Starting phenix.real_space_refine on Fri Sep 19 10:35:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lj3_23388/09_2025/7lj3_23388.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lj3_23388/09_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_23388/09_2025/7lj3_23388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lj3_23388/09_2025/7lj3_23388.map" model { file = "/net/cci-nas-00/data/ceres_data/7lj3_23388/09_2025/7lj3_23388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lj3_23388/09_2025/7lj3_23388.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 6.24, per 1000 atoms: 0.24 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: 2.18 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 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: 3.44 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: 4.18 Time building geometry restraints manager: 2.86 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.170 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (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 ARG 0.005 0.001 ARG 5 89 TYR 0.013 0.002 TYR y 94 PHE 0.016 0.002 PHE 7 179 TRP 0.016 0.002 TRP 6 217 HIS 0.006 0.001 HIS 8 69 Details of bonding type rmsd covalent geometry : bond 0.00519 (26605) covalent geometry : angle 0.71704 (37004) hydrogen bonds : bond 0.14726 ( 1521) hydrogen bonds : angle 5.18086 ( 4317) 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 : 0.883 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: 0.6836 time to fit residues: 467.1767 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 : 0.849 ------------------------------------------------------------------------------- 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 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 ** 0 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 4 193 ASN ** 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** 9 170 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 = 0.4514 r_free = 0.4514 target = 0.235306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.188443 restraints weight = 32500.169| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.50 r_work: 0.3933 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 26606 Z= 0.218 Angle : 0.836 10.015 37004 Z= 0.417 Chirality : 0.041 0.196 4397 Planarity : 0.006 0.098 3941 Dihedral : 22.447 160.289 6531 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.69 % Favored : 96.19 % Rotamer: Outliers : 5.30 % Allowed : 17.85 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.16), residues: 2546 helix: 1.59 (0.11), residues: 1766 sheet: None (None), residues: 0 loop : -0.27 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG 8 166 TYR 0.020 0.003 TYR 7 63 PHE 0.031 0.003 PHE 6 114 TRP 0.025 0.002 TRP 7 217 HIS 0.008 0.002 HIS 4 158 Details of bonding type rmsd covalent geometry : bond 0.00470 (26605) covalent geometry : angle 0.83635 (37004) hydrogen bonds : bond 0.06439 ( 1521) hydrogen bonds : angle 3.97108 ( 4317) Misc. bond : bond 0.00353 ( 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 699 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 577 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: z 21 ARG cc_start: 0.6878 (mmt-90) cc_final: 0.6546 (mmm-85) REVERT: z 36 LYS cc_start: 0.7735 (mptp) cc_final: 0.7480 (mttm) REVERT: z 169 GLU cc_start: 0.5891 (tt0) cc_final: 0.5624 (tt0) REVERT: z 171 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7301 (mt) REVERT: z 178 MET cc_start: 0.5540 (OUTLIER) cc_final: 0.4715 (ptp) REVERT: z 218 GLU cc_start: 0.7657 (tp30) cc_final: 0.7441 (tt0) REVERT: z 265 ASP cc_start: 0.7944 (m-30) cc_final: 0.7670 (m-30) REVERT: z 269 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7672 (mt-10) REVERT: 0 1 MET cc_start: 0.3376 (mmm) cc_final: 0.2699 (mmm) REVERT: 0 39 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6573 (ttmt) REVERT: 0 121 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: 0 135 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8455 (mt) REVERT: 0 150 GLN cc_start: 0.7096 (mt0) cc_final: 0.6292 (mm-40) REVERT: 0 170 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8251 (t0) REVERT: 0 175 ARG cc_start: 0.7323 (ttp-170) cc_final: 0.7080 (ttm-80) REVERT: 0 273 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7636 (tp30) REVERT: y 18 ASN cc_start: 0.7814 (m-40) cc_final: 0.7467 (m-40) REVERT: y 186 LEU cc_start: 0.3441 (OUTLIER) cc_final: 0.2907 (mm) REVERT: y 237 LYS cc_start: 0.8124 (ptmt) cc_final: 0.7441 (ptpt) REVERT: y 265 ASP cc_start: 0.6808 (t70) cc_final: 0.6330 (m-30) REVERT: y 269 GLU cc_start: 0.7484 (tp30) cc_final: 0.7230 (tp30) REVERT: 5 17 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7921 (t) REVERT: 5 79 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: 5 145 VAL cc_start: 0.4887 (OUTLIER) cc_final: 0.4512 (p) REVERT: 5 179 PHE cc_start: 0.7865 (m-10) cc_final: 0.7412 (m-10) REVERT: 5 187 ASN cc_start: 0.6947 (OUTLIER) cc_final: 0.5857 (t0) REVERT: 6 1 MET cc_start: 0.5009 (OUTLIER) cc_final: 0.4511 (tmt) REVERT: 6 11 ARG cc_start: 0.5737 (OUTLIER) cc_final: 0.5397 (mmp80) REVERT: 6 218 GLU cc_start: 0.7610 (tp30) cc_final: 0.7363 (tp30) REVERT: 4 4 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6763 (tp-100) REVERT: 4 19 PHE cc_start: 0.5998 (t80) cc_final: 0.5759 (t80) REVERT: 4 48 ARG cc_start: 0.6840 (mmm160) cc_final: 0.6564 (mmm160) REVERT: 4 163 GLU cc_start: 0.7107 (tp30) cc_final: 0.6279 (mt-10) REVERT: 4 219 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7280 (tt0) REVERT: 4 229 GLN cc_start: 0.8108 (mt0) cc_final: 0.7821 (mt0) REVERT: 8 21 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7451 (mmt-90) REVERT: 8 123 GLU cc_start: 0.7881 (pt0) cc_final: 0.7651 (pm20) REVERT: 8 127 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7837 (mtt180) REVERT: 8 241 MET cc_start: 0.7507 (mtp) cc_final: 0.7295 (mtt) REVERT: 9 18 ASN cc_start: 0.7416 (m-40) cc_final: 0.7188 (m110) REVERT: 9 45 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6762 (ttt90) REVERT: 9 47 HIS cc_start: 0.5654 (OUTLIER) cc_final: 0.5369 (t-170) REVERT: 9 241 MET cc_start: 0.6723 (mmm) cc_final: 0.6510 (mmm) REVERT: 9 253 ILE cc_start: 0.8775 (mm) cc_final: 0.8363 (mt) REVERT: 7 110 ASP cc_start: 0.7509 (m-30) cc_final: 0.7296 (m-30) REVERT: 7 111 ARG cc_start: 0.7923 (ptp-110) cc_final: 0.7673 (ptp90) REVERT: 7 165 GLN cc_start: 0.7643 (tp40) cc_final: 0.6636 (mt0) REVERT: 7 170 ASN cc_start: 0.7858 (t0) cc_final: 0.7644 (t0) REVERT: 7 229 GLN cc_start: 0.7866 (mt0) cc_final: 0.7630 (mt0) outliers start: 122 outliers final: 23 residues processed: 652 average time/residue: 0.7919 time to fit residues: 577.5287 Evaluate side-chains 416 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 376 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 z residue 246 ASP Chi-restraints excluded: chain 0 residue 39 LYS 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 135 LEU Chi-restraints excluded: chain 0 residue 170 ASN Chi-restraints excluded: chain 0 residue 244 SER Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 266 THR 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 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 116 THR 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 234 LEU Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 9 residue 45 ARG Chi-restraints excluded: chain 9 residue 47 HIS 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 181 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 30 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 5 69 HIS 8 22 HIS 8 170 ASN 9 25 GLN 7 105 HIS 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 = 0.4424 r_free = 0.4424 target = 0.224869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.176794 restraints weight = 31487.147| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.32 r_work: 0.3793 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.9916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26606 Z= 0.179 Angle : 0.667 9.151 37004 Z= 0.341 Chirality : 0.037 0.162 4397 Planarity : 0.005 0.099 3941 Dihedral : 22.103 172.075 6508 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.65 % Favored : 96.19 % Rotamer: Outliers : 5.91 % Allowed : 23.14 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.16), residues: 2546 helix: 2.06 (0.12), residues: 1797 sheet: None (None), residues: 0 loop : -0.38 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG 8 166 TYR 0.025 0.002 TYR z 278 PHE 0.030 0.002 PHE 6 114 TRP 0.019 0.002 TRP 4 217 HIS 0.007 0.001 HIS 7 22 Details of bonding type rmsd covalent geometry : bond 0.00398 (26605) covalent geometry : angle 0.66653 (37004) hydrogen bonds : bond 0.06782 ( 1521) hydrogen bonds : angle 3.63852 ( 4317) Misc. bond : bond 0.00247 ( 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 619 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 483 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: z 21 ARG cc_start: 0.7822 (mmt-90) cc_final: 0.7534 (mmp80) REVERT: z 36 LYS cc_start: 0.8138 (mptp) cc_final: 0.7904 (mttm) REVERT: z 44 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.6203 (mmpt) REVERT: z 166 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7274 (mtp85) REVERT: z 178 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7310 (ptp) REVERT: z 190 ARG cc_start: 0.6612 (mtp85) cc_final: 0.6350 (mpt90) REVERT: z 219 GLU cc_start: 0.7617 (tt0) cc_final: 0.7271 (tp30) REVERT: 0 39 LYS cc_start: 0.7109 (mptp) cc_final: 0.6491 (ttmm) REVERT: 0 175 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7480 (ttm-80) REVERT: 0 241 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6729 (mtp) REVERT: 0 273 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: y 18 ASN cc_start: 0.7812 (m-40) cc_final: 0.7585 (m110) REVERT: y 62 TYR cc_start: 0.8371 (t80) cc_final: 0.7560 (t80) REVERT: y 92 TYR cc_start: 0.8838 (m-80) cc_final: 0.8588 (m-80) REVERT: y 161 ASP cc_start: 0.6786 (t0) cc_final: 0.6122 (t0) REVERT: y 186 LEU cc_start: 0.3870 (OUTLIER) cc_final: 0.3036 (mm) REVERT: y 219 GLU cc_start: 0.7592 (tp30) cc_final: 0.7282 (tp30) REVERT: y 231 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.6896 (mtm-85) REVERT: y 237 LYS cc_start: 0.8315 (ptmt) cc_final: 0.8059 (mtmt) REVERT: 5 70 ASN cc_start: 0.7925 (t0) cc_final: 0.7678 (t160) REVERT: 5 98 ASP cc_start: 0.5955 (p0) cc_final: 0.5702 (p0) REVERT: 5 103 ARG cc_start: 0.6464 (tpp80) cc_final: 0.6073 (ttm170) REVERT: 5 166 ARG cc_start: 0.5965 (OUTLIER) cc_final: 0.5703 (mtm-85) REVERT: 5 187 ASN cc_start: 0.7203 (m110) cc_final: 0.6250 (t0) REVERT: 5 229 GLN cc_start: 0.8756 (mt0) cc_final: 0.8415 (mt0) REVERT: 6 28 ASP cc_start: 0.7020 (m-30) cc_final: 0.6751 (m-30) REVERT: 6 150 GLN cc_start: 0.5703 (mm-40) cc_final: 0.5359 (tp40) REVERT: 6 161 ASP cc_start: 0.7363 (m-30) cc_final: 0.7011 (m-30) REVERT: 6 175 ARG cc_start: 0.7787 (ttm170) cc_final: 0.7362 (ttt-90) REVERT: 4 48 ARG cc_start: 0.7718 (mmm160) cc_final: 0.7326 (tpt90) REVERT: 4 81 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: 4 90 ARG cc_start: 0.7663 (ptp-110) cc_final: 0.7429 (ptm160) REVERT: 4 141 ARG cc_start: 0.7373 (mtm180) cc_final: 0.7061 (mtp180) REVERT: 4 165 GLN cc_start: 0.7617 (tp40) cc_final: 0.7078 (pt0) REVERT: 4 191 HIS cc_start: 0.6163 (m-70) cc_final: 0.5857 (p90) REVERT: 4 219 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7915 (tt0) REVERT: 4 275 PHE cc_start: 0.7895 (t80) cc_final: 0.7322 (t80) REVERT: 8 21 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7954 (mmt-90) REVERT: 8 36 LYS cc_start: 0.7834 (mptt) cc_final: 0.7417 (mttt) REVERT: 8 37 ILE cc_start: 0.7228 (mm) cc_final: 0.6979 (mm) REVERT: 8 119 ARG cc_start: 0.7485 (mpt-90) cc_final: 0.7153 (mtt-85) REVERT: 8 144 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6601 (pp) REVERT: 9 47 HIS cc_start: 0.6749 (OUTLIER) cc_final: 0.6036 (t-170) REVERT: 9 48 ARG cc_start: 0.7064 (pmt-80) cc_final: 0.6691 (pmt-80) REVERT: 9 123 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: 9 184 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6184 (pt) REVERT: 7 18 ASN cc_start: 0.6879 (m-40) cc_final: 0.6104 (t0) REVERT: 7 39 LYS cc_start: 0.6706 (OUTLIER) cc_final: 0.6374 (mmtp) REVERT: 7 44 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6585 (tmtt) REVERT: 7 57 MET cc_start: 0.8448 (mmt) cc_final: 0.8242 (tpp) REVERT: 7 111 ARG cc_start: 0.7782 (ptp-110) cc_final: 0.7498 (ptp90) REVERT: 7 121 ASP cc_start: 0.8064 (m-30) cc_final: 0.7632 (m-30) REVERT: 7 165 GLN cc_start: 0.7705 (tp40) cc_final: 0.6860 (mt0) REVERT: 7 222 ARG cc_start: 0.7517 (ttp-110) cc_final: 0.7126 (mtm180) REVERT: 7 229 GLN cc_start: 0.8340 (mt0) cc_final: 0.8032 (mt0) outliers start: 136 outliers final: 45 residues processed: 569 average time/residue: 0.7842 time to fit residues: 499.9912 Evaluate side-chains 430 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 371 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 44 LYS 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 178 MET Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain 0 residue 93 THR Chi-restraints excluded: chain 0 residue 108 VAL 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 83 ARG Chi-restraints excluded: chain y residue 165 GLN 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 116 THR Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 159 LEU Chi-restraints excluded: chain 5 residue 166 ARG Chi-restraints excluded: chain 5 residue 194 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 24 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 232 CYS 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 108 VAL 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 47 HIS Chi-restraints excluded: chain 9 residue 65 GLU Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 184 LEU Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 39 LYS Chi-restraints excluded: chain 7 residue 44 LYS Chi-restraints excluded: chain 7 residue 140 VAL Chi-restraints excluded: chain 7 residue 146 THR Chi-restraints excluded: chain 7 residue 168 GLU Chi-restraints excluded: chain 7 residue 213 VAL Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 265 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 195 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 269 optimal weight: 50.0000 chunk 119 optimal weight: 3.9990 chunk 211 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 254 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 4 34 HIS 4 229 GLN 8 4 GLN ** 9 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 187 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.221035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.172526 restraints weight = 30762.424| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.31 r_work: 0.3754 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 1.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26606 Z= 0.173 Angle : 0.642 9.108 37004 Z= 0.328 Chirality : 0.036 0.168 4397 Planarity : 0.005 0.047 3941 Dihedral : 21.890 161.427 6504 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.89 % Favored : 95.95 % Rotamer: Outliers : 6.30 % Allowed : 24.75 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.16), residues: 2546 helix: 2.23 (0.12), residues: 1802 sheet: None (None), residues: 0 loop : -0.64 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG 8 166 TYR 0.021 0.002 TYR z 94 PHE 0.014 0.002 PHE 7 19 TRP 0.010 0.002 TRP 9 217 HIS 0.009 0.001 HIS 6 158 Details of bonding type rmsd covalent geometry : bond 0.00391 (26605) covalent geometry : angle 0.64233 (37004) hydrogen bonds : bond 0.06650 ( 1521) hydrogen bonds : angle 3.54498 ( 4317) Misc. bond : bond 0.00370 ( 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 549 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 404 time to evaluate : 0.879 Fit side-chains REVERT: z 21 ARG cc_start: 0.7843 (mmt-90) cc_final: 0.7564 (mmp80) REVERT: z 46 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8459 (mp) REVERT: z 141 ARG cc_start: 0.6516 (mtm-85) cc_final: 0.6314 (mtm-85) REVERT: z 190 ARG cc_start: 0.6523 (mtp85) cc_final: 0.6319 (mtt180) REVERT: z 237 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7323 (mtpp) REVERT: 0 4 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7715 (mp10) REVERT: 0 39 LYS cc_start: 0.7369 (mptp) cc_final: 0.6579 (ttmm) REVERT: 0 166 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7898 (mtm-85) REVERT: 0 175 ARG cc_start: 0.7891 (ttp-170) cc_final: 0.7540 (ttt180) REVERT: 0 273 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8186 (tp30) REVERT: y 18 ASN cc_start: 0.7975 (m-40) cc_final: 0.7739 (m110) REVERT: y 62 TYR cc_start: 0.8410 (t80) cc_final: 0.7768 (t80) REVERT: y 89 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7868 (ttt-90) REVERT: y 92 TYR cc_start: 0.8825 (m-80) cc_final: 0.8572 (m-80) REVERT: y 151 THR cc_start: 0.7290 (m) cc_final: 0.7054 (p) REVERT: y 190 ARG cc_start: 0.6468 (mtp85) cc_final: 0.6220 (mmp-170) REVERT: y 219 GLU cc_start: 0.7770 (tp30) cc_final: 0.7388 (tp30) REVERT: y 222 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7481 (mtm180) REVERT: y 227 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8027 (mmt-90) REVERT: y 231 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.6729 (mtm-85) REVERT: y 265 ASP cc_start: 0.7940 (t70) cc_final: 0.7498 (OUTLIER) REVERT: 5 79 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: 5 103 ARG cc_start: 0.7194 (tpp80) cc_final: 0.6696 (ttm170) REVERT: 5 104 ASP cc_start: 0.6319 (m-30) cc_final: 0.6074 (m-30) REVERT: 5 166 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.6229 (mtm-85) REVERT: 5 187 ASN cc_start: 0.7247 (m110) cc_final: 0.6761 (t0) REVERT: 5 229 GLN cc_start: 0.8773 (mt0) cc_final: 0.8426 (mt0) REVERT: 6 18 ASN cc_start: 0.7728 (m-40) cc_final: 0.7524 (m-40) REVERT: 6 25 GLN cc_start: 0.7411 (pt0) cc_final: 0.7147 (pt0) REVERT: 6 150 GLN cc_start: 0.5850 (mm-40) cc_final: 0.5204 (tt0) REVERT: 6 161 ASP cc_start: 0.7599 (m-30) cc_final: 0.7184 (m-30) REVERT: 6 166 ARG cc_start: 0.8165 (mtm180) cc_final: 0.7751 (mmm-85) REVERT: 6 175 ARG cc_start: 0.7898 (ttm170) cc_final: 0.7472 (ttt-90) REVERT: 6 211 MET cc_start: 0.8894 (mtp) cc_final: 0.8691 (mtp) REVERT: 4 45 ARG cc_start: 0.5425 (ptt90) cc_final: 0.5141 (ptt180) REVERT: 4 81 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: 4 90 ARG cc_start: 0.7685 (ptp-110) cc_final: 0.7435 (ptm160) REVERT: 4 111 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7528 (mtm-85) REVERT: 4 141 ARG cc_start: 0.7439 (mtm180) cc_final: 0.7226 (mtp180) REVERT: 4 165 GLN cc_start: 0.7569 (tp40) cc_final: 0.7099 (pt0) REVERT: 4 176 ARG cc_start: 0.7200 (tpp80) cc_final: 0.6983 (tpp80) REVERT: 4 191 HIS cc_start: 0.6458 (m-70) cc_final: 0.6008 (p90) REVERT: 4 237 LYS cc_start: 0.7414 (ttmt) cc_final: 0.7010 (ttpt) REVERT: 4 278 TYR cc_start: 0.8201 (p90) cc_final: 0.7804 (p90) REVERT: 8 25 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: 8 30 ASP cc_start: 0.7178 (p0) cc_final: 0.6809 (t0) REVERT: 8 36 LYS cc_start: 0.7795 (mptt) cc_final: 0.7414 (mttt) REVERT: 8 40 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7041 (ttmp) REVERT: 8 89 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7106 (mmm-85) REVERT: 8 90 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7004 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7673 (mpt-90) cc_final: 0.7290 (mtt-85) REVERT: 9 18 ASN cc_start: 0.8142 (m-40) cc_final: 0.7727 (m-40) REVERT: 9 184 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6631 (pt) REVERT: 9 255 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7927 (mtmt) REVERT: 7 12 ASP cc_start: 0.6425 (m-30) cc_final: 0.6150 (m-30) REVERT: 7 39 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6648 (mmtp) REVERT: 7 111 ARG cc_start: 0.7658 (ptp-110) cc_final: 0.7420 (ptp90) REVERT: 7 165 GLN cc_start: 0.7780 (tp40) cc_final: 0.7209 (mt0) REVERT: 7 178 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7646 (mtm) REVERT: 7 222 ARG cc_start: 0.7425 (ttp-110) cc_final: 0.7017 (mtm180) REVERT: 7 277 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.7884 (pp) outliers start: 145 outliers final: 64 residues processed: 499 average time/residue: 0.7905 time to fit residues: 441.3030 Evaluate side-chains 427 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 344 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 44 LYS Chi-restraints excluded: chain z residue 46 LEU Chi-restraints excluded: chain z residue 108 VAL 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 197 VAL Chi-restraints excluded: chain z residue 237 LYS 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 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 83 ARG Chi-restraints excluded: chain y residue 89 ARG Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 222 ARG 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 6 ILE Chi-restraints excluded: chain 5 residue 52 LEU Chi-restraints excluded: chain 5 residue 57 MET Chi-restraints excluded: chain 5 residue 79 GLU 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 140 VAL Chi-restraints excluded: chain 5 residue 159 LEU Chi-restraints excluded: chain 5 residue 166 ARG Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 180 CYS 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 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 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 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 25 GLN 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 190 ARG Chi-restraints excluded: chain 8 residue 277 ILE Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 181 VAL Chi-restraints excluded: chain 9 residue 184 LEU Chi-restraints excluded: chain 9 residue 255 LYS 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 31 LEU Chi-restraints excluded: chain 7 residue 39 LYS Chi-restraints excluded: chain 7 residue 76 VAL 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 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 243 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 258 optimal weight: 50.0000 chunk 233 optimal weight: 10.0000 chunk 58 optimal weight: 30.0000 chunk 149 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 5 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 22 HIS 4 158 HIS 4 229 GLN 9 22 HIS 9 25 GLN 7 18 ASN 7 187 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.219467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.171396 restraints weight = 30715.630| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.19 r_work: 0.3744 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 1.1607 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= 0.165 Angle : 0.608 8.954 37004 Z= 0.309 Chirality : 0.035 0.162 4397 Planarity : 0.004 0.048 3941 Dihedral : 21.818 165.838 6504 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.36 % Favored : 95.52 % Rotamer: Outliers : 5.91 % Allowed : 25.97 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.16), residues: 2546 helix: 2.28 (0.12), residues: 1802 sheet: None (None), residues: 0 loop : -0.71 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG 8 166 TYR 0.015 0.002 TYR 5 94 PHE 0.024 0.002 PHE y 19 TRP 0.014 0.002 TRP 6 217 HIS 0.010 0.001 HIS 6 158 Details of bonding type rmsd covalent geometry : bond 0.00370 (26605) covalent geometry : angle 0.60799 (37004) hydrogen bonds : bond 0.06684 ( 1521) hydrogen bonds : angle 3.49947 ( 4317) Misc. bond : bond 0.00487 ( 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 501 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 365 time to evaluate : 0.786 Fit side-chains REVERT: z 21 ARG cc_start: 0.7784 (mmt-90) cc_final: 0.7524 (mmp80) REVERT: z 141 ARG cc_start: 0.6637 (mtm-85) cc_final: 0.6403 (mtm110) REVERT: z 159 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7359 (tp) REVERT: z 190 ARG cc_start: 0.6690 (mtp85) cc_final: 0.6137 (mtt180) REVERT: z 219 GLU cc_start: 0.7436 (tt0) cc_final: 0.7046 (tp30) REVERT: z 237 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7121 (mtpp) REVERT: 0 39 LYS cc_start: 0.7214 (mptp) cc_final: 0.6379 (ttmp) REVERT: 0 57 MET cc_start: 0.8610 (tpp) cc_final: 0.8375 (tpt) REVERT: 0 175 ARG cc_start: 0.7807 (ttp-170) cc_final: 0.7525 (ttt180) REVERT: 0 273 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: y 18 ASN cc_start: 0.8173 (m-40) cc_final: 0.7942 (m110) REVERT: y 62 TYR cc_start: 0.8351 (t80) cc_final: 0.7704 (t80) REVERT: y 92 TYR cc_start: 0.8864 (m-80) cc_final: 0.8562 (m-80) REVERT: y 186 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.3946 (mm) REVERT: y 190 ARG cc_start: 0.6523 (mtp85) cc_final: 0.6250 (mmp-170) REVERT: y 219 GLU cc_start: 0.7708 (tp30) cc_final: 0.7333 (tp30) REVERT: y 222 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7435 (mtm180) REVERT: y 231 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7046 (mtm-85) REVERT: 5 79 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: 5 99 ARG cc_start: 0.6634 (mmm160) cc_final: 0.5566 (mtp180) REVERT: 5 103 ARG cc_start: 0.7222 (tpp80) cc_final: 0.6702 (ttm170) REVERT: 5 104 ASP cc_start: 0.6475 (m-30) cc_final: 0.6272 (m-30) REVERT: 5 166 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.6253 (mtp85) REVERT: 5 187 ASN cc_start: 0.7241 (m110) cc_final: 0.6830 (t0) REVERT: 5 229 GLN cc_start: 0.8803 (mt0) cc_final: 0.8451 (mt0) REVERT: 6 150 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5204 (tt0) REVERT: 6 175 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7457 (ttt-90) REVERT: 6 211 MET cc_start: 0.8916 (mtp) cc_final: 0.8600 (mtp) REVERT: 4 21 ARG cc_start: 0.8076 (ttt-90) cc_final: 0.7283 (ttp80) REVERT: 4 26 LYS cc_start: 0.7490 (ptpp) cc_final: 0.7155 (ptmt) REVERT: 4 45 ARG cc_start: 0.5639 (ptt90) cc_final: 0.5299 (ptt180) REVERT: 4 81 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8153 (mm-30) REVERT: 4 90 ARG cc_start: 0.7566 (ptp-110) cc_final: 0.7214 (ptm160) REVERT: 4 123 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.6002 (tm-30) REVERT: 4 141 ARG cc_start: 0.7340 (mtm180) cc_final: 0.7090 (mtp180) REVERT: 4 165 GLN cc_start: 0.7587 (tp40) cc_final: 0.7319 (pt0) REVERT: 4 185 ASP cc_start: 0.2726 (OUTLIER) cc_final: 0.1918 (m-30) REVERT: 4 191 HIS cc_start: 0.6368 (m-70) cc_final: 0.5819 (p90) REVERT: 4 237 LYS cc_start: 0.7412 (ttmt) cc_final: 0.7077 (ttpt) REVERT: 8 30 ASP cc_start: 0.7409 (p0) cc_final: 0.7002 (t0) REVERT: 8 36 LYS cc_start: 0.7840 (mptt) cc_final: 0.7423 (mttt) REVERT: 8 40 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7004 (ttmp) REVERT: 8 90 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7005 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7789 (mpt-90) cc_final: 0.7517 (mtt-85) REVERT: 8 218 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7160 (mt-10) REVERT: 9 18 ASN cc_start: 0.8277 (m-40) cc_final: 0.7894 (m-40) REVERT: 9 30 ASP cc_start: 0.8240 (t0) cc_final: 0.7942 (t70) REVERT: 9 118 VAL cc_start: 0.6967 (m) cc_final: 0.6399 (t) REVERT: 9 123 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: 9 182 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.5639 (pttm) REVERT: 9 184 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6657 (pt) REVERT: 9 258 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7060 (p) REVERT: 7 12 ASP cc_start: 0.6326 (m-30) cc_final: 0.6096 (m-30) REVERT: 7 39 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6570 (mmmm) REVERT: 7 41 CYS cc_start: 0.5902 (m) cc_final: 0.5376 (m) REVERT: 7 165 GLN cc_start: 0.7810 (tp40) cc_final: 0.7308 (mt0) REVERT: 7 178 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7767 (mtm) outliers start: 136 outliers final: 71 residues processed: 451 average time/residue: 0.8237 time to fit residues: 413.8732 Evaluate side-chains 425 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 335 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 2 SER Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 41 CYS Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 159 LEU Chi-restraints excluded: chain z residue 162 THR Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 237 LYS 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 83 ARG Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 222 ARG Chi-restraints excluded: chain y residue 231 ARG 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 79 GLU Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 116 THR Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 159 LEU Chi-restraints excluded: chain 5 residue 166 ARG Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 180 CYS 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 131 SER Chi-restraints excluded: chain 6 residue 143 THR Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 4 residue 81 GLU 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 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 40 LYS Chi-restraints excluded: chain 8 residue 45 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 162 THR 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 108 VAL Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 182 LYS Chi-restraints excluded: chain 9 residue 184 LEU Chi-restraints excluded: chain 9 residue 234 LEU Chi-restraints excluded: chain 9 residue 258 VAL 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 17 VAL Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 39 LYS Chi-restraints excluded: chain 7 residue 76 VAL Chi-restraints excluded: chain 7 residue 89 ARG 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 258 VAL Chi-restraints excluded: chain 7 residue 265 ASP Chi-restraints excluded: chain 7 residue 274 ASP 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 75 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 56 optimal weight: 30.0000 chunk 251 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 264 optimal weight: 50.0000 chunk 210 optimal weight: 0.0870 chunk 3 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 overall best weight: 7.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 4 229 GLN 9 25 GLN 7 18 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.218112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.170270 restraints weight = 30811.970| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.27 r_work: 0.3714 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 1.1995 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= 0.172 Angle : 0.619 9.822 37004 Z= 0.315 Chirality : 0.035 0.174 4397 Planarity : 0.004 0.048 3941 Dihedral : 21.730 162.547 6503 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.37 % Rotamer: Outliers : 6.47 % Allowed : 25.58 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.16), residues: 2546 helix: 2.23 (0.12), residues: 1798 sheet: None (None), residues: 0 loop : -0.75 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG 8 166 TYR 0.013 0.002 TYR y 205 PHE 0.016 0.002 PHE 8 275 TRP 0.012 0.002 TRP 6 217 HIS 0.011 0.001 HIS 6 158 Details of bonding type rmsd covalent geometry : bond 0.00391 (26605) covalent geometry : angle 0.61935 (37004) hydrogen bonds : bond 0.06766 ( 1521) hydrogen bonds : angle 3.53568 ( 4317) Misc. bond : bond 0.00255 ( 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 503 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 354 time to evaluate : 0.836 Fit side-chains REVERT: z 21 ARG cc_start: 0.7892 (mmt-90) cc_final: 0.7636 (mmp80) REVERT: z 190 ARG cc_start: 0.7000 (mtp85) cc_final: 0.6262 (mtt180) REVERT: z 219 GLU cc_start: 0.7477 (tt0) cc_final: 0.7052 (tp30) REVERT: z 238 GLU cc_start: 0.7903 (tp30) cc_final: 0.7626 (mm-30) REVERT: 0 39 LYS cc_start: 0.7180 (mptp) cc_final: 0.6369 (ttmm) REVERT: 0 57 MET cc_start: 0.8621 (tpp) cc_final: 0.8377 (tpt) REVERT: 0 169 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7287 (mt-10) REVERT: 0 175 ARG cc_start: 0.7923 (ttp-170) cc_final: 0.7587 (ttm-80) REVERT: 0 273 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8070 (tp30) REVERT: y 62 TYR cc_start: 0.8358 (t80) cc_final: 0.7733 (t80) REVERT: y 103 ARG cc_start: 0.8213 (tpp-160) cc_final: 0.7910 (ttm170) REVERT: y 163 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7129 (tp30) REVERT: y 186 LEU cc_start: 0.4965 (OUTLIER) cc_final: 0.3861 (mm) REVERT: y 219 GLU cc_start: 0.7646 (tp30) cc_final: 0.7373 (tp30) REVERT: y 222 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7449 (mtm180) REVERT: y 231 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7078 (mtm-85) REVERT: 5 1 MET cc_start: 0.6423 (tpp) cc_final: 0.5940 (tmt) REVERT: 5 11 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.7585 (ttp-110) REVERT: 5 94 TYR cc_start: 0.6878 (t80) cc_final: 0.6647 (t80) REVERT: 5 99 ARG cc_start: 0.6900 (mmm160) cc_final: 0.5582 (mtp180) REVERT: 5 104 ASP cc_start: 0.6531 (m-30) cc_final: 0.6250 (m-30) REVERT: 5 166 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.6130 (mtp85) REVERT: 5 187 ASN cc_start: 0.7276 (m110) cc_final: 0.6821 (t0) REVERT: 5 208 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7751 (mtp85) REVERT: 5 229 GLN cc_start: 0.8827 (mt0) cc_final: 0.8454 (mt0) REVERT: 6 115 ASP cc_start: 0.6648 (t0) cc_final: 0.6394 (t70) REVERT: 6 175 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7607 (ttt-90) REVERT: 6 211 MET cc_start: 0.8981 (mtp) cc_final: 0.8594 (mtp) REVERT: 4 21 ARG cc_start: 0.8188 (ttt-90) cc_final: 0.7306 (ttp80) REVERT: 4 26 LYS cc_start: 0.7414 (ptpp) cc_final: 0.7160 (ptmt) REVERT: 4 45 ARG cc_start: 0.5726 (ptt90) cc_final: 0.5435 (ptt180) REVERT: 4 81 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: 4 90 ARG cc_start: 0.7651 (ptp-110) cc_final: 0.7333 (ptm160) REVERT: 4 123 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6102 (tm-30) REVERT: 4 141 ARG cc_start: 0.7333 (mtm180) cc_final: 0.7093 (mtp180) REVERT: 4 164 VAL cc_start: 0.8353 (p) cc_final: 0.8151 (m) REVERT: 4 165 GLN cc_start: 0.7637 (tp40) cc_final: 0.7300 (pt0) REVERT: 4 191 HIS cc_start: 0.6118 (m-70) cc_final: 0.5584 (p90) REVERT: 4 237 LYS cc_start: 0.7529 (ttmt) cc_final: 0.7168 (ttpt) REVERT: 8 36 LYS cc_start: 0.7776 (mptt) cc_final: 0.7374 (mttt) REVERT: 8 40 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7068 (ttmp) REVERT: 8 89 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6940 (mmm-85) REVERT: 8 90 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7126 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7885 (mpt-90) cc_final: 0.7586 (mtt-85) REVERT: 8 189 ASP cc_start: 0.5644 (p0) cc_final: 0.5044 (m-30) REVERT: 9 18 ASN cc_start: 0.8203 (m-40) cc_final: 0.7850 (m-40) REVERT: 9 30 ASP cc_start: 0.8305 (t0) cc_final: 0.8020 (t70) REVERT: 9 99 ARG cc_start: 0.7597 (ttp-170) cc_final: 0.7196 (mtp180) REVERT: 9 118 VAL cc_start: 0.6952 (m) cc_final: 0.6308 (t) REVERT: 9 182 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.5644 (pttm) REVERT: 9 222 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7367 (tpp80) REVERT: 9 255 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7977 (mtmt) REVERT: 9 258 VAL cc_start: 0.7414 (OUTLIER) cc_final: 0.7134 (p) REVERT: 7 4 GLN cc_start: 0.8550 (tp40) cc_final: 0.8143 (mm-40) REVERT: 7 12 ASP cc_start: 0.6489 (m-30) cc_final: 0.6273 (m-30) REVERT: 7 31 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8103 (tm) REVERT: 7 39 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6734 (mmmm) REVERT: 7 165 GLN cc_start: 0.7880 (tp40) cc_final: 0.7454 (mt0) REVERT: 7 178 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7900 (mtm) REVERT: 7 277 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.7843 (pp) outliers start: 149 outliers final: 87 residues processed: 454 average time/residue: 0.8237 time to fit residues: 416.0999 Evaluate side-chains 445 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 340 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 41 CYS Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 139 SER Chi-restraints excluded: chain z residue 161 ASP Chi-restraints excluded: chain z residue 162 THR Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 237 LYS 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 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 83 ARG Chi-restraints excluded: chain y residue 118 VAL Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 222 ARG 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 31 LEU 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 159 LEU Chi-restraints excluded: chain 5 residue 166 ARG Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 180 CYS Chi-restraints excluded: chain 5 residue 194 THR 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 113 GLU Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 81 GLU Chi-restraints excluded: chain 4 residue 113 GLU 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 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 162 THR 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 108 VAL Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 182 LYS Chi-restraints excluded: chain 9 residue 222 ARG Chi-restraints excluded: chain 9 residue 234 LEU Chi-restraints excluded: chain 9 residue 255 LYS Chi-restraints excluded: chain 9 residue 258 VAL Chi-restraints excluded: chain 9 residue 262 ASP Chi-restraints excluded: chain 9 residue 284 GLN Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 39 LYS Chi-restraints excluded: chain 7 residue 89 ARG 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 258 VAL Chi-restraints excluded: chain 7 residue 265 ASP Chi-restraints excluded: chain 7 residue 274 ASP 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 215 optimal weight: 0.7980 chunk 272 optimal weight: 50.0000 chunk 264 optimal weight: 50.0000 chunk 96 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS y 193 ASN 4 229 GLN 9 25 GLN 7 18 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.221415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.173979 restraints weight = 30958.539| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.21 r_work: 0.3774 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 1.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26606 Z= 0.121 Angle : 0.536 8.591 37004 Z= 0.272 Chirality : 0.032 0.162 4397 Planarity : 0.004 0.078 3941 Dihedral : 21.540 160.926 6503 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.20 % Favored : 95.68 % Rotamer: Outliers : 4.47 % Allowed : 27.18 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.16), residues: 2546 helix: 2.58 (0.12), residues: 1801 sheet: None (None), residues: 0 loop : -0.68 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG 8 166 TYR 0.011 0.001 TYR y 205 PHE 0.027 0.001 PHE y 19 TRP 0.015 0.001 TRP z 217 HIS 0.009 0.001 HIS 0 22 Details of bonding type rmsd covalent geometry : bond 0.00247 (26605) covalent geometry : angle 0.53575 (37004) hydrogen bonds : bond 0.05524 ( 1521) hydrogen bonds : angle 3.29048 ( 4317) Misc. bond : bond 0.00400 ( 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 484 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 381 time to evaluate : 0.894 Fit side-chains REVERT: z 21 ARG cc_start: 0.7829 (mmt-90) cc_final: 0.7572 (mmp80) REVERT: z 70 ASN cc_start: 0.7873 (t0) cc_final: 0.7401 (t160) REVERT: z 190 ARG cc_start: 0.6874 (mtp85) cc_final: 0.6261 (mtt180) REVERT: z 219 GLU cc_start: 0.7414 (tt0) cc_final: 0.7071 (tp30) REVERT: z 238 GLU cc_start: 0.7681 (tp30) cc_final: 0.7405 (tp30) REVERT: 0 39 LYS cc_start: 0.7112 (mptp) cc_final: 0.6241 (ttmp) REVERT: 0 57 MET cc_start: 0.8529 (tpp) cc_final: 0.8295 (tpt) REVERT: 0 169 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7250 (mt-10) REVERT: 0 175 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7438 (ttm-80) REVERT: 0 273 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7974 (tp30) REVERT: y 62 TYR cc_start: 0.8347 (t80) cc_final: 0.7691 (t80) REVERT: y 92 TYR cc_start: 0.8869 (m-80) cc_final: 0.8549 (m-80) REVERT: y 103 ARG cc_start: 0.8116 (tpp-160) cc_final: 0.7889 (ttm170) REVERT: y 126 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8219 (tp30) REVERT: y 186 LEU cc_start: 0.4929 (OUTLIER) cc_final: 0.3946 (mm) REVERT: y 190 ARG cc_start: 0.6409 (mtp85) cc_final: 0.6192 (mmp-170) REVERT: y 219 GLU cc_start: 0.7567 (tp30) cc_final: 0.7366 (tp30) REVERT: 5 10 ARG cc_start: 0.6879 (tpp80) cc_final: 0.6640 (ttt90) REVERT: 5 94 TYR cc_start: 0.6919 (t80) cc_final: 0.6389 (t80) REVERT: 5 99 ARG cc_start: 0.6701 (mmm160) cc_final: 0.5576 (mtp180) REVERT: 5 166 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.6118 (mtp85) REVERT: 5 187 ASN cc_start: 0.7223 (m110) cc_final: 0.6858 (t0) REVERT: 5 229 GLN cc_start: 0.8797 (mt0) cc_final: 0.8483 (mt0) REVERT: 6 57 MET cc_start: 0.8964 (mmt) cc_final: 0.8722 (mmt) REVERT: 6 115 ASP cc_start: 0.6450 (t0) cc_final: 0.6221 (t70) REVERT: 6 134 ILE cc_start: 0.9157 (mt) cc_final: 0.8871 (mm) REVERT: 6 175 ARG cc_start: 0.7814 (ttm170) cc_final: 0.7404 (ttt-90) REVERT: 6 211 MET cc_start: 0.8887 (mtp) cc_final: 0.8549 (mtp) REVERT: 4 21 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7365 (ttp80) REVERT: 4 45 ARG cc_start: 0.5576 (ptt90) cc_final: 0.5369 (ptt180) REVERT: 4 176 ARG cc_start: 0.7055 (tpp80) cc_final: 0.6705 (ttp80) REVERT: 4 185 ASP cc_start: 0.2495 (OUTLIER) cc_final: 0.1683 (m-30) REVERT: 4 191 HIS cc_start: 0.5804 (m-70) cc_final: 0.5414 (p90) REVERT: 4 222 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7253 (mtp180) REVERT: 4 234 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7852 (mt) REVERT: 4 237 LYS cc_start: 0.7137 (ttmt) cc_final: 0.6788 (ttpt) REVERT: 4 259 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5253 (pm20) REVERT: 8 36 LYS cc_start: 0.7813 (mptt) cc_final: 0.7397 (mttt) REVERT: 8 90 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6941 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7656 (mpt-90) cc_final: 0.7435 (mtt-85) REVERT: 9 18 ASN cc_start: 0.8234 (m-40) cc_final: 0.7819 (m-40) REVERT: 9 30 ASP cc_start: 0.8230 (t0) cc_final: 0.7949 (t70) REVERT: 9 57 MET cc_start: 0.8670 (tpt) cc_final: 0.8246 (mmp) REVERT: 9 99 ARG cc_start: 0.7632 (ttp-170) cc_final: 0.7211 (mtp180) REVERT: 9 118 VAL cc_start: 0.6726 (m) cc_final: 0.6170 (t) REVERT: 9 258 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7152 (p) REVERT: 7 39 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6833 (mmtp) REVERT: 7 41 CYS cc_start: 0.6300 (m) cc_final: 0.5718 (m) REVERT: 7 165 GLN cc_start: 0.7975 (tp40) cc_final: 0.7517 (mt0) REVERT: 7 178 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7694 (mtm) REVERT: 7 277 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7641 (pp) outliers start: 103 outliers final: 54 residues processed: 453 average time/residue: 0.8137 time to fit residues: 411.1924 Evaluate side-chains 414 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 349 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 28 ASP Chi-restraints excluded: chain z residue 41 CYS 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 197 VAL Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain 0 residue 108 VAL 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 y residue 39 LYS Chi-restraints excluded: chain y residue 118 VAL Chi-restraints excluded: chain y residue 124 ILE Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 250 CYS Chi-restraints excluded: chain y residue 265 ASP Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain 5 residue 31 LEU Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 116 THR Chi-restraints excluded: chain 5 residue 166 ARG Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 180 CYS Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 143 THR Chi-restraints excluded: chain 4 residue 31 LEU 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 259 GLU Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU 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 162 THR 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 24 THR Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 258 VAL Chi-restraints excluded: chain 9 residue 284 GLN Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 39 LYS Chi-restraints excluded: chain 7 residue 76 VAL 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 178 MET Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 274 ASP 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 198 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 255 optimal weight: 50.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 0 25 GLN 0 229 GLN y 165 GLN 4 229 GLN 8 158 HIS 9 25 GLN 7 18 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.216815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.169017 restraints weight = 30633.119| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.30 r_work: 0.3698 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 1.2365 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= 0.183 Angle : 0.636 9.012 37004 Z= 0.322 Chirality : 0.035 0.221 4397 Planarity : 0.005 0.052 3941 Dihedral : 21.581 160.580 6503 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.89 % Rotamer: Outliers : 5.43 % Allowed : 26.70 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.16), residues: 2546 helix: 2.28 (0.12), residues: 1799 sheet: None (None), residues: 0 loop : -0.80 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG 8 166 TYR 0.015 0.002 TYR y 205 PHE 0.017 0.002 PHE 9 179 TRP 0.011 0.002 TRP 6 217 HIS 0.012 0.001 HIS 0 22 Details of bonding type rmsd covalent geometry : bond 0.00421 (26605) covalent geometry : angle 0.63621 (37004) hydrogen bonds : bond 0.06974 ( 1521) hydrogen bonds : angle 3.55511 ( 4317) Misc. bond : bond 0.00564 ( 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 478 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 353 time to evaluate : 0.928 Fit side-chains REVERT: z 21 ARG cc_start: 0.7996 (mmt-90) cc_final: 0.7733 (mmp80) REVERT: z 190 ARG cc_start: 0.7016 (mtp85) cc_final: 0.6217 (mtt180) REVERT: z 219 GLU cc_start: 0.7526 (tt0) cc_final: 0.7098 (tp30) REVERT: 0 1 MET cc_start: 0.5659 (tpp) cc_final: 0.5364 (tpt) REVERT: 0 39 LYS cc_start: 0.7156 (mptp) cc_final: 0.6338 (ttmm) REVERT: 0 57 MET cc_start: 0.8662 (tpp) cc_final: 0.8414 (tpt) REVERT: 0 90 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7593 (mmt90) REVERT: 0 123 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: 0 169 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7275 (mt-10) REVERT: 0 175 ARG cc_start: 0.7897 (ttp-170) cc_final: 0.7587 (ttm-80) REVERT: 0 247 SER cc_start: 0.8388 (t) cc_final: 0.8186 (m) REVERT: 0 273 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8081 (tp30) REVERT: y 1 MET cc_start: 0.1579 (mtm) cc_final: -0.0727 (ppp) REVERT: y 62 TYR cc_start: 0.8383 (t80) cc_final: 0.7608 (t80) REVERT: y 92 TYR cc_start: 0.8916 (m-80) cc_final: 0.8476 (m-80) REVERT: y 103 ARG cc_start: 0.8180 (tpp-160) cc_final: 0.7899 (ttm170) REVERT: y 167 ILE cc_start: 0.8279 (mt) cc_final: 0.7969 (mt) REVERT: y 186 LEU cc_start: 0.5111 (OUTLIER) cc_final: 0.4049 (mm) REVERT: y 218 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: y 219 GLU cc_start: 0.7646 (tp30) cc_final: 0.7431 (tp30) REVERT: 5 94 TYR cc_start: 0.6879 (t80) cc_final: 0.6631 (t80) REVERT: 5 99 ARG cc_start: 0.6700 (mmm160) cc_final: 0.5589 (mtp180) REVERT: 5 104 ASP cc_start: 0.6489 (m-30) cc_final: 0.6196 (m-30) REVERT: 5 187 ASN cc_start: 0.7297 (m110) cc_final: 0.6782 (t0) REVERT: 5 208 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7884 (mtp180) REVERT: 5 229 GLN cc_start: 0.8826 (mt0) cc_final: 0.8537 (mt0) REVERT: 6 115 ASP cc_start: 0.6740 (t0) cc_final: 0.6483 (t70) REVERT: 6 175 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7550 (ttt-90) REVERT: 6 211 MET cc_start: 0.8941 (mtp) cc_final: 0.8628 (mtp) REVERT: 6 273 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: 4 21 ARG cc_start: 0.8317 (ttt-90) cc_final: 0.7352 (ttp80) REVERT: 4 45 ARG cc_start: 0.5635 (ptt90) cc_final: 0.5398 (ptt180) REVERT: 4 90 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7616 (ttp-170) REVERT: 4 191 HIS cc_start: 0.6196 (m-70) cc_final: 0.5824 (p90) REVERT: 4 237 LYS cc_start: 0.7562 (ttmt) cc_final: 0.7199 (ttpt) REVERT: 4 259 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5509 (pm20) REVERT: 8 25 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: 8 36 LYS cc_start: 0.7774 (mptt) cc_final: 0.7382 (mtmt) REVERT: 8 40 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7806 (ttmm) REVERT: 8 89 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6980 (mmm-85) REVERT: 8 90 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7210 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7882 (mpt-90) cc_final: 0.7668 (mtt-85) REVERT: 8 189 ASP cc_start: 0.5635 (p0) cc_final: 0.5260 (m-30) REVERT: 8 269 GLU cc_start: 0.7793 (mp0) cc_final: 0.7495 (mt-10) REVERT: 9 18 ASN cc_start: 0.8248 (m-40) cc_final: 0.7873 (m-40) REVERT: 9 30 ASP cc_start: 0.8349 (t0) cc_final: 0.8100 (t70) REVERT: 9 99 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7196 (mtp180) REVERT: 9 118 VAL cc_start: 0.7126 (m) cc_final: 0.6480 (t) REVERT: 9 258 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.7094 (p) REVERT: 7 4 GLN cc_start: 0.8622 (tp40) cc_final: 0.8227 (mm-40) REVERT: 7 28 ASP cc_start: 0.7693 (t0) cc_final: 0.7332 (t0) REVERT: 7 39 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6748 (mmmm) REVERT: 7 48 ARG cc_start: 0.7010 (tpt170) cc_final: 0.6504 (tpt170) REVERT: 7 165 GLN cc_start: 0.8035 (tp40) cc_final: 0.7532 (mt0) REVERT: 7 178 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7989 (mtm) outliers start: 125 outliers final: 81 residues processed: 443 average time/residue: 0.8812 time to fit residues: 432.9609 Evaluate side-chains 430 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 334 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 28 ASP 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 151 THR Chi-restraints excluded: chain z residue 162 THR Chi-restraints excluded: chain z residue 197 VAL 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 90 ARG Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 116 THR Chi-restraints excluded: chain 0 residue 118 VAL 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 250 CYS Chi-restraints excluded: chain y residue 83 ARG Chi-restraints excluded: chain y residue 118 VAL 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 250 CYS Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain 5 residue 31 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 180 CYS 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 2 SER Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 143 THR Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 182 LYS Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 273 GLU Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 41 CYS 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 131 SER 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 246 ASP Chi-restraints excluded: chain 4 residue 259 GLU 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 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 160 LYS Chi-restraints excluded: chain 8 residue 162 THR 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 99 ARG Chi-restraints excluded: chain 9 residue 108 VAL Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 258 VAL Chi-restraints excluded: chain 9 residue 262 ASP Chi-restraints excluded: chain 9 residue 284 GLN Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 39 LYS Chi-restraints excluded: chain 7 residue 76 VAL Chi-restraints excluded: chain 7 residue 89 ARG 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 174 VAL Chi-restraints excluded: chain 7 residue 178 MET Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 265 ASP Chi-restraints excluded: chain 7 residue 274 ASP 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 100 optimal weight: 30.0000 chunk 95 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 265 optimal weight: 50.0000 chunk 154 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 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 y 165 GLN 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 = 0.4365 r_free = 0.4365 target = 0.218851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.171236 restraints weight = 31015.316| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.23 r_work: 0.3740 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 1.2485 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= 0.142 Angle : 0.578 8.427 37004 Z= 0.292 Chirality : 0.033 0.202 4397 Planarity : 0.004 0.095 3941 Dihedral : 21.491 159.665 6503 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.67 % Favored : 95.21 % Rotamer: Outliers : 4.56 % Allowed : 27.79 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.16), residues: 2546 helix: 2.46 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -0.77 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG 8 166 TYR 0.013 0.002 TYR y 205 PHE 0.026 0.001 PHE y 19 TRP 0.015 0.002 TRP 6 217 HIS 0.013 0.001 HIS 0 22 Details of bonding type rmsd covalent geometry : bond 0.00311 (26605) covalent geometry : angle 0.57766 (37004) hydrogen bonds : bond 0.06041 ( 1521) hydrogen bonds : angle 3.41067 ( 4317) Misc. bond : bond 0.00413 ( 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 450 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 345 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: z 21 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.7741 (mmp80) REVERT: z 70 ASN cc_start: 0.8259 (t0) cc_final: 0.7916 (t160) REVERT: z 190 ARG cc_start: 0.6895 (mtp85) cc_final: 0.6156 (mtt180) REVERT: z 219 GLU cc_start: 0.7473 (tt0) cc_final: 0.7100 (tp30) REVERT: 0 1 MET cc_start: 0.5633 (tpp) cc_final: 0.5334 (tpt) REVERT: 0 21 ARG cc_start: 0.7692 (ptp-110) cc_final: 0.7367 (ptp90) REVERT: 0 39 LYS cc_start: 0.7164 (mptp) cc_final: 0.6299 (ttmm) REVERT: 0 57 MET cc_start: 0.8585 (tpp) cc_final: 0.8345 (tpt) REVERT: 0 123 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: 0 169 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7296 (mt-10) REVERT: 0 175 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7540 (ttm-80) REVERT: 0 273 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8071 (tp30) REVERT: y 1 MET cc_start: 0.1638 (mtm) cc_final: -0.0401 (ppp) REVERT: y 62 TYR cc_start: 0.8375 (t80) cc_final: 0.7727 (t80) REVERT: y 92 TYR cc_start: 0.8878 (m-80) cc_final: 0.8496 (m-80) REVERT: y 103 ARG cc_start: 0.8167 (tpp-160) cc_final: 0.7847 (ttm170) REVERT: y 186 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.3990 (mm) REVERT: y 218 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: y 219 GLU cc_start: 0.7562 (tp30) cc_final: 0.7285 (tp30) REVERT: y 222 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7428 (mtm180) REVERT: y 231 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7130 (ttm-80) REVERT: 5 10 ARG cc_start: 0.6986 (tpp80) cc_final: 0.6667 (ttt90) REVERT: 5 79 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7904 (tp30) REVERT: 5 94 TYR cc_start: 0.6807 (t80) cc_final: 0.6509 (t80) REVERT: 5 99 ARG cc_start: 0.6772 (mmm160) cc_final: 0.5642 (mtp180) REVERT: 5 104 ASP cc_start: 0.6295 (m-30) cc_final: 0.5989 (m-30) REVERT: 5 187 ASN cc_start: 0.7206 (m110) cc_final: 0.6637 (t0) REVERT: 5 229 GLN cc_start: 0.8810 (mt0) cc_final: 0.8500 (mt0) REVERT: 6 57 MET cc_start: 0.8981 (mmt) cc_final: 0.8747 (mmt) REVERT: 6 115 ASP cc_start: 0.6418 (t0) cc_final: 0.6186 (t70) REVERT: 6 175 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7484 (ttt-90) REVERT: 6 211 MET cc_start: 0.8895 (mtp) cc_final: 0.8588 (mtp) REVERT: 4 21 ARG cc_start: 0.8276 (ttt-90) cc_final: 0.7447 (ttp80) REVERT: 4 45 ARG cc_start: 0.5626 (ptt90) cc_final: 0.5414 (ptt180) REVERT: 4 90 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7427 (ttp-170) REVERT: 4 168 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7693 (mm-30) REVERT: 4 176 ARG cc_start: 0.7320 (tpp80) cc_final: 0.6971 (ttp80) REVERT: 4 185 ASP cc_start: 0.2773 (OUTLIER) cc_final: 0.1860 (m-30) REVERT: 4 191 HIS cc_start: 0.5882 (m-70) cc_final: 0.5673 (p90) REVERT: 4 234 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7930 (mt) REVERT: 4 237 LYS cc_start: 0.7282 (ttmt) cc_final: 0.6899 (ttpt) REVERT: 4 259 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5436 (pm20) REVERT: 8 36 LYS cc_start: 0.7667 (mptt) cc_final: 0.7455 (mtmt) REVERT: 8 90 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6978 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7750 (mpt-90) cc_final: 0.7470 (mtt-85) REVERT: 9 18 ASN cc_start: 0.8227 (m-40) cc_final: 0.7861 (m-40) REVERT: 9 30 ASP cc_start: 0.8264 (t0) cc_final: 0.8021 (t70) REVERT: 9 57 MET cc_start: 0.8787 (tpt) cc_final: 0.8172 (mmp) REVERT: 9 99 ARG cc_start: 0.7808 (ttp-170) cc_final: 0.7396 (mtp180) REVERT: 9 118 VAL cc_start: 0.6939 (m) cc_final: 0.6332 (t) REVERT: 9 182 LYS cc_start: 0.6281 (OUTLIER) cc_final: 0.5650 (pttm) REVERT: 9 258 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7202 (p) REVERT: 7 28 ASP cc_start: 0.7651 (t0) cc_final: 0.7248 (t0) REVERT: 7 39 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6718 (mmmm) REVERT: 7 165 GLN cc_start: 0.7999 (tp40) cc_final: 0.7552 (mt0) REVERT: 7 178 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8018 (mtm) REVERT: 7 277 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7733 (pp) outliers start: 105 outliers final: 75 residues processed: 417 average time/residue: 0.9070 time to fit residues: 420.1173 Evaluate side-chains 424 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 332 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 28 ASP Chi-restraints excluded: chain z residue 41 CYS Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 139 SER Chi-restraints excluded: chain z residue 141 ARG Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 162 THR Chi-restraints excluded: chain z residue 197 VAL 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 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 250 CYS Chi-restraints excluded: chain 0 residue 258 VAL Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 118 VAL 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 222 ARG 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 31 LEU Chi-restraints excluded: chain 5 residue 57 MET Chi-restraints excluded: chain 5 residue 79 GLU 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 180 CYS 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 131 SER Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 182 LYS 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 131 SER 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 246 ASP Chi-restraints excluded: chain 4 residue 259 GLU Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 45 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 162 THR Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 189 ASP 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 123 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 182 LYS Chi-restraints excluded: chain 9 residue 258 VAL Chi-restraints excluded: chain 9 residue 284 GLN Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 39 LYS Chi-restraints excluded: chain 7 residue 76 VAL 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 258 VAL Chi-restraints excluded: chain 7 residue 274 ASP 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 218 optimal weight: 5.9990 chunk 140 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 160 optimal weight: 8.9990 chunk 242 optimal weight: 0.2980 chunk 157 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 169 optimal weight: 0.0070 chunk 235 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 overall best weight: 4.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 47 HIS y 165 GLN 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 = 0.4376 r_free = 0.4376 target = 0.220023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.172581 restraints weight = 30914.844| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.24 r_work: 0.3750 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 1.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26606 Z= 0.130 Angle : 0.560 8.041 37004 Z= 0.283 Chirality : 0.032 0.186 4397 Planarity : 0.004 0.053 3941 Dihedral : 21.347 158.511 6503 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.67 % Favored : 95.29 % Rotamer: Outliers : 4.08 % Allowed : 28.09 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.16), residues: 2546 helix: 2.55 (0.12), residues: 1798 sheet: None (None), residues: 0 loop : -0.75 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG 8 166 TYR 0.012 0.002 TYR y 205 PHE 0.013 0.001 PHE 4 275 TRP 0.012 0.001 TRP 6 217 HIS 0.015 0.001 HIS 0 22 Details of bonding type rmsd covalent geometry : bond 0.00278 (26605) covalent geometry : angle 0.55953 (37004) hydrogen bonds : bond 0.05746 ( 1521) hydrogen bonds : angle 3.34341 ( 4317) Misc. bond : bond 0.00528 ( 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 443 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 349 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: z 21 ARG cc_start: 0.7958 (mmt-90) cc_final: 0.7700 (mmp80) REVERT: z 70 ASN cc_start: 0.8124 (t0) cc_final: 0.7744 (t160) REVERT: z 190 ARG cc_start: 0.6852 (mtp85) cc_final: 0.6566 (mtt-85) REVERT: z 219 GLU cc_start: 0.7501 (tt0) cc_final: 0.7148 (tp30) REVERT: z 238 GLU cc_start: 0.7811 (tp30) cc_final: 0.7475 (mm-30) REVERT: 0 1 MET cc_start: 0.5543 (tpp) cc_final: 0.5252 (tpt) REVERT: 0 21 ARG cc_start: 0.7745 (ptp-110) cc_final: 0.7459 (ttm170) REVERT: 0 39 LYS cc_start: 0.7153 (mptp) cc_final: 0.6274 (ttmm) REVERT: 0 57 MET cc_start: 0.8576 (tpp) cc_final: 0.8345 (tpt) REVERT: 0 169 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7261 (mt-10) REVERT: 0 175 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7477 (ttt180) REVERT: 0 273 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8058 (tp30) REVERT: y 1 MET cc_start: 0.0949 (mtm) cc_final: 0.0182 (pmm) REVERT: y 55 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7968 (mt-10) REVERT: y 62 TYR cc_start: 0.8342 (t80) cc_final: 0.7687 (t80) REVERT: y 89 ARG cc_start: 0.8111 (ptm160) cc_final: 0.7746 (ttt-90) REVERT: y 92 TYR cc_start: 0.8905 (m-80) cc_final: 0.8545 (m-80) REVERT: y 186 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.3973 (mm) REVERT: y 218 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: y 219 GLU cc_start: 0.7561 (tp30) cc_final: 0.7309 (tp30) REVERT: y 231 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.6864 (ttm-80) REVERT: 5 10 ARG cc_start: 0.6989 (tpp80) cc_final: 0.6669 (ttt90) REVERT: 5 79 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7905 (tp30) REVERT: 5 94 TYR cc_start: 0.6877 (t80) cc_final: 0.6490 (t80) REVERT: 5 99 ARG cc_start: 0.6729 (mmm160) cc_final: 0.5554 (mtp180) REVERT: 5 104 ASP cc_start: 0.6387 (m-30) cc_final: 0.6027 (m-30) REVERT: 5 187 ASN cc_start: 0.7185 (m110) cc_final: 0.6649 (t0) REVERT: 5 229 GLN cc_start: 0.8778 (mt0) cc_final: 0.8519 (mt0) REVERT: 6 57 MET cc_start: 0.8977 (mmt) cc_final: 0.8734 (mmt) REVERT: 6 98 ASP cc_start: 0.7706 (t70) cc_final: 0.7447 (t0) REVERT: 6 115 ASP cc_start: 0.6364 (t0) cc_final: 0.6161 (t70) REVERT: 6 175 ARG cc_start: 0.7814 (ttm170) cc_final: 0.7425 (ttt-90) REVERT: 6 211 MET cc_start: 0.8907 (mtp) cc_final: 0.8598 (mtp) REVERT: 4 21 ARG cc_start: 0.8219 (ttt-90) cc_final: 0.7392 (ttp80) REVERT: 4 90 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7419 (ttp-170) REVERT: 4 168 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7800 (mm-30) REVERT: 4 176 ARG cc_start: 0.7267 (tpp80) cc_final: 0.6925 (ttp80) REVERT: 4 185 ASP cc_start: 0.2421 (OUTLIER) cc_final: 0.1561 (m-30) REVERT: 4 191 HIS cc_start: 0.6012 (m-70) cc_final: 0.5741 (p90) REVERT: 4 234 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7866 (mt) REVERT: 4 237 LYS cc_start: 0.7246 (ttmt) cc_final: 0.6887 (ttpt) REVERT: 8 36 LYS cc_start: 0.7605 (mptt) cc_final: 0.7387 (mtmt) REVERT: 8 68 PHE cc_start: 0.8551 (t80) cc_final: 0.8225 (t80) REVERT: 8 90 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7003 (tpp-160) REVERT: 8 119 ARG cc_start: 0.7683 (mpt-90) cc_final: 0.7468 (mtt-85) REVERT: 8 269 GLU cc_start: 0.7805 (mp0) cc_final: 0.7587 (mt-10) REVERT: 9 18 ASN cc_start: 0.8203 (m-40) cc_final: 0.7841 (m-40) REVERT: 9 57 MET cc_start: 0.8735 (tpt) cc_final: 0.8122 (mmp) REVERT: 9 99 ARG cc_start: 0.7751 (ttp-170) cc_final: 0.7321 (mtp180) REVERT: 9 118 VAL cc_start: 0.6689 (m) cc_final: 0.6123 (t) REVERT: 9 182 LYS cc_start: 0.6257 (OUTLIER) cc_final: 0.5632 (pttm) REVERT: 7 39 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6670 (mmmm) REVERT: 7 165 GLN cc_start: 0.7948 (tp40) cc_final: 0.7528 (mt0) REVERT: 7 178 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7981 (mtm) REVERT: 7 277 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7627 (pp) outliers start: 94 outliers final: 69 residues processed: 414 average time/residue: 0.9045 time to fit residues: 415.6734 Evaluate side-chains 418 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 337 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 28 ASP Chi-restraints excluded: chain z residue 108 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 162 THR Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 265 ASP 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 y residue 118 VAL 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 79 GLU 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 180 CYS 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 162 THR Chi-restraints excluded: chain 6 residue 182 LYS 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 131 SER 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 246 ASP Chi-restraints excluded: chain 8 residue 23 LEU 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 24 THR Chi-restraints excluded: chain 9 residue 50 THR Chi-restraints excluded: chain 9 residue 123 GLU Chi-restraints excluded: chain 9 residue 151 THR Chi-restraints excluded: chain 9 residue 182 LYS Chi-restraints excluded: chain 9 residue 189 ASP Chi-restraints excluded: chain 9 residue 262 ASP Chi-restraints excluded: chain 9 residue 284 GLN Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 39 LYS Chi-restraints excluded: chain 7 residue 89 ARG 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 174 VAL Chi-restraints excluded: chain 7 residue 178 MET Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 265 ASP Chi-restraints excluded: chain 7 residue 274 ASP 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 125 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 268 optimal weight: 50.0000 chunk 254 optimal weight: 50.0000 chunk 144 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 chunk 142 optimal weight: 4.9990 chunk 256 optimal weight: 50.0000 chunk 28 optimal weight: 30.0000 chunk 146 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 47 HIS y 165 GLN 4 229 GLN 9 25 GLN 7 18 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.217151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.169520 restraints weight = 30514.076| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.22 r_work: 0.3715 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 1.2765 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 : 0.613 8.897 37004 Z= 0.311 Chirality : 0.035 0.340 4397 Planarity : 0.004 0.071 3941 Dihedral : 21.407 159.182 6503 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.66 % Rotamer: Outliers : 4.60 % Allowed : 27.75 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.16), residues: 2546 helix: 2.34 (0.12), residues: 1797 sheet: None (None), residues: 0 loop : -0.74 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG 8 166 TYR 0.013 0.002 TYR y 205 PHE 0.026 0.002 PHE y 19 TRP 0.012 0.002 TRP 6 217 HIS 0.016 0.001 HIS 0 22 Details of bonding type rmsd covalent geometry : bond 0.00375 (26605) covalent geometry : angle 0.61342 (37004) hydrogen bonds : bond 0.06718 ( 1521) hydrogen bonds : angle 3.51730 ( 4317) Misc. bond : bond 0.00469 ( 1) =============================================================================== Job complete usr+sys time: 13016.19 seconds wall clock time: 220 minutes 55.29 seconds (13255.29 seconds total)