719 (m-30) cc_final: 0.9487 (m-30) REVERT: U 142 LYS cc_start: 0.9701 (tttt) cc_final: 0.9469 (ttmm) REVERT: U 219 MET cc_start: 0.9754 (ttt) cc_final: 0.9354 (tpp) REVERT: W 63 GLN cc_start: 0.9780 (mt0) cc_final: 0.9357 (mm110) REVERT: W 219 MET cc_start: 0.9429 (ppp) cc_final: 0.9085 (ppp) REVERT: W 223 LEU cc_start: 0.9714 (tt) cc_final: 0.9364 (pp) REVERT: Y 63 GLN cc_start: 0.9492 (mt0) cc_final: 0.9158 (mm110) REVERT: Y 196 LEU cc_start: 0.9681 (mt) cc_final: 0.9425 (mt) REVERT: 0 102 GLU cc_start: 0.9743 (pm20) cc_final: 0.9471 (pm20) REVERT: 0 219 MET cc_start: 0.9695 (ttm) cc_final: 0.9483 (ttm) outliers start: 2 outliers final: 0 residues processed: 114 average time/residue: 0.2121 time to fit residues: 36.1645 Evaluate side-chains 75 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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: 0.9990 chunk 214 optimal weight: 10.0000 chunk 113 optimal weight: 0.3980 chunk 283 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 311 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN ** O 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.020534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2077 r_free = 0.2077 target = 0.014305 restraints weight = 319187.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2097 r_free = 0.2097 target = 0.014685 restraints weight = 235891.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2113 r_free = 0.2113 target = 0.014963 restraints weight = 189270.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2125 r_free = 0.2125 target = 0.015225 restraints weight = 160472.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2133 r_free = 0.2133 target = 0.015383 restraints weight = 140944.316| |-----------------------------------------------------------------------------| r_work (final): 0.2125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 26754 Z= 0.119 Angle : 0.609 10.781 37016 Z= 0.287 Chirality : 0.038 0.240 4984 Planarity : 0.002 0.030 4480 Dihedral : 6.629 53.900 6776 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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 aren not related in a simple way. whole: 2.01 (0.15), residues: 3360 helix: 2.05 (0.11), residues: 2478 sheet: None (None), residues: 0 loop : -0.76 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 104 TYR 0.018 0.001 TYR O 65 PHE 0.029 0.002 PHE Y 105 Details of bonding type rmsd covalent geometry : bond 0.00249 (26600) covalent geometry : angle 0.58300 (36554) hydrogen bonds : bond 0.02538 ( 1638) hydrogen bonds : angle 4.73231 ( 4830) glycosidic custom : bond 0.00256 ( 112) glycosidic custom : angle 1.49978 ( 336) link_BETA1-3 : bond 0.00273 ( 42) link_BETA1-3 : angle 2.09710 ( 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 114 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.811 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 223 LEU cc_start: 0.9836 (tt) cc_final: 0.9609 (pp) REVERT: C 142 LYS cc_start: 0.9777 (tttt) cc_final: 0.9433 (tmtt) REVERT: E 134 GLN cc_start: 0.9734 (mt0) cc_final: 0.9433 (mt0) REVERT: E 219 MET cc_start: 0.9636 (tmm) cc_final: 0.9387 (tmm) REVERT: E 223 LEU cc_start: 0.9763 (tt) cc_final: 0.9553 (pp) REVERT: G 30 ASP cc_start: 0.9522 (m-30) cc_final: 0.9236 (m-30) REVERT: G 99 PHE cc_start: 0.9527 (m-80) cc_final: 0.9134 (m-80) REVERT: I 201 LEU cc_start: 0.9802 (mt) cc_final: 0.9477 (tp) REVERT: I 223 LEU cc_start: 0.9821 (tp) cc_final: 0.9503 (pp) REVERT: K 63 GLN cc_start: 0.9645 (mt0) cc_final: 0.9256 (mt0) REVERT: K 127 TYR cc_start: 0.9119 (m-80) cc_final: 0.8794 (m-80) REVERT: K 221 ASN cc_start: 0.9472 (m110) cc_final: 0.9213 (m110) REVERT: K 223 LEU cc_start: 0.9777 (tp) cc_final: 0.9430 (pp) REVERT: M 63 GLN cc_start: 0.9583 (mt0) cc_final: 0.9312 (mt0) REVERT: M 96 TYR cc_start: 0.9145 (m-80) cc_final: 0.8845 (m-80) REVERT: M 196 LEU cc_start: 0.9437 (mt) cc_final: 0.9184 (mt) REVERT: O 63 GLN cc_start: 0.9651 (pt0) cc_final: 0.9378 (pp30) REVERT: Q 134 GLN cc_start: 0.9726 (mt0) cc_final: 0.9408 (mt0) REVERT: Q 219 MET cc_start: 0.9479 (ppp) cc_final: 0.9183 (ppp) REVERT: Q 231 ASP cc_start: 0.9280 (t0) cc_final: 0.8481 (p0) REVERT: U 30 ASP cc_start: 0.9719 (m-30) cc_final: 0.9491 (m-30) REVERT: U 63 GLN cc_start: 0.9688 (mt0) cc_final: 0.9112 (pt0) REVERT: U 142 LYS cc_start: 0.9713 (tttt) cc_final: 0.9475 (ttmm) REVERT: U 219 MET cc_start: 0.9794 (ttt) cc_final: 0.9410 (tpp) REVERT: U 223 LEU cc_start: 0.9661 (mt) cc_final: 0.9314 (tt) REVERT: W 63 GLN cc_start: 0.9768 (mt0) cc_final: 0.9349 (mm110) REVERT: W 219 MET cc_start: 0.9473 (ppp) cc_final: 0.9101 (ppp) REVERT: W 223 LEU cc_start: 0.9731 (tt) cc_final: 0.9386 (pp) REVERT: Y 63 GLN cc_start: 0.9511 (mt0) cc_final: 0.9170 (mm110) REVERT: Y 196 LEU cc_start: 0.9651 (mt) cc_final: 0.9360 (mt) REVERT: Y 219 MET cc_start: 0.9393 (ppp) cc_final: 0.9164 (ppp) REVERT: 0 102 GLU cc_start: 0.9771 (pm20) cc_final: 0.9497 (pm20) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1837 time to fit residues: 31.2425 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 : 0.798 ------------------------------------------------------------------------------- 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: 1.9990 chunk 254 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 258 optimal weight: 0.0470 chunk 117 optimal weight: 0.7980 chunk 229 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 overall best weight: 1.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 GLN E 202 ASN G 179 ASN I 63 GLN W 134 GLN Y 134 GLN 0 202 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.020517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2077 r_free = 0.2077 target = 0.014275 restraints weight = 334032.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2098 r_free = 0.2098 target = 0.014673 restraints weight = 243442.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2114 r_free = 0.2114 target = 0.014990 restraints weight = 193395.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2126 r_free = 0.2126 target = 0.015206 restraints weight = 162761.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2136 r_free = 0.2136 target = 0.015404 restraints weight = 143242.453| |-----------------------------------------------------------------------------| r_work (final): 0.2124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 26754 Z= 0.106 Angle : 0.575 9.631 37016 Z= 0.271 Chirality : 0.037 0.240 4984 Planarity : 0.002 0.031 4480 Dihedral : 6.284 53.523 6776 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.04 % Allowed : 0.94 % Favored : 99.02 % 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 aren not related in a simple way. whole: 2.18 (0.15), residues: 3360 helix: 2.18 (0.11), residues: 2478 sheet: None (None), residues: 0 loop : -0.71 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 177 TYR 0.019 0.001 TYR K 171 PHE 0.018 0.001 PHE G 175 Details of bonding type rmsd covalent geometry : bond 0.00224 (26600) covalent geometry : angle 0.55212 (36554) hydrogen bonds : bond 0.02380 ( 1638) hydrogen bonds : angle 4.62373 ( 4830) glycosidic custom : bond 0.00199 ( 112) glycosidic custom : angle 1.37416 ( 336) link_BETA1-3 : bond 0.00297 ( 42) link_BETA1-3 : angle 1.94595 ( 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 : 0.882 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: A 223 LEU cc_start: 0.9828 (tt) cc_final: 0.9598 (pp) REVERT: C 142 LYS cc_start: 0.9779 (tttt) cc_final: 0.9490 (ttmm) REVERT: E 134 GLN cc_start: 0.9747 (mt0) cc_final: 0.9472 (mt0) REVERT: E 219 MET cc_start: 0.9660 (tmm) cc_final: 0.9405 (tmm) REVERT: G 30 ASP cc_start: 0.9551 (m-30) cc_final: 0.9258 (m-30) REVERT: I 63 GLN cc_start: 0.9687 (mt0) cc_final: 0.9096 (mm110) REVERT: I 201 LEU cc_start: 0.9798 (mt) cc_final: 0.9570 (tp) REVERT: I 223 LEU cc_start: 0.9834 (tp) cc_final: 0.9499 (pp) REVERT: K 63 GLN cc_start: 0.9662 (mt0) cc_final: 0.9282 (mt0) REVERT: K 127 TYR cc_start: 0.9171 (m-80) cc_final: 0.8869 (m-80) REVERT: K 134 GLN cc_start: 0.9712 (mt0) cc_final: 0.9468 (mt0) REVERT: K 221 ASN cc_start: 0.9495 (m110) cc_final: 0.9271 (m-40) REVERT: K 223 LEU cc_start: 0.9775 (tp) cc_final: 0.9474 (pp) REVERT: M 63 GLN cc_start: 0.9576 (mt0) cc_final: 0.9284 (mt0) REVERT: M 96 TYR cc_start: 0.9181 (m-80) cc_final: 0.8850 (m-80) REVERT: M 196 LEU cc_start: 0.9446 (mt) cc_final: 0.9200 (mt) REVERT: O 63 GLN cc_start: 0.9716 (pt0) cc_final: 0.9491 (pp30) REVERT: Q 134 GLN cc_start: 0.9727 (mt0) cc_final: 0.9406 (mt0) REVERT: Q 219 MET cc_start: 0.9469 (ppp) cc_final: 0.9146 (ppp) REVERT: Q 231 ASP cc_start: 0.9328 (t0) cc_final: 0.8590 (p0) REVERT: U 30 ASP cc_start: 0.9721 (m-30) cc_final: 0.9489 (m-30) REVERT: U 63 GLN cc_start: 0.9690 (mt0) cc_final: 0.9108 (pt0) REVERT: U 142 LYS cc_start: 0.9721 (tttt) cc_final: 0.9471 (ttmm) REVERT: U 219 MET cc_start: 0.9811 (ttt) cc_final: 0.9434 (tpp) REVERT: U 223 LEU cc_start: 0.9674 (mt) cc_final: 0.9291 (tt) REVERT: W 63 GLN cc_start: 0.9774 (mt0) cc_final: 0.9362 (mm110) REVERT: W 219 MET cc_start: 0.9495 (ppp) cc_final: 0.9094 (ppp) REVERT: W 223 LEU cc_start: 0.9738 (tt) cc_final: 0.9422 (pp) REVERT: Y 63 GLN cc_start: 0.9505 (mt0) cc_final: 0.9180 (mm-40) REVERT: Y 196 LEU cc_start: 0.9681 (mt) cc_final: 0.9398 (mt) REVERT: 0 102 GLU cc_start: 0.9797 (pm20) cc_final: 0.9547 (pm20) REVERT: 0 202 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8808 (t0) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1976 time to fit residues: 35.2726 Evaluate side-chains 80 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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: 0.7980 chunk 201 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 274 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 267 optimal weight: 0.3980 chunk 332 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 7 GLN I 146 ASN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 134 GLN 0 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.020698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2102 r_free = 0.2102 target = 0.014474 restraints weight = 317968.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2121 r_free = 0.2121 target = 0.014863 restraints weight = 234506.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2137 r_free = 0.2137 target = 0.015172 restraints weight = 188040.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2148 r_free = 0.2148 target = 0.015373 restraints weight = 158862.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2157 r_free = 0.2157 target = 0.015569 restraints weight = 140470.966| |-----------------------------------------------------------------------------| r_work (final): 0.2148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.5668 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= 0.100 Angle : 0.573 11.321 37016 Z= 0.272 Chirality : 0.037 0.240 4984 Planarity : 0.002 0.059 4480 Dihedral : 6.047 53.197 6776 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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 aren not related in a simple way. whole: 2.17 (0.15), residues: 3360 helix: 2.13 (0.11), residues: 2492 sheet: None (None), residues: 0 loop : -0.63 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 0 177 TYR 0.010 0.001 TYR Q 3 PHE 0.015 0.001 PHE G 175 Details of bonding type rmsd covalent geometry : bond 0.00212 (26600) covalent geometry : angle 0.55160 (36554) hydrogen bonds : bond 0.02379 ( 1638) hydrogen bonds : angle 4.59908 ( 4830) glycosidic custom : bond 0.00159 ( 112) glycosidic custom : angle 1.30554 ( 336) link_BETA1-3 : bond 0.00345 ( 42) link_BETA1-3 : angle 1.90771 ( 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 : 0.743 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: A 223 LEU cc_start: 0.9827 (tt) cc_final: 0.9592 (pp) REVERT: C 142 LYS cc_start: 0.9780 (tttt) cc_final: 0.9419 (tmtt) REVERT: E 134 GLN cc_start: 0.9753 (mt0) cc_final: 0.9427 (mt0) REVERT: E 146 ASN cc_start: 0.9689 (t0) cc_final: 0.9454 (m110) REVERT: G 30 ASP cc_start: 0.9517 (m-30) cc_final: 0.9241 (m-30) REVERT: G 99 PHE cc_start: 0.9541 (m-80) cc_final: 0.9213 (m-80) REVERT: I 201 LEU cc_start: 0.9803 (mt) cc_final: 0.9480 (tp) REVERT: I 223 LEU cc_start: 0.9832 (tp) cc_final: 0.9516 (pp) REVERT: K 63 GLN cc_start: 0.9627 (mt0) cc_final: 0.9278 (mt0) REVERT: K 127 TYR cc_start: 0.9133 (m-80) cc_final: 0.8863 (m-80) REVERT: K 134 GLN cc_start: 0.9738 (mt0) cc_final: 0.9510 (mt0) REVERT: K 223 LEU cc_start: 0.9785 (tp) cc_final: 0.9452 (pp) REVERT: M 63 GLN cc_start: 0.9591 (mt0) cc_final: 0.9351 (mt0) REVERT: M 96 TYR cc_start: 0.9141 (m-80) cc_final: 0.8826 (m-80) REVERT: M 196 LEU cc_start: 0.9435 (mt) cc_final: 0.9178 (mt) REVERT: O 63 GLN cc_start: 0.9699 (pt0) cc_final: 0.9400 (pp30) REVERT: O 134 GLN cc_start: 0.9728 (mt0) cc_final: 0.9443 (mt0) REVERT: O 196 LEU cc_start: 0.9620 (mt) cc_final: 0.9420 (mt) REVERT: Q 30 ASP cc_start: 0.9760 (m-30) cc_final: 0.9558 (m-30) REVERT: Q 134 GLN cc_start: 0.9731 (mt0) cc_final: 0.9407 (mt0) REVERT: Q 219 MET cc_start: 0.9456 (ppp) cc_final: 0.9139 (ppp) REVERT: Q 231 ASP cc_start: 0.9283 (t0) cc_final: 0.8529 (p0) REVERT: S 219 MET cc_start: 0.9398 (ppp) cc_final: 0.9170 (ppp) REVERT: U 30 ASP cc_start: 0.9714 (m-30) cc_final: 0.9478 (m-30) REVERT: U 63 GLN cc_start: 0.9683 (mt0) cc_final: 0.9100 (pt0) REVERT: U 142 LYS cc_start: 0.9717 (tttt) cc_final: 0.9472 (ttmm) REVERT: U 219 MET cc_start: 0.9802 (ttt) cc_final: 0.9455 (tpp) REVERT: U 223 LEU cc_start: 0.9670 (mt) cc_final: 0.9284 (tt) REVERT: W 63 GLN cc_start: 0.9764 (mt0) cc_final: 0.9351 (mm110) REVERT: W 219 MET cc_start: 0.9498 (ppp) cc_final: 0.9087 (ppp) REVERT: W 223 LEU cc_start: 0.9734 (tt) cc_final: 0.9431 (pp) REVERT: Y 63 GLN cc_start: 0.9509 (mt0) cc_final: 0.9198 (mm-40) REVERT: Y 196 LEU cc_start: 0.9671 (mt) cc_final: 0.9391 (mt) REVERT: 0 134 GLN cc_start: 0.9658 (tp-100) cc_final: 0.9412 (tp-100) REVERT: 0 166 GLN cc_start: 0.9595 (mm-40) cc_final: 0.8875 (tp-100) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2077 time to fit residues: 36.5580 Evaluate side-chains 82 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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: 5.9990 chunk 100 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 227 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 323 optimal weight: 30.0000 chunk 237 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 202 ASN O 101 GLN Y 134 GLN 0 63 GLN 0 107 ASN 0 202 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.019633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2042 r_free = 0.2042 target = 0.013698 restraints weight = 342929.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2063 r_free = 0.2063 target = 0.014066 restraints weight = 249444.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2078 r_free = 0.2078 target = 0.014365 restraints weight = 198726.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2090 r_free = 0.2090 target = 0.014592 restraints weight = 167957.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2098 r_free = 0.2098 target = 0.014740 restraints weight = 147549.560| |-----------------------------------------------------------------------------| r_work (final): 0.2089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 26754 Z= 0.221 Angle : 0.702 9.712 37016 Z= 0.335 Chirality : 0.040 0.250 4984 Planarity : 0.003 0.041 4480 Dihedral : 6.336 55.103 6776 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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 aren not related in a simple way. whole: 2.04 (0.15), residues: 3360 helix: 2.09 (0.10), residues: 2492 sheet: None (None), residues: 0 loop : -0.84 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 0 177 TYR 0.018 0.002 TYR K 171 PHE 0.020 0.002 PHE E 239 Details of bonding type rmsd covalent geometry : bond 0.00426 (26600) covalent geometry : angle 0.66947 (36554) hydrogen bonds : bond 0.02641 ( 1638) hydrogen bonds : angle 4.77555 ( 4830) glycosidic custom : bond 0.00634 ( 112) glycosidic custom : angle 1.97233 ( 336) link_BETA1-3 : bond 0.00385 ( 42) link_BETA1-3 : angle 2.07514 ( 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 100 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.781 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: C 142 LYS cc_start: 0.9780 (tttt) cc_final: 0.9485 (ttmm) REVERT: E 30 ASP cc_start: 0.9685 (m-30) cc_final: 0.9465 (m-30) REVERT: E 134 GLN cc_start: 0.9743 (mt0) cc_final: 0.9448 (mt0) REVERT: G 30 ASP cc_start: 0.9562 (m-30) cc_final: 0.9288 (m-30) REVERT: I 63 GLN cc_start: 0.9668 (mt0) cc_final: 0.9186 (mm110) REVERT: I 201 LEU cc_start: 0.9800 (mt) cc_final: 0.9569 (tp) REVERT: I 223 LEU cc_start: 0.9849 (tp) cc_final: 0.9570 (pp) REVERT: K 223 LEU cc_start: 0.9812 (tp) cc_final: 0.9507 (pp) REVERT: M 63 GLN cc_start: 0.9645 (mt0) cc_final: 0.9331 (mt0) REVERT: M 196 LEU cc_start: 0.9512 (mt) cc_final: 0.9246 (mt) REVERT: O 63 GLN cc_start: 0.9731 (pt0) cc_final: 0.9521 (pp30) REVERT: Q 134 GLN cc_start: 0.9726 (mt0) cc_final: 0.9398 (mt0) REVERT: Q 196 LEU cc_start: 0.9605 (mt) cc_final: 0.9387 (mt) REVERT: Q 219 MET cc_start: 0.9482 (ppp) cc_final: 0.9156 (ppp) REVERT: Q 231 ASP cc_start: 0.9212 (t0) cc_final: 0.8320 (p0) REVERT: S 219 MET cc_start: 0.9421 (ppp) cc_final: 0.9200 (ppp) REVERT: U 30 ASP cc_start: 0.9712 (m-30) cc_final: 0.9482 (m-30) REVERT: U 63 GLN cc_start: 0.9722 (mt0) cc_final: 0.9189 (pt0) REVERT: U 142 LYS cc_start: 0.9724 (tttt) cc_final: 0.9510 (ttmm) REVERT: U 219 MET cc_start: 0.9806 (ttt) cc_final: 0.9426 (tpp) REVERT: W 63 GLN cc_start: 0.9790 (mt0) cc_final: 0.9378 (mm110) REVERT: W 219 MET cc_start: 0.9544 (ppp) cc_final: 0.9173 (ppp) REVERT: W 223 LEU cc_start: 0.9785 (tt) cc_final: 0.9504 (pp) REVERT: Y 196 LEU cc_start: 0.9677 (mt) cc_final: 0.9395 (mt) REVERT: 0 134 GLN cc_start: 0.9675 (tp-100) cc_final: 0.9419 (tp-100) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2276 time to fit residues: 33.7561 Evaluate side-chains 69 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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: 0.0970 chunk 265 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 281 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 303 optimal weight: 20.0000 chunk 301 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 202 ASN O 101 GLN S 107 ASN Y 134 GLN 0 202 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.019783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2065 r_free = 0.2065 target = 0.013884 restraints weight = 322043.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2085 r_free = 0.2085 target = 0.014246 restraints weight = 236848.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2100 r_free = 0.2100 target = 0.014542 restraints weight = 189999.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2109 r_free = 0.2109 target = 0.014717 restraints weight = 161115.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2119 r_free = 0.2119 target = 0.014912 restraints weight = 143657.804| |-----------------------------------------------------------------------------| r_work (final): 0.2110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26754 Z= 0.142 Angle : 0.602 9.649 37016 Z= 0.288 Chirality : 0.038 0.346 4984 Planarity : 0.003 0.038 4480 Dihedral : 6.243 55.236 6776 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 aren not related in a simple way. whole: 2.15 (0.15), residues: 3360 helix: 2.15 (0.11), residues: 2492 sheet: None (None), residues: 0 loop : -0.74 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 0 177 TYR 0.025 0.001 TYR K 127 PHE 0.015 0.002 PHE E 239 Details of bonding type rmsd covalent geometry : bond 0.00286 (26600) covalent geometry : angle 0.57953 (36554) hydrogen bonds : bond 0.02507 ( 1638) hydrogen bonds : angle 4.68506 ( 4830) glycosidic custom : bond 0.00354 ( 112) glycosidic custom : angle 1.44148 ( 336) link_BETA1-3 : bond 0.00231 ( 42) link_BETA1-3 : angle 1.88508 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3530.81 seconds wall clock time: 62 minutes 39.76 seconds (3759.76 seconds total)