Starting phenix.real_space_refine on Sat Jun 21 20:51:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lj3_23388/06_2025/7lj3_23388.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lj3_23388/06_2025/7lj3_23388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lj3_23388/06_2025/7lj3_23388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lj3_23388/06_2025/7lj3_23388.map" model { file = "/net/cci-nas-00/data/ceres_data/7lj3_23388/06_2025/7lj3_23388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lj3_23388/06_2025/7lj3_23388.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 222 5.49 5 S 116 5.16 5 C 15334 2.51 5 N 4661 2.21 5 O 5381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25714 Number of models: 1 Model: "" Number of chains: 12 Chain: "z" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2320 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 276} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "0" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "y" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "4" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "9" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "7" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1590 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 27, 'rna3p_pyr': 35} Link IDs: {'rna2p': 13, 'rna3p': 61} Chain: "B" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1590 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 27, 'rna3p_pyr': 35} Link IDs: {'rna2p': 13, 'rna3p': 61} Chain: "C" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1590 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 27, 'rna3p_pyr': 35} Link IDs: {'rna2p': 13, 'rna3p': 61} Time building chain proxies: 14.76, per 1000 atoms: 0.57 Number of scatterers: 25714 At special positions: 0 Unit cell: (198.56, 306, 106.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 222 15.00 O 5381 8.00 N 4661 7.00 C 15334 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.24 Conformation dependent library (CDL) restraints added in 2.5 seconds 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4948 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 0 sheets defined 72.5% alpha, 0.0% beta 67 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 9.19 Creating SS restraints... Processing helix chain 'z' and resid 9 through 22 Processing helix chain 'z' and resid 23 through 26 Processing helix chain 'z' and resid 34 through 40 removed outlier: 4.074A pdb=" N LEU z 38 " --> pdb=" O HIS z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 47 through 70 Processing helix chain 'z' and resid 73 through 94 removed outlier: 3.534A pdb=" N TYR z 92 " --> pdb=" O ALA z 88 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR z 93 " --> pdb=" O ARG z 89 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR z 94 " --> pdb=" O ARG z 90 " (cutoff:3.500A) Processing helix chain 'z' and resid 98 through 111 removed outlier: 4.421A pdb=" N ASP z 104 " --> pdb=" O GLY z 100 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL z 108 " --> pdb=" O ASP z 104 " (cutoff:3.500A) Processing helix chain 'z' and resid 120 through 141 removed outlier: 3.654A pdb=" N ARG z 127 " --> pdb=" O GLU z 123 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER z 131 " --> pdb=" O ARG z 127 " (cutoff:3.500A) Processing helix chain 'z' and resid 160 through 175 Processing helix chain 'z' and resid 194 through 241 removed outlier: 3.666A pdb=" N VAL z 213 " --> pdb=" O LEU z 209 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS z 237 " --> pdb=" O LYS z 233 " (cutoff:3.500A) Processing helix chain 'z' and resid 244 through 254 Processing helix chain 'z' and resid 258 through 261 removed outlier: 4.406A pdb=" N GLY z 261 " --> pdb=" O VAL z 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 258 through 261' Processing helix chain 'z' and resid 262 through 274 removed outlier: 3.766A pdb=" N ASP z 274 " --> pdb=" O LEU z 270 " (cutoff:3.500A) Processing helix chain 'z' and resid 275 through 278 removed outlier: 3.555A pdb=" N TYR z 278 " --> pdb=" O PHE z 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 275 through 278' Processing helix chain '0' and resid 9 through 22 Processing helix chain '0' and resid 34 through 40 removed outlier: 4.036A pdb=" N LEU 0 38 " --> pdb=" O HIS 0 34 " (cutoff:3.500A) Processing helix chain '0' and resid 49 through 70 removed outlier: 3.616A pdb=" N GLU 0 55 " --> pdb=" O VAL 0 51 " (cutoff:3.500A) Processing helix chain '0' and resid 73 through 92 removed outlier: 3.644A pdb=" N ARG 0 90 " --> pdb=" O ALA 0 86 " (cutoff:3.500A) Processing helix chain '0' and resid 98 through 112 removed outlier: 3.558A pdb=" N VAL 0 108 " --> pdb=" O ASP 0 104 " (cutoff:3.500A) Processing helix chain '0' and resid 117 through 119 No H-bonds generated for 'chain '0' and resid 117 through 119' Processing helix chain '0' and resid 120 through 141 removed outlier: 3.649A pdb=" N ALA 0 128 " --> pdb=" O ILE 0 124 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU 0 135 " --> pdb=" O SER 0 131 " (cutoff:3.500A) Processing helix chain '0' and resid 160 through 177 Processing helix chain '0' and resid 194 through 241 removed outlier: 3.562A pdb=" N VAL 0 213 " --> pdb=" O LEU 0 209 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU 0 225 " --> pdb=" O GLU 0 221 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG 0 231 " --> pdb=" O ARG 0 227 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS 0 237 " --> pdb=" O LYS 0 233 " (cutoff:3.500A) Processing helix chain '0' and resid 244 through 254 removed outlier: 3.637A pdb=" N ARG 0 251 " --> pdb=" O SER 0 247 " (cutoff:3.500A) Processing helix chain '0' and resid 259 through 274 removed outlier: 4.138A pdb=" N SER 0 263 " --> pdb=" O GLU 0 259 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA 0 264 " --> pdb=" O ASN 0 260 " (cutoff:3.500A) Processing helix chain '0' and resid 274 through 279 removed outlier: 3.953A pdb=" N TYR 0 278 " --> pdb=" O ASP 0 274 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 22 Processing helix chain 'y' and resid 30 through 33 Processing helix chain 'y' and resid 34 through 40 removed outlier: 3.648A pdb=" N LEU y 38 " --> pdb=" O HIS y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 47 through 70 Processing helix chain 'y' and resid 73 through 94 removed outlier: 3.851A pdb=" N GLU y 81 " --> pdb=" O LEU y 77 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR y 93 " --> pdb=" O ARG y 89 " (cutoff:3.500A) Processing helix chain 'y' and resid 98 through 111 removed outlier: 3.843A pdb=" N ALA y 102 " --> pdb=" O ASP y 98 " (cutoff:3.500A) Processing helix chain 'y' and resid 117 through 119 No H-bonds generated for 'chain 'y' and resid 117 through 119' Processing helix chain 'y' and resid 120 through 141 removed outlier: 3.545A pdb=" N ARG y 127 " --> pdb=" O GLU y 123 " (cutoff:3.500A) Processing helix chain 'y' and resid 160 through 177 Processing helix chain 'y' and resid 194 through 241 Processing helix chain 'y' and resid 244 through 255 Processing helix chain 'y' and resid 260 through 274 removed outlier: 3.660A pdb=" N ALA y 264 " --> pdb=" O ASN y 260 " (cutoff:3.500A) Processing helix chain 'y' and resid 274 through 279 removed outlier: 3.704A pdb=" N TYR y 278 " --> pdb=" O ASP y 274 " (cutoff:3.500A) Processing helix chain 'y' and resid 280 through 282 No H-bonds generated for 'chain 'y' and resid 280 through 282' Processing helix chain '5' and resid 9 through 22 removed outlier: 3.514A pdb=" N ALA 5 15 " --> pdb=" O ARG 5 11 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU 5 20 " --> pdb=" O LEU 5 16 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 33 Processing helix chain '5' and resid 34 through 40 removed outlier: 3.544A pdb=" N LEU 5 38 " --> pdb=" O HIS 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 70 Processing helix chain '5' and resid 73 through 94 Processing helix chain '5' and resid 98 through 111 removed outlier: 3.819A pdb=" N HIS 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 118 through 140 removed outlier: 3.650A pdb=" N SER 5 131 " --> pdb=" O ARG 5 127 " (cutoff:3.500A) Processing helix chain '5' and resid 160 through 177 Processing helix chain '5' and resid 194 through 240 Processing helix chain '5' and resid 244 through 255 Processing helix chain '5' and resid 260 through 274 removed outlier: 3.667A pdb=" N ALA 5 264 " --> pdb=" O ASN 5 260 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 279 removed outlier: 3.765A pdb=" N TYR 5 278 " --> pdb=" O ASP 5 274 " (cutoff:3.500A) Processing helix chain '6' and resid 9 through 23 removed outlier: 3.531A pdb=" N ARG 6 21 " --> pdb=" O VAL 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 24 through 26 No H-bonds generated for 'chain '6' and resid 24 through 26' Processing helix chain '6' and resid 30 through 33 Processing helix chain '6' and resid 34 through 41 removed outlier: 3.713A pdb=" N LEU 6 38 " --> pdb=" O HIS 6 34 " (cutoff:3.500A) Processing helix chain '6' and resid 47 through 70 Processing helix chain '6' and resid 73 through 92 Processing helix chain '6' and resid 98 through 111 Processing helix chain '6' and resid 117 through 140 Processing helix chain '6' and resid 160 through 177 Processing helix chain '6' and resid 194 through 242 removed outlier: 3.972A pdb=" N CYS 6 242 " --> pdb=" O GLU 6 238 " (cutoff:3.500A) Processing helix chain '6' and resid 244 through 254 Processing helix chain '6' and resid 261 through 274 Processing helix chain '6' and resid 274 through 279 removed outlier: 3.730A pdb=" N TYR 6 278 " --> pdb=" O ASP 6 274 " (cutoff:3.500A) Processing helix chain '6' and resid 280 through 282 No H-bonds generated for 'chain '6' and resid 280 through 282' Processing helix chain '4' and resid 9 through 22 Processing helix chain '4' and resid 34 through 42 removed outlier: 3.873A pdb=" N LEU 4 38 " --> pdb=" O HIS 4 34 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY 4 42 " --> pdb=" O LEU 4 38 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 69 Processing helix chain '4' and resid 73 through 94 removed outlier: 3.985A pdb=" N THR 4 93 " --> pdb=" O ARG 4 89 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR 4 94 " --> pdb=" O ARG 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 98 through 112 removed outlier: 3.661A pdb=" N ALA 4 102 " --> pdb=" O ASP 4 98 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR 4 112 " --> pdb=" O VAL 4 108 " (cutoff:3.500A) Processing helix chain '4' and resid 119 through 141 removed outlier: 4.649A pdb=" N GLU 4 123 " --> pdb=" O ARG 4 119 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 177 Processing helix chain '4' and resid 194 through 241 Processing helix chain '4' and resid 244 through 254 Processing helix chain '4' and resid 261 through 274 Processing helix chain '4' and resid 274 through 279 removed outlier: 3.780A pdb=" N TYR 4 278 " --> pdb=" O ASP 4 274 " (cutoff:3.500A) Processing helix chain '4' and resid 280 through 282 No H-bonds generated for 'chain '4' and resid 280 through 282' Processing helix chain '8' and resid 9 through 22 Processing helix chain '8' and resid 34 through 41 removed outlier: 4.150A pdb=" N LEU 8 38 " --> pdb=" O HIS 8 34 " (cutoff:3.500A) Processing helix chain '8' and resid 47 through 70 Processing helix chain '8' and resid 73 through 94 removed outlier: 3.553A pdb=" N THR 8 93 " --> pdb=" O ARG 8 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR 8 94 " --> pdb=" O ARG 8 90 " (cutoff:3.500A) Processing helix chain '8' and resid 100 through 111 Processing helix chain '8' and resid 120 through 140 removed outlier: 3.819A pdb=" N ALA 8 128 " --> pdb=" O ILE 8 124 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU 8 135 " --> pdb=" O SER 8 131 " (cutoff:3.500A) Processing helix chain '8' and resid 160 through 177 Processing helix chain '8' and resid 194 through 241 removed outlier: 3.922A pdb=" N MET 8 241 " --> pdb=" O LYS 8 237 " (cutoff:3.500A) Processing helix chain '8' and resid 244 through 254 Processing helix chain '8' and resid 261 through 274 removed outlier: 3.566A pdb=" N ASP 8 265 " --> pdb=" O GLY 8 261 " (cutoff:3.500A) Processing helix chain '8' and resid 274 through 280 removed outlier: 3.796A pdb=" N TYR 8 278 " --> pdb=" O ASP 8 274 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP 8 280 " --> pdb=" O ASP 8 276 " (cutoff:3.500A) Processing helix chain '9' and resid 9 through 22 Processing helix chain '9' and resid 30 through 33 Processing helix chain '9' and resid 34 through 41 removed outlier: 3.568A pdb=" N LEU 9 38 " --> pdb=" O HIS 9 34 " (cutoff:3.500A) Processing helix chain '9' and resid 47 through 70 Processing helix chain '9' and resid 73 through 92 Processing helix chain '9' and resid 98 through 111 Processing helix chain '9' and resid 117 through 141 removed outlier: 3.728A pdb=" N ASP 9 121 " --> pdb=" O ASP 9 117 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA 9 122 " --> pdb=" O VAL 9 118 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG 9 127 " --> pdb=" O GLU 9 123 " (cutoff:3.500A) Processing helix chain '9' and resid 160 through 176 Processing helix chain '9' and resid 194 through 241 removed outlier: 3.919A pdb=" N MET 9 241 " --> pdb=" O LYS 9 237 " (cutoff:3.500A) Processing helix chain '9' and resid 244 through 254 Processing helix chain '9' and resid 261 through 274 Processing helix chain '9' and resid 274 through 279 removed outlier: 3.832A pdb=" N TYR 9 278 " --> pdb=" O ASP 9 274 " (cutoff:3.500A) Processing helix chain '9' and resid 280 through 282 No H-bonds generated for 'chain '9' and resid 280 through 282' Processing helix chain '7' and resid 9 through 22 Processing helix chain '7' and resid 30 through 33 Processing helix chain '7' and resid 34 through 41 removed outlier: 3.738A pdb=" N LEU 7 38 " --> pdb=" O HIS 7 34 " (cutoff:3.500A) Processing helix chain '7' and resid 47 through 69 Processing helix chain '7' and resid 73 through 94 removed outlier: 3.645A pdb=" N THR 7 93 " --> pdb=" O ARG 7 89 " (cutoff:3.500A) Processing helix chain '7' and resid 98 through 112 removed outlier: 3.821A pdb=" N ALA 7 102 " --> pdb=" O ASP 7 98 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL 7 108 " --> pdb=" O ASP 7 104 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR 7 112 " --> pdb=" O VAL 7 108 " (cutoff:3.500A) Processing helix chain '7' and resid 120 through 141 removed outlier: 3.673A pdb=" N ALA 7 128 " --> pdb=" O ILE 7 124 " (cutoff:3.500A) Processing helix chain '7' and resid 160 through 177 removed outlier: 3.607A pdb=" N ARG 7 176 " --> pdb=" O GLU 7 172 " (cutoff:3.500A) Processing helix chain '7' and resid 194 through 241 Processing helix chain '7' and resid 244 through 255 Processing helix chain '7' and resid 260 through 274 removed outlier: 3.943A pdb=" N ALA 7 264 " --> pdb=" O ASN 7 260 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP 7 265 " --> pdb=" O GLY 7 261 " (cutoff:3.500A) Processing helix chain '7' and resid 274 through 279 removed outlier: 3.723A pdb=" N TYR 7 278 " --> pdb=" O ASP 7 274 " (cutoff:3.500A) Processing helix chain '7' and resid 280 through 282 No H-bonds generated for 'chain '7' and resid 280 through 282' 1341 hydrogen bonds defined for protein. 4005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 180 hydrogen bonds 312 hydrogen bond angles 0 basepair planarities 67 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 8.54 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7306 1.33 - 1.46: 5363 1.46 - 1.58: 13323 1.58 - 1.70: 444 1.70 - 1.82: 169 Bond restraints: 26605 Sorted by residual: bond pdb=" C ASN 4 70 " pdb=" N PRO 4 71 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.23e-02 6.61e+03 8.95e+00 bond pdb=" CB GLN z 9 " pdb=" CG GLN z 9 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.45e+00 bond pdb=" CD ARG 8 10 " pdb=" NE ARG 8 10 " ideal model delta sigma weight residual 1.458 1.425 0.033 1.40e-02 5.10e+03 5.44e+00 bond pdb=" CG ARG z 10 " pdb=" CD ARG z 10 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.10e+00 bond pdb=" CG GLN z 9 " pdb=" CD GLN z 9 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.45e+00 ... (remaining 26600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 36213 2.03 - 4.07: 720 4.07 - 6.10: 60 6.10 - 8.14: 8 8.14 - 10.17: 3 Bond angle restraints: 37004 Sorted by residual: angle pdb=" N ILE z 6 " pdb=" CA ILE z 6 " pdb=" C ILE z 6 " ideal model delta sigma weight residual 110.62 119.93 -9.31 1.02e+00 9.61e-01 8.33e+01 angle pdb=" N ARG z 11 " pdb=" CA ARG z 11 " pdb=" C ARG z 11 " ideal model delta sigma weight residual 111.07 105.86 5.21 1.07e+00 8.73e-01 2.37e+01 angle pdb=" N LEU z 46 " pdb=" CA LEU z 46 " pdb=" C LEU z 46 " ideal model delta sigma weight residual 109.63 115.25 -5.62 1.49e+00 4.50e-01 1.42e+01 angle pdb=" N ASN 4 193 " pdb=" CA ASN 4 193 " pdb=" CB ASN 4 193 " ideal model delta sigma weight residual 110.49 104.13 6.36 1.69e+00 3.50e-01 1.42e+01 angle pdb=" N GLN 5 150 " pdb=" CA GLN 5 150 " pdb=" C GLN 5 150 " ideal model delta sigma weight residual 110.80 103.05 7.75 2.13e+00 2.20e-01 1.32e+01 ... (remaining 36999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 15633 35.08 - 70.16: 944 70.16 - 105.24: 123 105.24 - 140.32: 18 140.32 - 175.41: 4 Dihedral angle restraints: 16722 sinusoidal: 9156 harmonic: 7566 Sorted by residual: dihedral pdb=" O4' U A 33 " pdb=" C1' U A 33 " pdb=" N1 U A 33 " pdb=" C2 U A 33 " ideal model delta sinusoidal sigma weight residual -160.00 -34.18 -125.82 1 1.50e+01 4.44e-03 6.76e+01 dihedral pdb=" O4' U B 33 " pdb=" C1' U B 33 " pdb=" N1 U B 33 " pdb=" C2 U B 33 " ideal model delta sinusoidal sigma weight residual -160.00 -38.21 -121.79 1 1.50e+01 4.44e-03 6.51e+01 dihedral pdb=" O4' U C 33 " pdb=" C1' U C 33 " pdb=" N1 U C 33 " pdb=" C2 U C 33 " ideal model delta sinusoidal sigma weight residual -160.00 -40.58 -119.42 1 1.50e+01 4.44e-03 6.36e+01 ... (remaining 16719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3294 0.041 - 0.081: 924 0.081 - 0.122: 125 0.122 - 0.162: 34 0.162 - 0.203: 20 Chirality restraints: 4397 Sorted by residual: chirality pdb=" C1' G A 10 " pdb=" O4' G A 10 " pdb=" C2' G A 10 " pdb=" N9 G A 10 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2' C B 34 " pdb=" C3' C B 34 " pdb=" O2' C B 34 " pdb=" C1' C B 34 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2' C C 34 " pdb=" C3' C C 34 " pdb=" O2' C C 34 " pdb=" C1' C C 34 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4394 not shown) Planarity restraints: 3941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN 4 70 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO 4 71 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO 4 71 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO 4 71 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN y 70 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO y 71 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO y 71 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO y 71 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G C 18 " -0.028 2.00e-02 2.50e+03 1.37e-02 5.63e+00 pdb=" N9 G C 18 " 0.037 2.00e-02 2.50e+03 pdb=" C8 G C 18 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G C 18 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G C 18 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G C 18 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G C 18 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G C 18 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G C 18 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G C 18 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G C 18 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G C 18 " 0.000 2.00e-02 2.50e+03 ... (remaining 3938 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 11 1.81 - 2.58: 364 2.58 - 3.36: 34332 3.36 - 4.13: 61759 4.13 - 4.90: 108606 Nonbonded interactions: 205072 Sorted by model distance: nonbonded pdb=" NH2 ARG 6 119 " pdb=" OE2 GLU 6 218 " model vdw 1.041 3.120 nonbonded pdb=" OD2 ASP 5 98 " pdb=" CE LYS 5 101 " model vdw 1.160 3.440 nonbonded pdb=" OE2 GLU 0 163 " pdb=" CD2 LEU 0 186 " model vdw 1.284 3.460 nonbonded pdb=" NH2 ARG 0 11 " pdb=" C8 A A 37 " model vdw 1.333 3.340 nonbonded pdb=" CD GLU 0 163 " pdb=" CD2 LEU 0 186 " model vdw 1.344 3.690 ... (remaining 205067 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: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 285) selection = (chain '4' and resid 2 through 285) selection = (chain '5' and resid 2 through 285) selection = (chain '6' and resid 2 through 285) selection = (chain '7' and resid 2 through 285) selection = (chain '8' and resid 2 through 285) selection = (chain '9' and resid 2 through 285) selection = (chain 'y' and resid 2 through 285) selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 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: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 61.000 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.100 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2158 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.237 26606 Z= 0.282 Angle : 0.717 10.170 37004 Z= 0.415 Chirality : 0.040 0.203 4397 Planarity : 0.005 0.109 3941 Dihedral : 20.498 175.406 11774 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.61 % Favored : 95.95 % Rotamer: Outliers : 3.30 % Allowed : 9.21 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2546 helix: 0.67 (0.11), residues: 1783 sheet: None (None), residues: 0 loop : -0.77 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 6 217 HIS 0.006 0.001 HIS 8 69 PHE 0.016 0.002 PHE 7 179 TYR 0.013 0.002 TYR y 94 ARG 0.005 0.001 ARG 5 89 Details of bonding type rmsd hydrogen bonds : bond 0.14726 ( 1521) hydrogen bonds : angle 5.18086 ( 4317) covalent geometry : bond 0.00519 (26605) covalent geometry : angle 0.71704 (37004) Misc. bond : bond 0.23679 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 539 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.2491 (mmm) cc_final: 0.2288 (mmm) REVERT: 0 18 ASN cc_start: 0.4593 (m-40) cc_final: 0.4352 (m-40) REVERT: 0 120 HIS cc_start: 0.4444 (m90) cc_final: 0.4086 (m-70) REVERT: 0 167 ILE cc_start: 0.5516 (OUTLIER) cc_final: 0.5285 (tt) REVERT: 0 206 THR cc_start: 0.4784 (OUTLIER) cc_final: 0.4429 (p) REVERT: 0 256 HIS cc_start: 0.5249 (m-70) cc_final: 0.4996 (t70) REVERT: 0 259 GLU cc_start: 0.3378 (OUTLIER) cc_final: 0.3145 (pm20) REVERT: y 162 THR cc_start: 0.5902 (m) cc_final: 0.5672 (t) REVERT: y 211 MET cc_start: 0.5629 (mtm) cc_final: 0.5306 (mpp) REVERT: y 230 GLU cc_start: 0.5266 (mm-30) cc_final: 0.4802 (mm-30) REVERT: y 234 LEU cc_start: 0.6536 (mt) cc_final: 0.6102 (mm) REVERT: y 238 GLU cc_start: 0.4828 (mm-30) cc_final: 0.4495 (mm-30) REVERT: y 280 ASP cc_start: 0.7178 (m-30) cc_final: 0.6929 (m-30) REVERT: 5 103 ARG cc_start: 0.5004 (tpp80) cc_final: 0.4652 (mtt-85) REVERT: 5 116 THR cc_start: 0.6904 (m) cc_final: 0.6462 (p) REVERT: 5 123 GLU cc_start: 0.4742 (tp30) cc_final: 0.4412 (pt0) REVERT: 5 175 ARG cc_start: 0.6723 (ttt-90) cc_final: 0.6457 (ttp-110) REVERT: 5 179 PHE cc_start: 0.5696 (m-10) cc_final: 0.5283 (m-80) REVERT: 6 189 ASP cc_start: 0.5701 (m-30) cc_final: 0.5311 (m-30) REVERT: 6 215 ARG cc_start: 0.6963 (mtp180) cc_final: 0.6438 (ttp-170) REVERT: 6 219 GLU cc_start: 0.6941 (tt0) cc_final: 0.5995 (tp30) REVERT: 4 4 GLN cc_start: 0.4548 (OUTLIER) cc_final: 0.4200 (tp-100) REVERT: 4 273 GLU cc_start: 0.6801 (tp30) cc_final: 0.6366 (tp30) REVERT: 4 274 ASP cc_start: 0.7000 (m-30) cc_final: 0.6680 (t0) REVERT: 4 276 ASP cc_start: 0.5010 (m-30) cc_final: 0.4296 (p0) REVERT: 8 28 ASP cc_start: 0.4646 (t0) cc_final: 0.4391 (t0) REVERT: 8 123 GLU cc_start: 0.5055 (pt0) cc_final: 0.4258 (pm20) REVERT: 8 124 ILE cc_start: 0.5361 (mm) cc_final: 0.5067 (mt) REVERT: 9 4 GLN cc_start: 0.3628 (OUTLIER) cc_final: 0.2343 (mt0) REVERT: 9 162 THR cc_start: 0.5884 (m) cc_final: 0.5629 (t) REVERT: 9 211 MET cc_start: 0.4322 (mtp) cc_final: 0.3933 (mmt) REVERT: 9 215 ARG cc_start: 0.4885 (mmm-85) cc_final: 0.4662 (ptp-110) REVERT: 9 219 GLU cc_start: 0.7108 (tt0) cc_final: 0.6886 (tm-30) REVERT: 9 237 LYS cc_start: 0.5539 (mttt) cc_final: 0.5174 (mmpt) REVERT: 9 241 MET cc_start: 0.3844 (mmm) cc_final: 0.3586 (mmt) REVERT: 7 170 ASN cc_start: 0.5624 (t0) cc_final: 0.5179 (t0) REVERT: 7 266 THR cc_start: 0.4483 (m) cc_final: 0.3997 (t) REVERT: 7 269 GLU cc_start: 0.5138 (tt0) cc_final: 0.4708 (pt0) REVERT: 7 273 GLU cc_start: 0.6243 (tt0) cc_final: 0.5983 (pt0) outliers start: 76 outliers final: 11 residues processed: 601 average time/residue: 1.4764 time to fit residues: 1014.2679 Evaluate side-chains 298 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 282 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 167 ILE Chi-restraints excluded: chain 0 residue 206 THR Chi-restraints excluded: chain 0 residue 259 GLU Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 272 ILE Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 145 VAL Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 41 CYS Chi-restraints excluded: chain 4 residue 258 VAL Chi-restraints excluded: chain 8 residue 72 ASP Chi-restraints excluded: chain 9 residue 4 GLN Chi-restraints excluded: chain 9 residue 11 ARG Chi-restraints excluded: chain 9 residue 157 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 159 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 252 ASN 0 22 HIS 0 47 HIS y 22 HIS y 105 HIS y 165 GLN y 193 ASN 5 34 HIS 5 193 ASN 5 284 GLN 6 70 ASN 6 193 ASN 4 4 GLN 4 25 GLN 4 158 HIS ** 4 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 252 ASN 8 25 GLN 8 198 ASN 8 252 ASN ** 9 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 34 HIS 9 170 ASN 9 256 HIS 7 22 HIS ** 7 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 150 GLN 7 193 ASN 7 260 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.236357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.191480 restraints weight = 32549.242| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.41 r_work: 0.3956 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26606 Z= 0.209 Angle : 0.810 11.680 37004 Z= 0.406 Chirality : 0.041 0.206 4397 Planarity : 0.006 0.093 3941 Dihedral : 22.436 159.674 6531 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.61 % Favored : 96.27 % Rotamer: Outliers : 4.99 % Allowed : 17.76 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.16), residues: 2546 helix: 1.64 (0.11), residues: 1764 sheet: None (None), residues: 0 loop : -0.27 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 7 217 HIS 0.008 0.002 HIS 7 120 PHE 0.023 0.002 PHE 6 114 TYR 0.020 0.003 TYR 7 63 ARG 0.010 0.001 ARG 5 214 Details of bonding type rmsd hydrogen bonds : bond 0.06276 ( 1521) hydrogen bonds : angle 3.90674 ( 4317) covalent geometry : bond 0.00441 (26605) covalent geometry : angle 0.80965 (37004) Misc. bond : bond 0.00262 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 563 time to evaluate : 2.533 Fit side-chains revert: symmetry clash REVERT: z 21 ARG cc_start: 0.6952 (mmt-90) cc_final: 0.6600 (mmm-85) REVERT: z 36 LYS cc_start: 0.7637 (mptp) cc_final: 0.7350 (mttm) REVERT: z 70 ASN cc_start: 0.8550 (t0) cc_final: 0.8268 (t160) REVERT: z 178 MET cc_start: 0.4982 (OUTLIER) cc_final: 0.4170 (ptp) REVERT: z 218 GLU cc_start: 0.7581 (tp30) cc_final: 0.7321 (tt0) REVERT: 0 1 MET cc_start: 0.3036 (mmm) cc_final: 0.2381 (mmm) REVERT: 0 121 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7043 (m-30) REVERT: 0 150 GLN cc_start: 0.6910 (mt0) cc_final: 0.6175 (mm-40) REVERT: 0 170 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8168 (t0) REVERT: 0 273 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: y 165 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6407 (pt0) REVERT: y 186 LEU cc_start: 0.4078 (OUTLIER) cc_final: 0.3661 (mm) REVERT: y 237 LYS cc_start: 0.8057 (ptmt) cc_final: 0.7345 (ptpp) REVERT: y 265 ASP cc_start: 0.6716 (t70) cc_final: 0.6260 (m-30) REVERT: y 269 GLU cc_start: 0.7200 (tp30) cc_final: 0.6948 (tp30) REVERT: 5 17 VAL cc_start: 0.8017 (OUTLIER) cc_final: 0.7712 (t) REVERT: 5 79 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: 5 145 VAL cc_start: 0.4347 (OUTLIER) cc_final: 0.4005 (p) REVERT: 5 179 PHE cc_start: 0.7679 (m-10) cc_final: 0.7181 (m-10) REVERT: 5 187 ASN cc_start: 0.7023 (OUTLIER) cc_final: 0.5853 (t0) REVERT: 6 1 MET cc_start: 0.4898 (OUTLIER) cc_final: 0.4442 (tmt) REVERT: 6 11 ARG cc_start: 0.5620 (OUTLIER) cc_final: 0.5263 (mmp80) REVERT: 6 211 MET cc_start: 0.7397 (mtp) cc_final: 0.7156 (mtm) REVERT: 6 218 GLU cc_start: 0.7507 (tp30) cc_final: 0.7260 (tp30) REVERT: 6 219 GLU cc_start: 0.8175 (tt0) cc_final: 0.7939 (tp30) REVERT: 6 234 LEU cc_start: 0.9139 (mt) cc_final: 0.8938 (mt) REVERT: 6 269 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: 4 4 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6614 (tm-30) REVERT: 4 19 PHE cc_start: 0.5784 (t80) cc_final: 0.5509 (t80) REVERT: 4 40 LYS cc_start: 0.4948 (ttmt) cc_final: 0.4685 (ttpp) REVERT: 4 163 GLU cc_start: 0.6975 (tp30) cc_final: 0.6211 (mt-10) REVERT: 4 229 GLN cc_start: 0.7998 (mt0) cc_final: 0.7312 (pt0) REVERT: 4 273 GLU cc_start: 0.7824 (tp30) cc_final: 0.7620 (mm-30) REVERT: 9 241 MET cc_start: 0.6452 (mmm) cc_final: 0.6225 (mmm) REVERT: 9 253 ILE cc_start: 0.8560 (mm) cc_final: 0.8175 (mt) REVERT: 7 263 SER cc_start: 0.7574 (OUTLIER) cc_final: 0.7374 (p) outliers start: 115 outliers final: 21 residues processed: 632 average time/residue: 1.9336 time to fit residues: 1379.0947 Evaluate side-chains 399 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 363 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 161 ASP Chi-restraints excluded: chain z residue 171 LEU Chi-restraints excluded: chain z residue 178 MET Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain 0 residue 84 CYS Chi-restraints excluded: chain 0 residue 118 VAL Chi-restraints excluded: chain 0 residue 121 ASP Chi-restraints excluded: chain 0 residue 170 ASN Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 165 GLN Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 79 GLU Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 145 VAL Chi-restraints excluded: chain 5 residue 159 LEU Chi-restraints excluded: chain 5 residue 187 ASN Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 11 ARG Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain 6 residue 269 GLU Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 4 residue 241 MET Chi-restraints excluded: chain 4 residue 278 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 9 residue 181 VAL Chi-restraints excluded: chain 7 residue 76 VAL Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 263 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 222 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 0 34 HIS ** 0 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 25 GLN 5 69 HIS 9 4 GLN 9 25 GLN 7 105 HIS 7 170 ASN 7 187 ASN 7 260 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.226947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.179082 restraints weight = 31356.140| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.27 r_work: 0.3834 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.9407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26606 Z= 0.171 Angle : 0.650 12.519 37004 Z= 0.331 Chirality : 0.036 0.164 4397 Planarity : 0.005 0.125 3941 Dihedral : 22.057 170.976 6508 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.61 % Favored : 96.23 % Rotamer: Outliers : 5.91 % Allowed : 22.97 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.16), residues: 2546 helix: 2.21 (0.12), residues: 1774 sheet: None (None), residues: 0 loop : -0.21 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 7 217 HIS 0.005 0.001 HIS 7 158 PHE 0.029 0.002 PHE 6 114 TYR 0.022 0.002 TYR y 63 ARG 0.011 0.001 ARG 8 166 Details of bonding type rmsd hydrogen bonds : bond 0.06438 ( 1521) hydrogen bonds : angle 3.58086 ( 4317) covalent geometry : bond 0.00372 (26605) covalent geometry : angle 0.65007 (37004) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 490 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: z 21 ARG cc_start: 0.7664 (mmt-90) cc_final: 0.7401 (mmp80) REVERT: z 190 ARG cc_start: 0.6491 (mtp85) cc_final: 0.6220 (mtt90) REVERT: z 211 MET cc_start: 0.8860 (mtp) cc_final: 0.8552 (mtp) REVERT: z 237 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7522 (ttmm) REVERT: z 240 ARG cc_start: 0.8115 (ttp-170) cc_final: 0.7728 (ttp80) REVERT: 0 48 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.7318 (mmm160) REVERT: 0 241 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7010 (mtp) REVERT: 0 273 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: y 18 ASN cc_start: 0.7914 (m-40) cc_final: 0.7702 (m110) REVERT: y 57 MET cc_start: 0.8801 (tpp) cc_final: 0.8520 (tpt) REVERT: y 62 TYR cc_start: 0.8308 (t80) cc_final: 0.7379 (t80) REVERT: y 92 TYR cc_start: 0.8767 (m-80) cc_final: 0.8546 (m-80) REVERT: y 186 LEU cc_start: 0.3652 (OUTLIER) cc_final: 0.2934 (mm) REVERT: y 230 GLU cc_start: 0.7534 (pt0) cc_final: 0.7228 (tt0) REVERT: y 237 LYS cc_start: 0.8454 (ptmt) cc_final: 0.8074 (mtmt) REVERT: 5 21 ARG cc_start: 0.7674 (ttm-80) cc_final: 0.7425 (ttt180) REVERT: 5 70 ASN cc_start: 0.7796 (t0) cc_final: 0.7325 (t160) REVERT: 5 187 ASN cc_start: 0.7181 (m110) cc_final: 0.6225 (t0) REVERT: 5 218 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7314 (mt-10) REVERT: 5 229 GLN cc_start: 0.8790 (mt0) cc_final: 0.8471 (mt0) REVERT: 6 11 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.4895 (mtm110) REVERT: 6 150 GLN cc_start: 0.5562 (mm-40) cc_final: 0.5163 (tp40) REVERT: 6 175 ARG cc_start: 0.7554 (ttm170) cc_final: 0.7087 (ttt-90) REVERT: 4 77 LEU cc_start: 0.6806 (tt) cc_final: 0.6561 (mt) REVERT: 4 81 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: 4 165 GLN cc_start: 0.7460 (tp40) cc_final: 0.7068 (pt0) REVERT: 4 219 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7712 (tt0) REVERT: 4 275 PHE cc_start: 0.7560 (t80) cc_final: 0.6640 (t80) REVERT: 8 12 ASP cc_start: 0.6573 (m-30) cc_final: 0.6349 (m-30) REVERT: 8 36 LYS cc_start: 0.7857 (mptt) cc_final: 0.7404 (mttt) REVERT: 8 48 ARG cc_start: 0.7572 (mtm180) cc_final: 0.7346 (ttp80) REVERT: 8 111 ARG cc_start: 0.7581 (mmm160) cc_final: 0.7304 (mtm110) REVERT: 8 119 ARG cc_start: 0.7453 (mpt-90) cc_final: 0.7067 (mtt-85) REVERT: 8 144 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6468 (pp) REVERT: 8 185 ASP cc_start: 0.6471 (m-30) cc_final: 0.6195 (m-30) REVERT: 9 103 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.8169 (mmt180) REVERT: 9 123 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: 9 184 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6248 (pt) REVERT: 9 219 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7524 (tm-30) REVERT: 9 237 LYS cc_start: 0.7622 (mmtt) cc_final: 0.7401 (mtpp) REVERT: 9 243 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7927 (tp) REVERT: 7 18 ASN cc_start: 0.6754 (m-40) cc_final: 0.6243 (m110) REVERT: 7 44 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.6306 (tmtt) REVERT: 7 121 ASP cc_start: 0.8012 (m-30) cc_final: 0.7576 (m-30) REVERT: 7 165 GLN cc_start: 0.7835 (tp40) cc_final: 0.7161 (mt0) REVERT: 7 176 ARG cc_start: 0.7092 (tpp80) cc_final: 0.6875 (tpp-160) outliers start: 136 outliers final: 39 residues processed: 576 average time/residue: 1.6740 time to fit residues: 1081.6321 Evaluate side-chains 420 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 370 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 140 VAL Chi-restraints excluded: chain z residue 161 ASP Chi-restraints excluded: chain z residue 196 LEU Chi-restraints excluded: chain z residue 237 LYS Chi-restraints excluded: chain 0 residue 241 MET Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 110 ASP Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 258 VAL Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain 5 residue 116 THR Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 159 LEU Chi-restraints excluded: chain 5 residue 194 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 11 ARG Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain 6 residue 93 THR Chi-restraints excluded: chain 6 residue 210 ILE Chi-restraints excluded: chain 4 residue 81 GLU Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 139 SER Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 151 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 222 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 116 THR Chi-restraints excluded: chain 8 residue 144 LEU Chi-restraints excluded: chain 8 residue 159 LEU Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 50 THR Chi-restraints excluded: chain 9 residue 108 VAL Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 184 LEU Chi-restraints excluded: chain 9 residue 243 LEU Chi-restraints excluded: chain 7 residue 37 ILE Chi-restraints excluded: chain 7 residue 44 LYS Chi-restraints excluded: chain 7 residue 76 VAL Chi-restraints excluded: chain 7 residue 146 THR Chi-restraints excluded: chain 7 residue 258 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 29 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 182 optimal weight: 40.0000 chunk 24 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 140 optimal weight: 30.0000 chunk 78 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 158 HIS 0 22 HIS ** 5 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 4 GLN 4 34 HIS 4 191 HIS 4 229 GLN 8 4 GLN 8 170 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.223574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.175285 restraints weight = 31312.043| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.34 r_work: 0.3774 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 1.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26606 Z= 0.156 Angle : 0.616 9.029 37004 Z= 0.314 Chirality : 0.035 0.168 4397 Planarity : 0.004 0.044 3941 Dihedral : 21.805 160.620 6504 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.73 % Favored : 96.11 % Rotamer: Outliers : 5.99 % Allowed : 24.97 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.16), residues: 2546 helix: 2.43 (0.12), residues: 1778 sheet: None (None), residues: 0 loop : -0.38 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP z 217 HIS 0.006 0.001 HIS 6 158 PHE 0.016 0.002 PHE 7 19 TYR 0.019 0.002 TYR y 63 ARG 0.033 0.001 ARG 8 166 Details of bonding type rmsd hydrogen bonds : bond 0.06209 ( 1521) hydrogen bonds : angle 3.44398 ( 4317) covalent geometry : bond 0.00343 (26605) covalent geometry : angle 0.61584 (37004) Misc. bond : bond 0.00268 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 409 time to evaluate : 2.783 Fit side-chains REVERT: z 45 ARG cc_start: 0.7646 (tmm-80) cc_final: 0.7043 (tmm160) REVERT: z 70 ASN cc_start: 0.8263 (t0) cc_final: 0.7761 (t160) REVERT: z 131 SER cc_start: 0.8109 (OUTLIER) cc_final: 0.7676 (p) REVERT: z 166 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7330 (mtp85) REVERT: z 190 ARG cc_start: 0.6595 (mtp85) cc_final: 0.6254 (mtt180) REVERT: z 211 MET cc_start: 0.8851 (mtp) cc_final: 0.8630 (mtp) REVERT: z 219 GLU cc_start: 0.7593 (tt0) cc_final: 0.7197 (tp30) REVERT: z 238 GLU cc_start: 0.7935 (tp30) cc_final: 0.7624 (mm-30) REVERT: 0 39 LYS cc_start: 0.7647 (tppp) cc_final: 0.6809 (ttmm) REVERT: 0 57 MET cc_start: 0.8567 (tpp) cc_final: 0.8209 (tpt) REVERT: 0 227 ARG cc_start: 0.8967 (mmt-90) cc_final: 0.8597 (tpp-160) REVERT: 0 241 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7143 (mtp) REVERT: 0 273 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8106 (tp30) REVERT: y 18 ASN cc_start: 0.7991 (m-40) cc_final: 0.7760 (m110) REVERT: y 62 TYR cc_start: 0.8382 (t80) cc_final: 0.7846 (t80) REVERT: y 161 ASP cc_start: 0.5826 (t0) cc_final: 0.5339 (t0) REVERT: y 164 VAL cc_start: 0.8772 (t) cc_final: 0.8463 (t) REVERT: y 186 LEU cc_start: 0.4423 (OUTLIER) cc_final: 0.3482 (mm) REVERT: y 219 GLU cc_start: 0.7703 (tp30) cc_final: 0.7323 (tp30) REVERT: y 227 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.6558 (mtt90) REVERT: 5 70 ASN cc_start: 0.7988 (t0) cc_final: 0.7686 (t160) REVERT: 5 166 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5847 (mtm-85) REVERT: 5 172 GLU cc_start: 0.7234 (tp30) cc_final: 0.6559 (tp30) REVERT: 5 187 ASN cc_start: 0.7344 (m110) cc_final: 0.6864 (t0) REVERT: 5 229 GLN cc_start: 0.8799 (mt0) cc_final: 0.8424 (mt0) REVERT: 6 39 LYS cc_start: 0.7738 (ttpt) cc_final: 0.7051 (tmtm) REVERT: 6 150 GLN cc_start: 0.5568 (mm-40) cc_final: 0.5113 (tt0) REVERT: 6 175 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7436 (ttt-90) REVERT: 4 45 ARG cc_start: 0.5511 (ptt90) cc_final: 0.5229 (ptt180) REVERT: 4 77 LEU cc_start: 0.6570 (tt) cc_final: 0.6254 (mp) REVERT: 4 81 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: 4 90 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6921 (ptm160) REVERT: 4 165 GLN cc_start: 0.7628 (tp40) cc_final: 0.7109 (pt0) REVERT: 4 237 LYS cc_start: 0.7097 (ttmm) cc_final: 0.6664 (ttpt) REVERT: 4 275 PHE cc_start: 0.8206 (t80) cc_final: 0.7806 (t80) REVERT: 4 278 TYR cc_start: 0.8078 (p90) cc_final: 0.7754 (p90) REVERT: 8 25 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: 8 36 LYS cc_start: 0.7961 (mptt) cc_final: 0.7531 (mttt) REVERT: 8 40 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.6942 (ttmp) REVERT: 8 43 GLU cc_start: 0.7152 (pp20) cc_final: 0.6729 (pm20) REVERT: 8 90 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7066 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7646 (mpt-90) cc_final: 0.7364 (mtt-85) REVERT: 8 175 ARG cc_start: 0.7436 (ttm170) cc_final: 0.7226 (ttp80) REVERT: 9 123 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: 9 219 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7525 (tm-30) REVERT: 7 18 ASN cc_start: 0.7232 (m-40) cc_final: 0.6723 (t0) REVERT: 7 165 GLN cc_start: 0.8013 (tp40) cc_final: 0.7390 (mt0) REVERT: 7 176 ARG cc_start: 0.7366 (tpp80) cc_final: 0.7089 (tpp-160) REVERT: 7 178 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7625 (mtm) REVERT: 7 276 ASP cc_start: 0.8126 (m-30) cc_final: 0.7854 (m-30) REVERT: 7 277 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.7930 (pp) outliers start: 138 outliers final: 58 residues processed: 503 average time/residue: 1.8376 time to fit residues: 1041.7863 Evaluate side-chains 423 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 351 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 41 CYS Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 131 SER Chi-restraints excluded: chain z residue 161 ASP Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 135 LEU Chi-restraints excluded: chain 0 residue 142 GLU Chi-restraints excluded: chain 0 residue 241 MET Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 227 ARG Chi-restraints excluded: chain y residue 231 ARG Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain 5 residue 52 LEU Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 116 THR Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 5 residue 166 ARG Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 194 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 5 residue 284 GLN Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 143 THR Chi-restraints excluded: chain 4 residue 41 CYS Chi-restraints excluded: chain 4 residue 81 GLU Chi-restraints excluded: chain 4 residue 90 ARG Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 123 GLU Chi-restraints excluded: chain 4 residue 139 SER Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 151 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 222 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 25 GLN Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 90 ARG Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 190 ARG Chi-restraints excluded: chain 8 residue 277 ILE Chi-restraints excluded: chain 8 residue 284 GLN Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 65 GLU Chi-restraints excluded: chain 9 residue 108 VAL Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 181 VAL Chi-restraints excluded: chain 9 residue 272 ILE Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 146 THR Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 168 GLU Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 178 MET Chi-restraints excluded: chain 7 residue 241 MET Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 52 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 39 optimal weight: 30.0000 chunk 202 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 253 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 4 191 HIS 4 229 GLN 9 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.221900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.173498 restraints weight = 30868.327| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.32 r_work: 0.3733 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 1.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26606 Z= 0.149 Angle : 0.583 8.455 37004 Z= 0.296 Chirality : 0.034 0.158 4397 Planarity : 0.004 0.043 3941 Dihedral : 21.704 163.760 6504 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 5.56 % Allowed : 25.88 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.16), residues: 2546 helix: 2.43 (0.12), residues: 1798 sheet: None (None), residues: 0 loop : -0.58 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 6 217 HIS 0.007 0.001 HIS 6 158 PHE 0.022 0.002 PHE y 19 TYR 0.014 0.002 TYR z 63 ARG 0.016 0.001 ARG 8 166 Details of bonding type rmsd hydrogen bonds : bond 0.06260 ( 1521) hydrogen bonds : angle 3.38784 ( 4317) covalent geometry : bond 0.00324 (26605) covalent geometry : angle 0.58307 (37004) Misc. bond : bond 0.00209 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 380 time to evaluate : 2.373 Fit side-chains revert: symmetry clash REVERT: z 70 ASN cc_start: 0.8233 (t0) cc_final: 0.7806 (t160) REVERT: z 141 ARG cc_start: 0.6784 (mtm-85) cc_final: 0.6391 (mtm-85) REVERT: z 166 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7349 (mtp180) REVERT: z 190 ARG cc_start: 0.6663 (mtp85) cc_final: 0.6073 (mtt180) REVERT: z 211 MET cc_start: 0.8915 (mtp) cc_final: 0.8684 (mtp) REVERT: z 219 GLU cc_start: 0.7653 (tt0) cc_final: 0.7303 (tp30) REVERT: 0 4 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: 0 39 LYS cc_start: 0.7397 (tppp) cc_final: 0.6584 (ttmm) REVERT: 0 57 MET cc_start: 0.8610 (tpp) cc_final: 0.8400 (tpt) REVERT: 0 175 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7272 (ttt180) REVERT: 0 227 ARG cc_start: 0.8969 (mmt-90) cc_final: 0.8687 (mmt180) REVERT: 0 273 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: y 18 ASN cc_start: 0.8166 (m-40) cc_final: 0.7945 (m110) REVERT: y 57 MET cc_start: 0.8786 (tpp) cc_final: 0.8526 (tpt) REVERT: y 62 TYR cc_start: 0.8403 (t80) cc_final: 0.7851 (t80) REVERT: y 92 TYR cc_start: 0.8887 (m-80) cc_final: 0.8558 (m-80) REVERT: y 103 ARG cc_start: 0.8307 (tpp-160) cc_final: 0.7965 (ttm170) REVERT: y 112 THR cc_start: 0.7623 (p) cc_final: 0.7126 (m) REVERT: y 169 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7022 (mt-10) REVERT: y 186 LEU cc_start: 0.4875 (OUTLIER) cc_final: 0.3913 (mm) REVERT: y 190 ARG cc_start: 0.6465 (mtp85) cc_final: 0.6254 (mmp-170) REVERT: y 218 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7485 (mt-10) REVERT: y 219 GLU cc_start: 0.7771 (tp30) cc_final: 0.7380 (tp30) REVERT: y 222 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7705 (mtm180) REVERT: 5 94 TYR cc_start: 0.6576 (t80) cc_final: 0.6333 (t80) REVERT: 5 99 ARG cc_start: 0.6707 (mmm160) cc_final: 0.5599 (mtp180) REVERT: 5 101 LYS cc_start: 0.6262 (OUTLIER) cc_final: 0.5390 (mtpt) REVERT: 5 163 GLU cc_start: 0.5904 (mp0) cc_final: 0.5657 (mp0) REVERT: 5 166 ARG cc_start: 0.6104 (OUTLIER) cc_final: 0.5874 (mtm-85) REVERT: 5 187 ASN cc_start: 0.7558 (m110) cc_final: 0.7012 (t0) REVERT: 5 229 GLN cc_start: 0.8819 (mt0) cc_final: 0.8533 (mt0) REVERT: 6 39 LYS cc_start: 0.7820 (ttpt) cc_final: 0.7063 (tmtm) REVERT: 6 150 GLN cc_start: 0.5775 (mm-40) cc_final: 0.5147 (tt0) REVERT: 6 175 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7492 (ttt-90) REVERT: 6 178 MET cc_start: 0.8047 (ptm) cc_final: 0.7794 (ptm) REVERT: 4 45 ARG cc_start: 0.5770 (ptt90) cc_final: 0.5483 (ptt180) REVERT: 4 90 ARG cc_start: 0.7243 (ptm160) cc_final: 0.6894 (ptm160) REVERT: 4 165 GLN cc_start: 0.7669 (tp40) cc_final: 0.7305 (pt0) REVERT: 4 234 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7868 (mt) REVERT: 4 237 LYS cc_start: 0.7173 (ttmm) cc_final: 0.6775 (ttpt) REVERT: 4 275 PHE cc_start: 0.8396 (t80) cc_final: 0.8141 (t80) REVERT: 4 278 TYR cc_start: 0.8400 (p90) cc_final: 0.8036 (p90) REVERT: 8 30 ASP cc_start: 0.7398 (p0) cc_final: 0.7083 (t0) REVERT: 8 36 LYS cc_start: 0.7851 (mptt) cc_final: 0.7418 (mttt) REVERT: 8 40 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.6962 (ttmp) REVERT: 8 43 GLU cc_start: 0.7040 (pp20) cc_final: 0.6704 (pm20) REVERT: 8 89 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7104 (mmm-85) REVERT: 8 90 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7050 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7764 (mpt-90) cc_final: 0.7531 (mtt-85) REVERT: 9 18 ASN cc_start: 0.8148 (m-40) cc_final: 0.7814 (m-40) REVERT: 9 45 ARG cc_start: 0.7763 (ttt90) cc_final: 0.7532 (ttp80) REVERT: 9 123 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: 9 219 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7597 (tm-30) REVERT: 9 284 GLN cc_start: 0.7116 (pt0) cc_final: 0.6797 (pt0) REVERT: 7 12 ASP cc_start: 0.6272 (m-30) cc_final: 0.6063 (m-30) REVERT: 7 18 ASN cc_start: 0.7281 (m-40) cc_final: 0.6822 (t0) REVERT: 7 31 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8118 (tm) REVERT: 7 165 GLN cc_start: 0.8042 (tp40) cc_final: 0.7477 (mt0) REVERT: 7 178 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7543 (mtm) REVERT: 7 277 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8016 (pp) outliers start: 128 outliers final: 68 residues processed: 473 average time/residue: 1.7578 time to fit residues: 932.8797 Evaluate side-chains 419 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 338 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 2 SER Chi-restraints excluded: chain z residue 28 ASP Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 104 ASP Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 161 ASP Chi-restraints excluded: chain z residue 162 THR Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 236 VAL Chi-restraints excluded: chain z residue 242 CYS Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 116 THR Chi-restraints excluded: chain 0 residue 135 LEU Chi-restraints excluded: chain 0 residue 222 ARG Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 231 ARG Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 57 MET Chi-restraints excluded: chain 5 residue 101 LYS Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 166 ARG Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 194 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 6 residue 2 SER Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 143 THR Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 123 GLU Chi-restraints excluded: chain 4 residue 139 SER Chi-restraints excluded: chain 4 residue 151 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 222 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 4 residue 241 MET Chi-restraints excluded: chain 4 residue 277 ILE Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 89 ARG Chi-restraints excluded: chain 8 residue 90 ARG Chi-restraints excluded: chain 8 residue 92 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 277 ILE Chi-restraints excluded: chain 8 residue 284 GLN Chi-restraints excluded: chain 9 residue 6 ILE Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 108 VAL Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 163 GLU Chi-restraints excluded: chain 9 residue 234 LEU Chi-restraints excluded: chain 9 residue 276 ASP Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 140 VAL Chi-restraints excluded: chain 7 residue 146 THR Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 168 GLU Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 178 MET Chi-restraints excluded: chain 7 residue 219 GLU Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 85 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 253 optimal weight: 50.0000 chunk 146 optimal weight: 0.9980 chunk 111 optimal weight: 0.0070 chunk 213 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 30.0000 chunk 131 optimal weight: 10.0000 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 0 47 HIS 0 229 GLN 4 191 HIS 4 229 GLN 9 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.222838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.174767 restraints weight = 30936.493| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.28 r_work: 0.3760 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 1.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26606 Z= 0.127 Angle : 0.545 8.225 37004 Z= 0.278 Chirality : 0.033 0.299 4397 Planarity : 0.004 0.099 3941 Dihedral : 21.585 159.716 6504 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 4.47 % Allowed : 27.53 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.16), residues: 2546 helix: 2.71 (0.12), residues: 1777 sheet: None (None), residues: 0 loop : -0.42 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 5 217 HIS 0.007 0.001 HIS 0 22 PHE 0.011 0.001 PHE 4 19 TYR 0.017 0.002 TYR z 63 ARG 0.010 0.001 ARG 8 166 Details of bonding type rmsd hydrogen bonds : bond 0.05667 ( 1521) hydrogen bonds : angle 3.28976 ( 4317) covalent geometry : bond 0.00268 (26605) covalent geometry : angle 0.54456 (37004) Misc. bond : bond 0.00501 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 370 time to evaluate : 2.373 Fit side-chains revert: symmetry clash REVERT: z 45 ARG cc_start: 0.7396 (tmm-80) cc_final: 0.6942 (tmm160) REVERT: z 70 ASN cc_start: 0.7906 (t0) cc_final: 0.7397 (t160) REVERT: z 166 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7321 (mtp180) REVERT: z 168 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: z 190 ARG cc_start: 0.6557 (mtp85) cc_final: 0.6018 (mtt180) REVERT: z 219 GLU cc_start: 0.7545 (tt0) cc_final: 0.7244 (tp30) REVERT: 0 39 LYS cc_start: 0.7361 (tppp) cc_final: 0.6545 (ttmm) REVERT: 0 169 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7388 (mt-10) REVERT: 0 273 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: y 18 ASN cc_start: 0.8196 (m-40) cc_final: 0.7939 (m110) REVERT: y 57 MET cc_start: 0.8733 (tpp) cc_final: 0.8479 (tpt) REVERT: y 62 TYR cc_start: 0.8377 (t80) cc_final: 0.7857 (t80) REVERT: y 92 TYR cc_start: 0.8893 (m-80) cc_final: 0.8580 (m-80) REVERT: y 103 ARG cc_start: 0.8227 (tpp-160) cc_final: 0.8009 (ttm170) REVERT: y 112 THR cc_start: 0.7563 (p) cc_final: 0.7115 (m) REVERT: y 169 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7068 (mt-10) REVERT: y 175 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7573 (ttp-110) REVERT: y 190 ARG cc_start: 0.6475 (mtp85) cc_final: 0.6259 (mmp-170) REVERT: y 219 GLU cc_start: 0.7628 (tp30) cc_final: 0.7237 (tp30) REVERT: y 222 ARG cc_start: 0.8021 (mtm180) cc_final: 0.7726 (mtm180) REVERT: y 227 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.6664 (mtt90) REVERT: 5 94 TYR cc_start: 0.6741 (t80) cc_final: 0.6491 (t80) REVERT: 5 99 ARG cc_start: 0.6642 (mmm160) cc_final: 0.5613 (mtp180) REVERT: 5 104 ASP cc_start: 0.6333 (m-30) cc_final: 0.5940 (m-30) REVERT: 5 166 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5725 (mtm-85) REVERT: 5 187 ASN cc_start: 0.7450 (m110) cc_final: 0.6989 (t0) REVERT: 5 229 GLN cc_start: 0.8818 (mt0) cc_final: 0.8562 (mt0) REVERT: 6 11 ARG cc_start: 0.5877 (mmp80) cc_final: 0.5058 (mtm-85) REVERT: 6 39 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7238 (tmtm) REVERT: 6 57 MET cc_start: 0.8972 (mmt) cc_final: 0.8747 (mmt) REVERT: 6 134 ILE cc_start: 0.9127 (mt) cc_final: 0.8851 (mm) REVERT: 6 150 GLN cc_start: 0.5710 (mm-40) cc_final: 0.5152 (tt0) REVERT: 6 175 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7496 (ttt-90) REVERT: 6 178 MET cc_start: 0.7923 (ptm) cc_final: 0.7690 (ptm) REVERT: 4 45 ARG cc_start: 0.5743 (ptt90) cc_final: 0.5426 (ppt170) REVERT: 4 90 ARG cc_start: 0.7121 (ptm160) cc_final: 0.6746 (ptm160) REVERT: 4 165 GLN cc_start: 0.7598 (tp40) cc_final: 0.7273 (pt0) REVERT: 4 176 ARG cc_start: 0.7097 (tpp80) cc_final: 0.6791 (ttp80) REVERT: 4 234 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7836 (mt) REVERT: 4 237 LYS cc_start: 0.7151 (ttmm) cc_final: 0.6729 (ttpt) REVERT: 4 278 TYR cc_start: 0.8335 (p90) cc_final: 0.8024 (p90) REVERT: 8 36 LYS cc_start: 0.7792 (mptt) cc_final: 0.7375 (mttt) REVERT: 8 40 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.6979 (ttmp) REVERT: 8 43 GLU cc_start: 0.7013 (pp20) cc_final: 0.6683 (pm20) REVERT: 8 89 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6854 (mmm-85) REVERT: 8 119 ARG cc_start: 0.7650 (mpt-90) cc_final: 0.7446 (mtt-85) REVERT: 9 18 ASN cc_start: 0.8140 (m-40) cc_final: 0.7784 (m-40) REVERT: 9 99 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7350 (mtp180) REVERT: 9 123 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: 9 219 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7566 (tm-30) REVERT: 9 284 GLN cc_start: 0.7142 (pt0) cc_final: 0.6893 (pt0) REVERT: 7 31 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7869 (tm) REVERT: 7 41 CYS cc_start: 0.5720 (m) cc_final: 0.5051 (m) REVERT: 7 74 SER cc_start: 0.7114 (t) cc_final: 0.6658 (m) REVERT: 7 165 GLN cc_start: 0.7832 (tp40) cc_final: 0.7368 (mt0) REVERT: 7 178 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7495 (mtm) REVERT: 7 230 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: 7 277 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.7932 (pp) outliers start: 103 outliers final: 52 residues processed: 445 average time/residue: 1.8040 time to fit residues: 897.3861 Evaluate side-chains 409 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 345 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 2 SER Chi-restraints excluded: chain z residue 28 ASP Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 162 THR Chi-restraints excluded: chain z residue 168 GLU Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 75 SER Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 116 THR Chi-restraints excluded: chain 0 residue 135 LEU Chi-restraints excluded: chain 0 residue 142 GLU Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 227 ARG Chi-restraints excluded: chain y residue 231 ARG Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain 5 residue 57 MET Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 166 ARG Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 5 residue 281 SER Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 123 GLU Chi-restraints excluded: chain 4 residue 151 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 222 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 4 residue 241 MET Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 89 ARG Chi-restraints excluded: chain 8 residue 92 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 277 ILE Chi-restraints excluded: chain 8 residue 284 GLN Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 262 ASP Chi-restraints excluded: chain 9 residue 276 ASP Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 89 ARG Chi-restraints excluded: chain 7 residue 140 VAL Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 168 GLU Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 178 MET Chi-restraints excluded: chain 7 residue 219 GLU Chi-restraints excluded: chain 7 residue 230 GLU Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 223 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 178 optimal weight: 40.0000 chunk 155 optimal weight: 0.9990 chunk 158 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 196 optimal weight: 30.0000 chunk 205 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 0 47 HIS 4 191 HIS 4 229 GLN 9 22 HIS 9 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.218660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.170332 restraints weight = 30857.265| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.30 r_work: 0.3721 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 1.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26606 Z= 0.170 Angle : 0.617 8.839 37004 Z= 0.314 Chirality : 0.035 0.302 4397 Planarity : 0.004 0.044 3941 Dihedral : 21.606 160.993 6503 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.33 % Rotamer: Outliers : 5.60 % Allowed : 26.23 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.16), residues: 2546 helix: 2.35 (0.12), residues: 1801 sheet: None (None), residues: 0 loop : -0.68 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 6 217 HIS 0.010 0.001 HIS 5 69 PHE 0.026 0.002 PHE y 19 TYR 0.016 0.002 TYR z 63 ARG 0.028 0.001 ARG 8 166 Details of bonding type rmsd hydrogen bonds : bond 0.06799 ( 1521) hydrogen bonds : angle 3.52768 ( 4317) covalent geometry : bond 0.00385 (26605) covalent geometry : angle 0.61716 (37004) Misc. bond : bond 0.00277 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 360 time to evaluate : 2.527 Fit side-chains revert: symmetry clash REVERT: z 111 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7236 (ttp-110) REVERT: z 168 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: z 190 ARG cc_start: 0.6870 (mtp85) cc_final: 0.6307 (mtt180) REVERT: z 219 GLU cc_start: 0.7581 (tt0) cc_final: 0.7179 (tp30) REVERT: 0 39 LYS cc_start: 0.7425 (tppp) cc_final: 0.6516 (ttmm) REVERT: 0 273 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8040 (tp30) REVERT: y 62 TYR cc_start: 0.8365 (t80) cc_final: 0.7822 (t80) REVERT: y 112 THR cc_start: 0.8093 (p) cc_final: 0.7795 (m) REVERT: y 169 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7436 (mt-10) REVERT: y 186 LEU cc_start: 0.5083 (OUTLIER) cc_final: 0.4035 (mm) REVERT: y 219 GLU cc_start: 0.7671 (tp30) cc_final: 0.7285 (tp30) REVERT: y 222 ARG cc_start: 0.8021 (mtm180) cc_final: 0.7630 (mtm-85) REVERT: y 265 ASP cc_start: 0.7840 (t70) cc_final: 0.7615 (t70) REVERT: 5 99 ARG cc_start: 0.6571 (mmm160) cc_final: 0.5580 (mtp180) REVERT: 5 104 ASP cc_start: 0.6333 (m-30) cc_final: 0.5977 (m-30) REVERT: 5 166 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.5709 (mtm-85) REVERT: 5 187 ASN cc_start: 0.7341 (m110) cc_final: 0.6823 (t0) REVERT: 5 229 GLN cc_start: 0.8880 (mt0) cc_final: 0.8606 (mt0) REVERT: 6 39 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7455 (tmtm) REVERT: 6 175 ARG cc_start: 0.7986 (ttm170) cc_final: 0.7612 (ttt-90) REVERT: 6 178 MET cc_start: 0.7962 (ptm) cc_final: 0.7700 (ptm) REVERT: 6 240 ARG cc_start: 0.7694 (ttt-90) cc_final: 0.7473 (ttp80) REVERT: 4 21 ARG cc_start: 0.8175 (ttt-90) cc_final: 0.7311 (ttp80) REVERT: 4 45 ARG cc_start: 0.5710 (ptt90) cc_final: 0.5382 (ppt170) REVERT: 4 90 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6936 (ptm160) REVERT: 4 165 GLN cc_start: 0.7639 (tp40) cc_final: 0.7368 (pt0) REVERT: 4 237 LYS cc_start: 0.7441 (ttmm) cc_final: 0.7035 (ttpt) REVERT: 8 36 LYS cc_start: 0.7827 (mptt) cc_final: 0.7421 (mttt) REVERT: 8 40 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7041 (ttmp) REVERT: 8 43 GLU cc_start: 0.7053 (pp20) cc_final: 0.6690 (pm20) REVERT: 8 89 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7137 (mmm-85) REVERT: 8 90 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7131 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7828 (mpt-90) cc_final: 0.7607 (mtt-85) REVERT: 9 18 ASN cc_start: 0.8202 (m-40) cc_final: 0.7873 (m-40) REVERT: 9 30 ASP cc_start: 0.8268 (t0) cc_final: 0.7990 (t70) REVERT: 9 99 ARG cc_start: 0.7744 (ttp-170) cc_final: 0.7493 (mtp180) REVERT: 9 118 VAL cc_start: 0.6709 (m) cc_final: 0.6138 (t) REVERT: 9 284 GLN cc_start: 0.7171 (pt0) cc_final: 0.6913 (pt0) REVERT: 7 4 GLN cc_start: 0.8606 (tp40) cc_final: 0.8238 (mm-40) REVERT: 7 31 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7917 (tm) REVERT: 7 165 GLN cc_start: 0.7950 (tp40) cc_final: 0.7444 (mt0) REVERT: 7 175 ARG cc_start: 0.7532 (ttm170) cc_final: 0.7097 (mmt-90) REVERT: 7 178 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7641 (mtm) REVERT: 7 230 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7685 (tt0) outliers start: 129 outliers final: 71 residues processed: 453 average time/residue: 1.8041 time to fit residues: 911.1133 Evaluate side-chains 408 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 326 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 2 SER Chi-restraints excluded: chain z residue 28 ASP Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 139 SER Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 161 ASP Chi-restraints excluded: chain z residue 162 THR Chi-restraints excluded: chain z residue 168 GLU Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 236 VAL Chi-restraints excluded: chain z residue 265 ASP Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 75 SER Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 116 THR Chi-restraints excluded: chain 0 residue 135 LEU Chi-restraints excluded: chain 0 residue 142 GLU Chi-restraints excluded: chain 0 residue 180 CYS Chi-restraints excluded: chain 0 residue 243 LEU Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 258 VAL Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 231 ARG Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 52 LEU Chi-restraints excluded: chain 5 residue 57 MET Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 166 ARG Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 5 residue 281 SER Chi-restraints excluded: chain 5 residue 284 GLN Chi-restraints excluded: chain 6 residue 2 SER Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 4 residue 90 ARG Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 123 GLU Chi-restraints excluded: chain 4 residue 139 SER Chi-restraints excluded: chain 4 residue 151 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 222 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 4 residue 241 MET Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 45 ARG Chi-restraints excluded: chain 8 residue 89 ARG Chi-restraints excluded: chain 8 residue 90 ARG Chi-restraints excluded: chain 8 residue 92 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 190 ARG Chi-restraints excluded: chain 8 residue 225 LEU Chi-restraints excluded: chain 8 residue 277 ILE Chi-restraints excluded: chain 8 residue 284 GLN Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 112 THR Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 76 VAL Chi-restraints excluded: chain 7 residue 146 THR Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 168 GLU Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 178 MET Chi-restraints excluded: chain 7 residue 219 GLU Chi-restraints excluded: chain 7 residue 230 GLU Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 181 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 265 optimal weight: 50.0000 chunk 130 optimal weight: 10.0000 chunk 267 optimal weight: 50.0000 chunk 231 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 chunk 263 optimal weight: 50.0000 chunk 244 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 0 47 HIS 4 191 HIS 4 229 GLN 9 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.217420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.169809 restraints weight = 30846.386| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.28 r_work: 0.3701 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 1.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26606 Z= 0.181 Angle : 0.635 9.274 37004 Z= 0.323 Chirality : 0.036 0.257 4397 Planarity : 0.004 0.060 3941 Dihedral : 21.610 159.345 6503 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.83 % Favored : 95.05 % Rotamer: Outliers : 4.95 % Allowed : 27.01 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.16), residues: 2546 helix: 2.21 (0.12), residues: 1798 sheet: None (None), residues: 0 loop : -0.78 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 6 217 HIS 0.013 0.001 HIS 0 22 PHE 0.018 0.002 PHE 9 179 TYR 0.022 0.002 TYR z 63 ARG 0.016 0.001 ARG 8 166 Details of bonding type rmsd hydrogen bonds : bond 0.06808 ( 1521) hydrogen bonds : angle 3.55844 ( 4317) covalent geometry : bond 0.00417 (26605) covalent geometry : angle 0.63497 (37004) Misc. bond : bond 0.00337 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 349 time to evaluate : 2.508 Fit side-chains REVERT: z 101 LYS cc_start: 0.8466 (mttt) cc_final: 0.7608 (tttt) REVERT: z 111 ARG cc_start: 0.7581 (ttm110) cc_final: 0.7319 (ttp-110) REVERT: z 168 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: z 190 ARG cc_start: 0.6848 (mtp85) cc_final: 0.6182 (mtt180) REVERT: z 219 GLU cc_start: 0.7597 (tt0) cc_final: 0.7211 (tp30) REVERT: 0 39 LYS cc_start: 0.7465 (tppp) cc_final: 0.6557 (ttmm) REVERT: 0 169 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7330 (mt-10) REVERT: 0 273 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: y 62 TYR cc_start: 0.8324 (t80) cc_final: 0.7838 (t80) REVERT: y 169 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7524 (mt-10) REVERT: y 175 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7832 (ttp-110) REVERT: y 190 ARG cc_start: 0.6448 (mtp85) cc_final: 0.6185 (mmp-170) REVERT: y 218 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: y 219 GLU cc_start: 0.7665 (tp30) cc_final: 0.7336 (tp30) REVERT: y 265 ASP cc_start: 0.7878 (t70) cc_final: 0.7673 (t70) REVERT: 5 10 ARG cc_start: 0.7087 (tpp80) cc_final: 0.6743 (ttt90) REVERT: 5 99 ARG cc_start: 0.6962 (mmm160) cc_final: 0.5788 (mtp180) REVERT: 5 104 ASP cc_start: 0.6327 (m-30) cc_final: 0.6015 (m-30) REVERT: 5 163 GLU cc_start: 0.6400 (pm20) cc_final: 0.6021 (pm20) REVERT: 5 187 ASN cc_start: 0.7375 (m110) cc_final: 0.6687 (t0) REVERT: 5 229 GLN cc_start: 0.8895 (mt0) cc_final: 0.8590 (mt0) REVERT: 6 19 PHE cc_start: 0.8206 (t80) cc_final: 0.7962 (t80) REVERT: 6 39 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7321 (tmtm) REVERT: 6 98 ASP cc_start: 0.7719 (t70) cc_final: 0.7472 (t0) REVERT: 6 103 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8127 (mpt180) REVERT: 6 175 ARG cc_start: 0.8032 (ttm170) cc_final: 0.7645 (ttt-90) REVERT: 6 178 MET cc_start: 0.7931 (ptm) cc_final: 0.7614 (ptm) REVERT: 6 240 ARG cc_start: 0.7728 (ttt-90) cc_final: 0.7514 (ttp80) REVERT: 4 21 ARG cc_start: 0.8338 (ttt-90) cc_final: 0.7297 (ttm170) REVERT: 4 45 ARG cc_start: 0.5730 (ptt90) cc_final: 0.5453 (ptt180) REVERT: 4 90 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6842 (ptm160) REVERT: 4 165 GLN cc_start: 0.7656 (tp40) cc_final: 0.7274 (pt0) REVERT: 4 176 ARG cc_start: 0.7307 (tpp80) cc_final: 0.7021 (ttp80) REVERT: 4 237 LYS cc_start: 0.7479 (ttmm) cc_final: 0.7076 (ttpt) REVERT: 8 25 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7310 (mp10) REVERT: 8 36 LYS cc_start: 0.7779 (mptt) cc_final: 0.7377 (mtmt) REVERT: 8 40 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.6988 (ttmp) REVERT: 8 43 GLU cc_start: 0.7031 (pp20) cc_final: 0.6771 (pm20) REVERT: 8 89 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7048 (mmm-85) REVERT: 8 90 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7163 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7851 (mpt-90) cc_final: 0.7571 (mtt-85) REVERT: 8 144 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6476 (mp) REVERT: 8 269 GLU cc_start: 0.7817 (mp0) cc_final: 0.7549 (mt-10) REVERT: 9 18 ASN cc_start: 0.8160 (m-40) cc_final: 0.7857 (m-40) REVERT: 9 30 ASP cc_start: 0.8260 (t0) cc_final: 0.7993 (t70) REVERT: 9 118 VAL cc_start: 0.7173 (m) cc_final: 0.6509 (t) REVERT: 9 237 LYS cc_start: 0.8786 (tptm) cc_final: 0.8393 (ttpt) REVERT: 9 284 GLN cc_start: 0.7367 (pt0) cc_final: 0.7152 (pt0) REVERT: 7 4 GLN cc_start: 0.8681 (tp40) cc_final: 0.8322 (mm-40) REVERT: 7 31 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7991 (tm) REVERT: 7 48 ARG cc_start: 0.7200 (tpt170) cc_final: 0.6552 (tpt170) REVERT: 7 165 GLN cc_start: 0.7964 (tp40) cc_final: 0.7475 (mt0) REVERT: 7 175 ARG cc_start: 0.7603 (ttm170) cc_final: 0.7214 (mmt-90) REVERT: 7 178 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7760 (mtm) REVERT: 7 230 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: 7 277 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.7891 (pp) outliers start: 114 outliers final: 72 residues processed: 427 average time/residue: 1.8845 time to fit residues: 895.7233 Evaluate side-chains 429 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 343 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 28 ASP Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 161 ASP Chi-restraints excluded: chain z residue 162 THR Chi-restraints excluded: chain z residue 168 GLU Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 242 CYS Chi-restraints excluded: chain z residue 265 ASP Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 75 SER Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 116 THR Chi-restraints excluded: chain 0 residue 135 LEU Chi-restraints excluded: chain 0 residue 180 CYS Chi-restraints excluded: chain 0 residue 243 LEU Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 258 VAL Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 218 GLU Chi-restraints excluded: chain y residue 231 ARG Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain 5 residue 52 LEU Chi-restraints excluded: chain 5 residue 57 MET Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 116 THR Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 5 residue 281 SER Chi-restraints excluded: chain 5 residue 284 GLN Chi-restraints excluded: chain 6 residue 2 SER Chi-restraints excluded: chain 6 residue 103 ARG Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 143 THR Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 90 ARG Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 139 SER Chi-restraints excluded: chain 4 residue 151 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 222 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 4 residue 241 MET Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 25 GLN Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 45 ARG Chi-restraints excluded: chain 8 residue 89 ARG Chi-restraints excluded: chain 8 residue 90 ARG Chi-restraints excluded: chain 8 residue 92 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 144 LEU Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 190 ARG Chi-restraints excluded: chain 8 residue 225 LEU Chi-restraints excluded: chain 8 residue 277 ILE Chi-restraints excluded: chain 8 residue 284 GLN Chi-restraints excluded: chain 9 residue 6 ILE Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 50 THR Chi-restraints excluded: chain 9 residue 112 THR Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 262 ASP Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 11 ARG Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 76 VAL Chi-restraints excluded: chain 7 residue 146 THR Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 168 GLU Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 178 MET Chi-restraints excluded: chain 7 residue 230 GLU Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 11 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 272 optimal weight: 50.0000 chunk 116 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 47 HIS y 47 HIS y 193 ASN 6 25 GLN 4 191 HIS 4 229 GLN 8 158 HIS 9 25 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.216892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.169289 restraints weight = 30654.782| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.29 r_work: 0.3704 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 1.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26606 Z= 0.182 Angle : 0.640 8.467 37004 Z= 0.326 Chirality : 0.036 0.257 4397 Planarity : 0.005 0.091 3941 Dihedral : 21.530 159.614 6503 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 4.39 % Allowed : 28.09 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.16), residues: 2546 helix: 2.17 (0.12), residues: 1798 sheet: None (None), residues: 0 loop : -0.85 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 6 217 HIS 0.016 0.002 HIS 0 22 PHE 0.028 0.002 PHE y 19 TYR 0.025 0.002 TYR z 63 ARG 0.025 0.001 ARG 8 166 Details of bonding type rmsd hydrogen bonds : bond 0.06926 ( 1521) hydrogen bonds : angle 3.60414 ( 4317) covalent geometry : bond 0.00418 (26605) covalent geometry : angle 0.64003 (37004) Misc. bond : bond 0.00378 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 353 time to evaluate : 2.734 Fit side-chains revert: symmetry clash REVERT: z 168 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: z 190 ARG cc_start: 0.6936 (mtp85) cc_final: 0.6223 (mtt180) REVERT: z 219 GLU cc_start: 0.7588 (tt0) cc_final: 0.7180 (tp30) REVERT: 0 21 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7370 (ptp90) REVERT: 0 39 LYS cc_start: 0.7234 (tppp) cc_final: 0.6517 (ttmp) REVERT: 0 123 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: 0 169 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7286 (mt-10) REVERT: 0 273 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8066 (tp30) REVERT: y 62 TYR cc_start: 0.8309 (t80) cc_final: 0.7824 (t80) REVERT: y 169 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7528 (mt-10) REVERT: y 186 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.3973 (mm) REVERT: y 218 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: 5 99 ARG cc_start: 0.6892 (mmm160) cc_final: 0.5650 (mtp180) REVERT: 5 104 ASP cc_start: 0.6167 (m-30) cc_final: 0.5899 (m-30) REVERT: 5 163 GLU cc_start: 0.6514 (pm20) cc_final: 0.6243 (pm20) REVERT: 5 187 ASN cc_start: 0.7461 (m110) cc_final: 0.6701 (t0) REVERT: 5 229 GLN cc_start: 0.8893 (mt0) cc_final: 0.8582 (mt0) REVERT: 6 19 PHE cc_start: 0.8184 (t80) cc_final: 0.7924 (t80) REVERT: 6 39 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7383 (tmtm) REVERT: 6 175 ARG cc_start: 0.7948 (ttm170) cc_final: 0.7595 (ttt-90) REVERT: 6 178 MET cc_start: 0.7957 (ptm) cc_final: 0.7623 (ptm) REVERT: 4 21 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.7266 (ttm170) REVERT: 4 45 ARG cc_start: 0.5629 (ptt90) cc_final: 0.5410 (ptt180) REVERT: 4 90 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6947 (ptm160) REVERT: 4 165 GLN cc_start: 0.7661 (tp40) cc_final: 0.7371 (pt0) REVERT: 4 176 ARG cc_start: 0.7328 (tpp80) cc_final: 0.7030 (ttp80) REVERT: 4 237 LYS cc_start: 0.7460 (ttmm) cc_final: 0.7036 (ttpt) REVERT: 8 25 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: 8 36 LYS cc_start: 0.7725 (mptt) cc_final: 0.7395 (mtmt) REVERT: 8 40 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7060 (ttmp) REVERT: 8 43 GLU cc_start: 0.7037 (pp20) cc_final: 0.6744 (pm20) REVERT: 8 89 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7011 (mmm-85) REVERT: 8 90 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7078 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7861 (mpt-90) cc_final: 0.7569 (mtt-85) REVERT: 9 18 ASN cc_start: 0.8189 (m-40) cc_final: 0.7872 (m-40) REVERT: 9 21 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.8044 (ttm110) REVERT: 9 30 ASP cc_start: 0.8310 (t0) cc_final: 0.8049 (t70) REVERT: 9 99 ARG cc_start: 0.7781 (ttp-170) cc_final: 0.7464 (mtp180) REVERT: 9 118 VAL cc_start: 0.7297 (m) cc_final: 0.6680 (t) REVERT: 9 123 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: 9 284 GLN cc_start: 0.7330 (pt0) cc_final: 0.7094 (pt0) REVERT: 7 4 GLN cc_start: 0.8695 (tp40) cc_final: 0.8346 (mm-40) REVERT: 7 12 ASP cc_start: 0.6266 (m-30) cc_final: 0.6044 (m-30) REVERT: 7 31 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7938 (tm) REVERT: 7 48 ARG cc_start: 0.6848 (tpt170) cc_final: 0.6597 (tpt170) REVERT: 7 165 GLN cc_start: 0.7905 (tp40) cc_final: 0.7405 (mt0) REVERT: 7 175 ARG cc_start: 0.7569 (ttm170) cc_final: 0.7219 (mmt-90) REVERT: 7 178 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8086 (mtm) REVERT: 7 230 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7709 (tt0) outliers start: 101 outliers final: 73 residues processed: 422 average time/residue: 1.9290 time to fit residues: 915.1215 Evaluate side-chains 424 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 336 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 28 ASP Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 162 THR Chi-restraints excluded: chain z residue 168 GLU Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 239 LEU Chi-restraints excluded: chain z residue 242 CYS Chi-restraints excluded: chain z residue 265 ASP Chi-restraints excluded: chain 0 residue 21 ARG Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 75 SER Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 116 THR Chi-restraints excluded: chain 0 residue 123 GLU Chi-restraints excluded: chain 0 residue 135 LEU Chi-restraints excluded: chain 0 residue 180 CYS Chi-restraints excluded: chain 0 residue 243 LEU Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 258 VAL Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 218 GLU Chi-restraints excluded: chain y residue 231 ARG Chi-restraints excluded: chain y residue 250 CYS Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain 5 residue 52 LEU Chi-restraints excluded: chain 5 residue 57 MET Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 116 THR Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 5 residue 284 GLN Chi-restraints excluded: chain 6 residue 2 SER Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 90 ARG Chi-restraints excluded: chain 4 residue 113 GLU Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 139 SER Chi-restraints excluded: chain 4 residue 151 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 193 ASN Chi-restraints excluded: chain 4 residue 222 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 4 residue 241 MET Chi-restraints excluded: chain 4 residue 262 ASP Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 25 GLN Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 45 ARG Chi-restraints excluded: chain 8 residue 89 ARG Chi-restraints excluded: chain 8 residue 90 ARG Chi-restraints excluded: chain 8 residue 92 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 190 ARG Chi-restraints excluded: chain 8 residue 277 ILE Chi-restraints excluded: chain 8 residue 284 GLN Chi-restraints excluded: chain 9 residue 6 ILE Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 50 THR Chi-restraints excluded: chain 9 residue 112 THR Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 262 ASP Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 76 VAL Chi-restraints excluded: chain 7 residue 146 THR Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 168 GLU Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 178 MET Chi-restraints excluded: chain 7 residue 230 GLU Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 260 optimal weight: 50.0000 chunk 246 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 172 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 43 optimal weight: 0.0040 chunk 229 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 overall best weight: 6.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 47 HIS y 47 HIS 4 191 HIS 4 229 GLN 9 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.218130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.170555 restraints weight = 30715.078| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.26 r_work: 0.3720 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 1.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26606 Z= 0.151 Angle : 0.597 10.607 37004 Z= 0.303 Chirality : 0.034 0.254 4397 Planarity : 0.004 0.116 3941 Dihedral : 21.433 158.018 6503 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 4.08 % Allowed : 28.53 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.16), residues: 2546 helix: 2.34 (0.12), residues: 1798 sheet: None (None), residues: 0 loop : -0.83 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 4 217 HIS 0.014 0.001 HIS 0 22 PHE 0.027 0.002 PHE y 19 TYR 0.035 0.002 TYR z 63 ARG 0.036 0.001 ARG 8 166 Details of bonding type rmsd hydrogen bonds : bond 0.06271 ( 1521) hydrogen bonds : angle 3.49693 ( 4317) covalent geometry : bond 0.00334 (26605) covalent geometry : angle 0.59655 (37004) Misc. bond : bond 0.00533 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 354 time to evaluate : 4.204 Fit side-chains REVERT: z 70 ASN cc_start: 0.8318 (t0) cc_final: 0.7969 (t160) REVERT: z 168 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: z 190 ARG cc_start: 0.6841 (mtp85) cc_final: 0.6158 (mtt180) REVERT: z 219 GLU cc_start: 0.7546 (tt0) cc_final: 0.7180 (tp30) REVERT: 0 21 ARG cc_start: 0.7719 (ptp-110) cc_final: 0.7325 (ptp90) REVERT: 0 39 LYS cc_start: 0.7337 (tppp) cc_final: 0.6640 (ttmm) REVERT: 0 169 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7302 (mt-10) REVERT: 0 273 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: y 1 MET cc_start: 0.1084 (mtm) cc_final: -0.0492 (ppp) REVERT: y 62 TYR cc_start: 0.8338 (t80) cc_final: 0.7792 (t80) REVERT: y 92 TYR cc_start: 0.8845 (m-80) cc_final: 0.8578 (m-80) REVERT: y 169 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7511 (mt-10) REVERT: y 175 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7760 (ttp-110) REVERT: y 186 LEU cc_start: 0.4970 (OUTLIER) cc_final: 0.3843 (mm) REVERT: y 190 ARG cc_start: 0.6432 (mtp85) cc_final: 0.6228 (mmp-170) REVERT: y 218 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: y 222 ARG cc_start: 0.7956 (mtm180) cc_final: 0.7579 (mtm-85) REVERT: 5 10 ARG cc_start: 0.7307 (tpp80) cc_final: 0.6864 (ttt90) REVERT: 5 99 ARG cc_start: 0.6880 (mmm160) cc_final: 0.5594 (mtp180) REVERT: 5 104 ASP cc_start: 0.6138 (m-30) cc_final: 0.5874 (m-30) REVERT: 5 163 GLU cc_start: 0.6420 (pm20) cc_final: 0.6167 (pm20) REVERT: 5 187 ASN cc_start: 0.7073 (m110) cc_final: 0.6458 (t0) REVERT: 5 229 GLN cc_start: 0.8881 (mt0) cc_final: 0.8565 (mt0) REVERT: 6 19 PHE cc_start: 0.8199 (t80) cc_final: 0.7938 (t80) REVERT: 6 39 LYS cc_start: 0.7894 (ttpt) cc_final: 0.7404 (tmtm) REVERT: 6 57 MET cc_start: 0.8970 (mmt) cc_final: 0.8701 (mmt) REVERT: 6 175 ARG cc_start: 0.7978 (ttm170) cc_final: 0.7592 (ttt-90) REVERT: 6 178 MET cc_start: 0.7926 (ptm) cc_final: 0.7588 (ptm) REVERT: 4 21 ARG cc_start: 0.8233 (ttt-90) cc_final: 0.7305 (ttm170) REVERT: 4 45 ARG cc_start: 0.5601 (ptt90) cc_final: 0.5386 (ptt180) REVERT: 4 90 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6808 (ptm160) REVERT: 4 165 GLN cc_start: 0.7613 (tp40) cc_final: 0.7371 (pt0) REVERT: 4 176 ARG cc_start: 0.7299 (tpp80) cc_final: 0.6952 (ttp80) REVERT: 4 234 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7957 (mt) REVERT: 4 237 LYS cc_start: 0.7364 (ttmm) cc_final: 0.6952 (ttpt) REVERT: 8 36 LYS cc_start: 0.7760 (mptt) cc_final: 0.7419 (mtmt) REVERT: 8 40 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7804 (ttmm) REVERT: 8 43 GLU cc_start: 0.7009 (pp20) cc_final: 0.6728 (pm20) REVERT: 8 89 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7009 (mmm-85) REVERT: 8 90 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7047 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7849 (mpt-90) cc_final: 0.7560 (mtt-85) REVERT: 8 144 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6445 (mp) REVERT: 8 269 GLU cc_start: 0.7719 (mp0) cc_final: 0.7448 (mt-10) REVERT: 9 18 ASN cc_start: 0.8141 (m-40) cc_final: 0.7847 (m-40) REVERT: 9 30 ASP cc_start: 0.8247 (t0) cc_final: 0.8011 (t70) REVERT: 9 57 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8060 (mmp) REVERT: 9 99 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7406 (mtp180) REVERT: 9 118 VAL cc_start: 0.7247 (m) cc_final: 0.6574 (t) REVERT: 9 123 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: 9 237 LYS cc_start: 0.8725 (tptm) cc_final: 0.8312 (ttpt) REVERT: 9 284 GLN cc_start: 0.7338 (pt0) cc_final: 0.7122 (pt0) REVERT: 7 31 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7952 (tm) REVERT: 7 175 ARG cc_start: 0.7510 (ttm170) cc_final: 0.7166 (mmt-90) REVERT: 7 178 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8002 (mtm) REVERT: 7 230 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: 7 277 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.7892 (pp) outliers start: 94 outliers final: 65 residues processed: 419 average time/residue: 2.7763 time to fit residues: 1308.4932 Evaluate side-chains 413 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 332 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 28 ASP Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 162 THR Chi-restraints excluded: chain z residue 168 GLU Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 242 CYS Chi-restraints excluded: chain z residue 265 ASP Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 75 SER Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 116 THR Chi-restraints excluded: chain 0 residue 135 LEU Chi-restraints excluded: chain 0 residue 180 CYS Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 258 VAL Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 218 GLU Chi-restraints excluded: chain y residue 231 ARG Chi-restraints excluded: chain y residue 250 CYS Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain 5 residue 57 MET Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 116 THR Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 5 residue 284 GLN Chi-restraints excluded: chain 6 residue 2 SER Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 90 ARG Chi-restraints excluded: chain 4 residue 113 GLU Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 139 SER Chi-restraints excluded: chain 4 residue 151 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 222 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 4 residue 241 MET Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 45 ARG Chi-restraints excluded: chain 8 residue 89 ARG Chi-restraints excluded: chain 8 residue 90 ARG Chi-restraints excluded: chain 8 residue 92 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 144 LEU Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 277 ILE Chi-restraints excluded: chain 8 residue 284 GLN Chi-restraints excluded: chain 9 residue 6 ILE Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 50 THR Chi-restraints excluded: chain 9 residue 57 MET Chi-restraints excluded: chain 9 residue 112 THR Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 262 ASP Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 76 VAL Chi-restraints excluded: chain 7 residue 146 THR Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 168 GLU Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 178 MET Chi-restraints excluded: chain 7 residue 219 GLU Chi-restraints excluded: chain 7 residue 230 GLU Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 217 optimal weight: 20.0000 chunk 234 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 269 optimal weight: 50.0000 chunk 41 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 47 HIS y 47 HIS 4 191 HIS 4 229 GLN 9 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.217034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.169220 restraints weight = 30678.719| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.24 r_work: 0.3714 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 1.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26606 Z= 0.166 Angle : 0.622 9.564 37004 Z= 0.316 Chirality : 0.035 0.265 4397 Planarity : 0.004 0.075 3941 Dihedral : 21.418 158.708 6503 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.82 % Rotamer: Outliers : 4.13 % Allowed : 28.70 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.16), residues: 2546 helix: 2.24 (0.12), residues: 1801 sheet: None (None), residues: 0 loop : -0.85 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 4 217 HIS 0.013 0.001 HIS 0 22 PHE 0.029 0.002 PHE y 19 TYR 0.035 0.002 TYR z 63 ARG 0.028 0.001 ARG 8 166 Details of bonding type rmsd hydrogen bonds : bond 0.06702 ( 1521) hydrogen bonds : angle 3.56059 ( 4317) covalent geometry : bond 0.00375 (26605) covalent geometry : angle 0.62204 (37004) Misc. bond : bond 0.00399 ( 1) =============================================================================== Job complete usr+sys time: 34289.53 seconds wall clock time: 600 minutes 52.23 seconds (36052.23 seconds total)