Starting phenix.real_space_refine on Tue Mar 19 23:26:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/03_2024/7lj3_23388.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/03_2024/7lj3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/03_2024/7lj3_23388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/03_2024/7lj3_23388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/03_2024/7lj3_23388.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/03_2024/7lj3_23388.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 222 5.49 5 S 116 5.16 5 C 15334 2.51 5 N 4661 2.21 5 O 5381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "z ARG 11": "NH1" <-> "NH2" Residue "z ARG 99": "NH1" <-> "NH2" Residue "z ARG 190": "NH1" <-> "NH2" Residue "0 ARG 11": "NH1" <-> "NH2" Residue "0 ARG 48": "NH1" <-> "NH2" Residue "0 GLU 113": "OE1" <-> "OE2" Residue "0 GLU 123": "OE1" <-> "OE2" Residue "0 GLU 168": "OE1" <-> "OE2" Residue "0 ARG 215": "NH1" <-> "NH2" Residue "0 ARG 222": "NH1" <-> "NH2" Residue "y ARG 89": "NH1" <-> "NH2" Residue "y ARG 111": "NH1" <-> "NH2" Residue "y GLU 126": "OE1" <-> "OE2" Residue "y GLU 219": "OE1" <-> "OE2" Residue "5 ARG 11": "NH1" <-> "NH2" Residue "5 ARG 48": "NH1" <-> "NH2" Residue "5 ARG 49": "NH1" <-> "NH2" Residue "5 ARG 103": "NH1" <-> "NH2" Residue "5 ARG 111": "NH1" <-> "NH2" Residue "5 ARG 119": "NH1" <-> "NH2" Residue "5 ARG 190": "NH1" <-> "NH2" Residue "5 ARG 240": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 GLU 81": "OE1" <-> "OE2" Residue "6 ARG 141": "NH1" <-> "NH2" Residue "6 GLU 163": "OE1" <-> "OE2" Residue "6 ARG 166": "NH1" <-> "NH2" Residue "6 ARG 227": "NH1" <-> "NH2" Residue "4 GLU 43": "OE1" <-> "OE2" Residue "4 ARG 49": "NH1" <-> "NH2" Residue "4 ARG 67": "NH1" <-> "NH2" Residue "4 ARG 111": "NH1" <-> "NH2" Residue "4 ARG 190": "NH1" <-> "NH2" Residue "4 GLU 273": "OE1" <-> "OE2" Residue "8 GLU 32": "OE1" <-> "OE2" Residue "8 ARG 45": "NH1" <-> "NH2" Residue "8 ARG 48": "NH1" <-> "NH2" Residue "8 ARG 64": "NH1" <-> "NH2" Residue "8 ARG 89": "NH1" <-> "NH2" Residue "8 ARG 99": "NH1" <-> "NH2" Residue "8 ARG 166": "NH1" <-> "NH2" Residue "8 ARG 222": "NH1" <-> "NH2" Residue "8 GLU 259": "OE1" <-> "OE2" Residue "9 ARG 21": "NH1" <-> "NH2" Residue "9 ARG 89": "NH1" <-> "NH2" Residue "9 GLU 113": "OE1" <-> "OE2" Residue "9 ARG 141": "NH1" <-> "NH2" Residue "9 ARG 190": "NH1" <-> "NH2" Residue "7 ARG 64": "NH1" <-> "NH2" Residue "7 ARG 89": "NH1" <-> "NH2" Residue "7 ARG 127": "NH1" <-> "NH2" Residue "7 ARG 175": "NH1" <-> "NH2" Residue "7 ARG 190": "NH1" <-> "NH2" Residue "7 ARG 227": "NH1" <-> "NH2" Residue "7 GLU 238": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25714 Number of models: 1 Model: "" Number of chains: 12 Chain: "z" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2320 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 276} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "0" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "y" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "4" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "9" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "7" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1590 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 27, 'rna3p_pyr': 35} Link IDs: {'rna2p': 13, 'rna3p': 61} Chain: "B" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1590 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 27, 'rna3p_pyr': 35} Link IDs: {'rna2p': 13, 'rna3p': 61} Chain: "C" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1590 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 27, 'rna3p_pyr': 35} Link IDs: {'rna2p': 13, 'rna3p': 61} Time building chain proxies: 13.95, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.72 Conformation dependent library (CDL) restraints added in 4.2 seconds 5092 Ramachandran restraints generated. 2546 Oldfield, 0 Emsley, 2546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4948 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 0 sheets defined 72.5% alpha, 0.0% beta 67 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 9.14 Creating SS restraints... Processing helix chain 'z' and resid 9 through 22 Processing helix chain 'z' and resid 23 through 26 Processing helix chain 'z' and resid 34 through 40 removed outlier: 4.074A pdb=" N LEU z 38 " --> pdb=" O HIS z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 47 through 70 Processing helix chain 'z' and resid 73 through 94 removed outlier: 3.534A pdb=" N TYR z 92 " --> pdb=" O ALA z 88 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR z 93 " --> pdb=" O ARG z 89 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR z 94 " --> pdb=" O ARG z 90 " (cutoff:3.500A) Processing helix chain 'z' and resid 98 through 111 removed outlier: 4.421A pdb=" N ASP z 104 " --> pdb=" O GLY z 100 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL z 108 " --> pdb=" O ASP z 104 " (cutoff:3.500A) Processing helix chain 'z' and resid 120 through 141 removed outlier: 3.654A pdb=" N ARG z 127 " --> pdb=" O GLU z 123 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER z 131 " --> pdb=" O ARG z 127 " (cutoff:3.500A) Processing helix chain 'z' and resid 160 through 175 Processing helix chain 'z' and resid 194 through 241 removed outlier: 3.666A pdb=" N VAL z 213 " --> pdb=" O LEU z 209 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS z 237 " --> pdb=" O LYS z 233 " (cutoff:3.500A) Processing helix chain 'z' and resid 244 through 254 Processing helix chain 'z' and resid 258 through 261 removed outlier: 4.406A pdb=" N GLY z 261 " --> pdb=" O VAL z 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 258 through 261' Processing helix chain 'z' and resid 262 through 274 removed outlier: 3.766A pdb=" N ASP z 274 " --> pdb=" O LEU z 270 " (cutoff:3.500A) Processing helix chain 'z' and resid 275 through 278 removed outlier: 3.555A pdb=" N TYR z 278 " --> pdb=" O PHE z 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 275 through 278' Processing helix chain '0' and resid 9 through 22 Processing helix chain '0' and resid 34 through 40 removed outlier: 4.036A pdb=" N LEU 0 38 " --> pdb=" O HIS 0 34 " (cutoff:3.500A) Processing helix chain '0' and resid 49 through 70 removed outlier: 3.616A pdb=" N GLU 0 55 " --> pdb=" O VAL 0 51 " (cutoff:3.500A) Processing helix chain '0' and resid 73 through 92 removed outlier: 3.644A pdb=" N ARG 0 90 " --> pdb=" O ALA 0 86 " (cutoff:3.500A) Processing helix chain '0' and resid 98 through 112 removed outlier: 3.558A pdb=" N VAL 0 108 " --> pdb=" O ASP 0 104 " (cutoff:3.500A) Processing helix chain '0' and resid 117 through 119 No H-bonds generated for 'chain '0' and resid 117 through 119' Processing helix chain '0' and resid 120 through 141 removed outlier: 3.649A pdb=" N ALA 0 128 " --> pdb=" O ILE 0 124 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU 0 135 " --> pdb=" O SER 0 131 " (cutoff:3.500A) Processing helix chain '0' and resid 160 through 177 Processing helix chain '0' and resid 194 through 241 removed outlier: 3.562A pdb=" N VAL 0 213 " --> pdb=" O LEU 0 209 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU 0 225 " --> pdb=" O GLU 0 221 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG 0 231 " --> pdb=" O ARG 0 227 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS 0 237 " --> pdb=" O LYS 0 233 " (cutoff:3.500A) Processing helix chain '0' and resid 244 through 254 removed outlier: 3.637A pdb=" N ARG 0 251 " --> pdb=" O SER 0 247 " (cutoff:3.500A) Processing helix chain '0' and resid 259 through 274 removed outlier: 4.138A pdb=" N SER 0 263 " --> pdb=" O GLU 0 259 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA 0 264 " --> pdb=" O ASN 0 260 " (cutoff:3.500A) Processing helix chain '0' and resid 274 through 279 removed outlier: 3.953A pdb=" N TYR 0 278 " --> pdb=" O ASP 0 274 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 22 Processing helix chain 'y' and resid 30 through 33 Processing helix chain 'y' and resid 34 through 40 removed outlier: 3.648A pdb=" N LEU y 38 " --> pdb=" O HIS y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 47 through 70 Processing helix chain 'y' and resid 73 through 94 removed outlier: 3.851A pdb=" N GLU y 81 " --> pdb=" O LEU y 77 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR y 93 " --> pdb=" O ARG y 89 " (cutoff:3.500A) Processing helix chain 'y' and resid 98 through 111 removed outlier: 3.843A pdb=" N ALA y 102 " --> pdb=" O ASP y 98 " (cutoff:3.500A) Processing helix chain 'y' and resid 117 through 119 No H-bonds generated for 'chain 'y' and resid 117 through 119' Processing helix chain 'y' and resid 120 through 141 removed outlier: 3.545A pdb=" N ARG y 127 " --> pdb=" O GLU y 123 " (cutoff:3.500A) Processing helix chain 'y' and resid 160 through 177 Processing helix chain 'y' and resid 194 through 241 Processing helix chain 'y' and resid 244 through 255 Processing helix chain 'y' and resid 260 through 274 removed outlier: 3.660A pdb=" N ALA y 264 " --> pdb=" O ASN y 260 " (cutoff:3.500A) Processing helix chain 'y' and resid 274 through 279 removed outlier: 3.704A pdb=" N TYR y 278 " --> pdb=" O ASP y 274 " (cutoff:3.500A) Processing helix chain 'y' and resid 280 through 282 No H-bonds generated for 'chain 'y' and resid 280 through 282' Processing helix chain '5' and resid 9 through 22 removed outlier: 3.514A pdb=" N ALA 5 15 " --> pdb=" O ARG 5 11 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU 5 20 " --> pdb=" O LEU 5 16 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 33 Processing helix chain '5' and resid 34 through 40 removed outlier: 3.544A pdb=" N LEU 5 38 " --> pdb=" O HIS 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 70 Processing helix chain '5' and resid 73 through 94 Processing helix chain '5' and resid 98 through 111 removed outlier: 3.819A pdb=" N HIS 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 118 through 140 removed outlier: 3.650A pdb=" N SER 5 131 " --> pdb=" O ARG 5 127 " (cutoff:3.500A) Processing helix chain '5' and resid 160 through 177 Processing helix chain '5' and resid 194 through 240 Processing helix chain '5' and resid 244 through 255 Processing helix chain '5' and resid 260 through 274 removed outlier: 3.667A pdb=" N ALA 5 264 " --> pdb=" O ASN 5 260 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 279 removed outlier: 3.765A pdb=" N TYR 5 278 " --> pdb=" O ASP 5 274 " (cutoff:3.500A) Processing helix chain '6' and resid 9 through 23 removed outlier: 3.531A pdb=" N ARG 6 21 " --> pdb=" O VAL 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 24 through 26 No H-bonds generated for 'chain '6' and resid 24 through 26' Processing helix chain '6' and resid 30 through 33 Processing helix chain '6' and resid 34 through 41 removed outlier: 3.713A pdb=" N LEU 6 38 " --> pdb=" O HIS 6 34 " (cutoff:3.500A) Processing helix chain '6' and resid 47 through 70 Processing helix chain '6' and resid 73 through 92 Processing helix chain '6' and resid 98 through 111 Processing helix chain '6' and resid 117 through 140 Processing helix chain '6' and resid 160 through 177 Processing helix chain '6' and resid 194 through 242 removed outlier: 3.972A pdb=" N CYS 6 242 " --> pdb=" O GLU 6 238 " (cutoff:3.500A) Processing helix chain '6' and resid 244 through 254 Processing helix chain '6' and resid 261 through 274 Processing helix chain '6' and resid 274 through 279 removed outlier: 3.730A pdb=" N TYR 6 278 " --> pdb=" O ASP 6 274 " (cutoff:3.500A) Processing helix chain '6' and resid 280 through 282 No H-bonds generated for 'chain '6' and resid 280 through 282' Processing helix chain '4' and resid 9 through 22 Processing helix chain '4' and resid 34 through 42 removed outlier: 3.873A pdb=" N LEU 4 38 " --> pdb=" O HIS 4 34 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY 4 42 " --> pdb=" O LEU 4 38 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 69 Processing helix chain '4' and resid 73 through 94 removed outlier: 3.985A pdb=" N THR 4 93 " --> pdb=" O ARG 4 89 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR 4 94 " --> pdb=" O ARG 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 98 through 112 removed outlier: 3.661A pdb=" N ALA 4 102 " --> pdb=" O ASP 4 98 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR 4 112 " --> pdb=" O VAL 4 108 " (cutoff:3.500A) Processing helix chain '4' and resid 119 through 141 removed outlier: 4.649A pdb=" N GLU 4 123 " --> pdb=" O ARG 4 119 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 177 Processing helix chain '4' and resid 194 through 241 Processing helix chain '4' and resid 244 through 254 Processing helix chain '4' and resid 261 through 274 Processing helix chain '4' and resid 274 through 279 removed outlier: 3.780A pdb=" N TYR 4 278 " --> pdb=" O ASP 4 274 " (cutoff:3.500A) Processing helix chain '4' and resid 280 through 282 No H-bonds generated for 'chain '4' and resid 280 through 282' Processing helix chain '8' and resid 9 through 22 Processing helix chain '8' and resid 34 through 41 removed outlier: 4.150A pdb=" N LEU 8 38 " --> pdb=" O HIS 8 34 " (cutoff:3.500A) Processing helix chain '8' and resid 47 through 70 Processing helix chain '8' and resid 73 through 94 removed outlier: 3.553A pdb=" N THR 8 93 " --> pdb=" O ARG 8 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR 8 94 " --> pdb=" O ARG 8 90 " (cutoff:3.500A) Processing helix chain '8' and resid 100 through 111 Processing helix chain '8' and resid 120 through 140 removed outlier: 3.819A pdb=" N ALA 8 128 " --> pdb=" O ILE 8 124 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU 8 135 " --> pdb=" O SER 8 131 " (cutoff:3.500A) Processing helix chain '8' and resid 160 through 177 Processing helix chain '8' and resid 194 through 241 removed outlier: 3.922A pdb=" N MET 8 241 " --> pdb=" O LYS 8 237 " (cutoff:3.500A) Processing helix chain '8' and resid 244 through 254 Processing helix chain '8' and resid 261 through 274 removed outlier: 3.566A pdb=" N ASP 8 265 " --> pdb=" O GLY 8 261 " (cutoff:3.500A) Processing helix chain '8' and resid 274 through 280 removed outlier: 3.796A pdb=" N TYR 8 278 " --> pdb=" O ASP 8 274 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP 8 280 " --> pdb=" O ASP 8 276 " (cutoff:3.500A) Processing helix chain '9' and resid 9 through 22 Processing helix chain '9' and resid 30 through 33 Processing helix chain '9' and resid 34 through 41 removed outlier: 3.568A pdb=" N LEU 9 38 " --> pdb=" O HIS 9 34 " (cutoff:3.500A) Processing helix chain '9' and resid 47 through 70 Processing helix chain '9' and resid 73 through 92 Processing helix chain '9' and resid 98 through 111 Processing helix chain '9' and resid 117 through 141 removed outlier: 3.728A pdb=" N ASP 9 121 " --> pdb=" O ASP 9 117 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA 9 122 " --> pdb=" O VAL 9 118 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG 9 127 " --> pdb=" O GLU 9 123 " (cutoff:3.500A) Processing helix chain '9' and resid 160 through 176 Processing helix chain '9' and resid 194 through 241 removed outlier: 3.919A pdb=" N MET 9 241 " --> pdb=" O LYS 9 237 " (cutoff:3.500A) Processing helix chain '9' and resid 244 through 254 Processing helix chain '9' and resid 261 through 274 Processing helix chain '9' and resid 274 through 279 removed outlier: 3.832A pdb=" N TYR 9 278 " --> pdb=" O ASP 9 274 " (cutoff:3.500A) Processing helix chain '9' and resid 280 through 282 No H-bonds generated for 'chain '9' and resid 280 through 282' Processing helix chain '7' and resid 9 through 22 Processing helix chain '7' and resid 30 through 33 Processing helix chain '7' and resid 34 through 41 removed outlier: 3.738A pdb=" N LEU 7 38 " --> pdb=" O HIS 7 34 " (cutoff:3.500A) Processing helix chain '7' and resid 47 through 69 Processing helix chain '7' and resid 73 through 94 removed outlier: 3.645A pdb=" N THR 7 93 " --> pdb=" O ARG 7 89 " (cutoff:3.500A) Processing helix chain '7' and resid 98 through 112 removed outlier: 3.821A pdb=" N ALA 7 102 " --> pdb=" O ASP 7 98 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL 7 108 " --> pdb=" O ASP 7 104 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR 7 112 " --> pdb=" O VAL 7 108 " (cutoff:3.500A) Processing helix chain '7' and resid 120 through 141 removed outlier: 3.673A pdb=" N ALA 7 128 " --> pdb=" O ILE 7 124 " (cutoff:3.500A) Processing helix chain '7' and resid 160 through 177 removed outlier: 3.607A pdb=" N ARG 7 176 " --> pdb=" O GLU 7 172 " (cutoff:3.500A) Processing helix chain '7' and resid 194 through 241 Processing helix chain '7' and resid 244 through 255 Processing helix chain '7' and resid 260 through 274 removed outlier: 3.943A pdb=" N ALA 7 264 " --> pdb=" O ASN 7 260 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP 7 265 " --> pdb=" O GLY 7 261 " (cutoff:3.500A) Processing helix chain '7' and resid 274 through 279 removed outlier: 3.723A pdb=" N TYR 7 278 " --> pdb=" O ASP 7 274 " (cutoff:3.500A) Processing helix chain '7' and resid 280 through 282 No H-bonds generated for 'chain '7' and resid 280 through 282' 1341 hydrogen bonds defined for protein. 4005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 180 hydrogen bonds 312 hydrogen bond angles 0 basepair planarities 67 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 8.33 Time building geometry restraints manager: 12.60 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: 98.81 - 105.86: 1366 105.86 - 112.90: 14991 112.90 - 119.94: 9041 119.94 - 126.98: 10970 126.98 - 134.02: 636 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: 12 1.81 - 2.58: 365 2.58 - 3.36: 34333 3.36 - 4.13: 61759 4.13 - 4.90: 108606 Nonbonded interactions: 205075 Sorted by model distance: nonbonded pdb=" NH2 ARG 6 119 " pdb=" OE2 GLU 6 218 " model vdw 1.041 2.520 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 205070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.160 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 73.430 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.210 ------------------------------------------------------------------------------- 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 0.076 26605 Z= 0.334 Angle : 0.717 10.170 37004 Z= 0.415 Chirality : 0.040 0.203 4397 Planarity : 0.005 0.109 3941 Dihedral : 20.498 175.406 11774 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.61 % Favored : 95.95 % Rotamer: Outliers : 3.30 % Allowed : 9.21 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2546 helix: 0.67 (0.11), residues: 1783 sheet: None (None), residues: 0 loop : -0.77 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 6 217 HIS 0.006 0.001 HIS 8 69 PHE 0.016 0.002 PHE 7 179 TYR 0.013 0.002 TYR y 94 ARG 0.005 0.001 ARG 5 89 *********************** 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 fitting. rotamer outliers: 76 poor density : 539 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.2491 (mmm) cc_final: 0.2288 (mmm) REVERT: 0 18 ASN cc_start: 0.4593 (m-40) cc_final: 0.4352 (m-40) REVERT: 0 120 HIS cc_start: 0.4444 (m90) cc_final: 0.4086 (m-70) REVERT: 0 167 ILE cc_start: 0.5516 (OUTLIER) cc_final: 0.5285 (tt) REVERT: 0 206 THR cc_start: 0.4784 (OUTLIER) cc_final: 0.4429 (p) REVERT: 0 256 HIS cc_start: 0.5249 (m-70) cc_final: 0.4996 (t70) REVERT: 0 259 GLU cc_start: 0.3378 (OUTLIER) cc_final: 0.3145 (pm20) REVERT: y 162 THR cc_start: 0.5902 (m) cc_final: 0.5672 (t) REVERT: y 211 MET cc_start: 0.5629 (mtm) cc_final: 0.5306 (mpp) REVERT: y 230 GLU cc_start: 0.5266 (mm-30) cc_final: 0.4802 (mm-30) REVERT: y 234 LEU cc_start: 0.6536 (mt) cc_final: 0.6102 (mm) REVERT: y 238 GLU cc_start: 0.4828 (mm-30) cc_final: 0.4495 (mm-30) REVERT: y 280 ASP cc_start: 0.7178 (m-30) cc_final: 0.6929 (m-30) REVERT: 5 103 ARG cc_start: 0.5004 (tpp80) cc_final: 0.4652 (mtt-85) REVERT: 5 116 THR cc_start: 0.6904 (m) cc_final: 0.6462 (p) REVERT: 5 123 GLU cc_start: 0.4742 (tp30) cc_final: 0.4412 (pt0) REVERT: 5 175 ARG cc_start: 0.6723 (ttt-90) cc_final: 0.6457 (ttp-110) REVERT: 5 179 PHE cc_start: 0.5696 (m-10) cc_final: 0.5283 (m-80) REVERT: 6 189 ASP cc_start: 0.5701 (m-30) cc_final: 0.5311 (m-30) REVERT: 6 215 ARG cc_start: 0.6963 (mtp180) cc_final: 0.6438 (ttp-170) REVERT: 6 219 GLU cc_start: 0.6941 (tt0) cc_final: 0.5995 (tp30) REVERT: 4 4 GLN cc_start: 0.4548 (OUTLIER) cc_final: 0.4200 (tp-100) REVERT: 4 273 GLU cc_start: 0.6801 (tp30) cc_final: 0.6366 (tp30) REVERT: 4 274 ASP cc_start: 0.7000 (m-30) cc_final: 0.6680 (t0) REVERT: 4 276 ASP cc_start: 0.5010 (m-30) cc_final: 0.4296 (p0) REVERT: 8 28 ASP cc_start: 0.4646 (t0) cc_final: 0.4391 (t0) REVERT: 8 123 GLU cc_start: 0.5055 (pt0) cc_final: 0.4258 (pm20) REVERT: 8 124 ILE cc_start: 0.5361 (mm) cc_final: 0.5067 (mt) REVERT: 9 4 GLN cc_start: 0.3628 (OUTLIER) cc_final: 0.2343 (mt0) REVERT: 9 162 THR cc_start: 0.5884 (m) cc_final: 0.5629 (t) REVERT: 9 211 MET cc_start: 0.4322 (mtp) cc_final: 0.3933 (mmt) REVERT: 9 215 ARG cc_start: 0.4885 (mmm-85) cc_final: 0.4662 (ptp-110) REVERT: 9 219 GLU cc_start: 0.7108 (tt0) cc_final: 0.6886 (tm-30) REVERT: 9 237 LYS cc_start: 0.5539 (mttt) cc_final: 0.5174 (mmpt) REVERT: 9 241 MET cc_start: 0.3844 (mmm) cc_final: 0.3586 (mmt) REVERT: 7 170 ASN cc_start: 0.5624 (t0) cc_final: 0.5179 (t0) REVERT: 7 266 THR cc_start: 0.4483 (m) cc_final: 0.3997 (t) REVERT: 7 269 GLU cc_start: 0.5138 (tt0) cc_final: 0.4708 (pt0) REVERT: 7 273 GLU cc_start: 0.6243 (tt0) cc_final: 0.5983 (pt0) outliers start: 76 outliers final: 11 residues processed: 601 average time/residue: 1.4302 time to fit residues: 981.1232 Evaluate side-chains 298 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 282 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 167 ILE Chi-restraints excluded: chain 0 residue 206 THR Chi-restraints excluded: chain 0 residue 259 GLU Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 272 ILE Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 145 VAL Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 41 CYS Chi-restraints excluded: chain 4 residue 258 VAL Chi-restraints excluded: chain 8 residue 72 ASP Chi-restraints excluded: chain 9 residue 4 GLN Chi-restraints excluded: chain 9 residue 11 ARG Chi-restraints excluded: chain 9 residue 157 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 40.0000 chunk 70 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 247 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 170 ASN z 252 ASN 0 22 HIS y 22 HIS y 105 HIS y 165 GLN y 193 ASN 5 34 HIS 5 193 ASN 5 284 GLN 6 70 ASN 6 193 ASN 4 4 GLN 4 25 GLN 4 158 HIS ** 4 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 34 HIS 9 170 ASN 9 256 HIS 7 22 HIS ** 7 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 150 GLN 7 260 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2751 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 26605 Z= 0.294 Angle : 0.813 11.174 37004 Z= 0.409 Chirality : 0.042 0.224 4397 Planarity : 0.006 0.072 3941 Dihedral : 22.446 171.963 6531 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.65 % Favored : 96.19 % Rotamer: Outliers : 5.43 % Allowed : 18.06 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.16), residues: 2546 helix: 1.42 (0.11), residues: 1768 sheet: None (None), residues: 0 loop : -0.39 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 7 217 HIS 0.010 0.002 HIS 4 158 PHE 0.020 0.003 PHE 8 275 TYR 0.026 0.003 TYR z 278 ARG 0.020 0.001 ARG 5 11 *********************** 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 708 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 583 time to evaluate : 2.612 Fit side-chains revert: symmetry clash REVERT: z 21 ARG cc_start: 0.6152 (mmt-90) cc_final: 0.5000 (mmm-85) REVERT: z 99 ARG cc_start: 0.4971 (mtt180) cc_final: 0.4644 (mtm-85) REVERT: z 113 GLU cc_start: 0.7835 (pt0) cc_final: 0.7524 (tt0) REVERT: z 154 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6692 (mt) REVERT: z 160 LYS cc_start: 0.4838 (tptt) cc_final: 0.4531 (tppt) REVERT: z 166 ARG cc_start: 0.6588 (mtt180) cc_final: 0.6123 (mtm180) REVERT: z 169 GLU cc_start: 0.5087 (tt0) cc_final: 0.4748 (tt0) REVERT: z 178 MET cc_start: 0.2325 (OUTLIER) cc_final: 0.1812 (ptp) REVERT: z 218 GLU cc_start: 0.5597 (tp30) cc_final: 0.5077 (tt0) REVERT: z 259 GLU cc_start: 0.5615 (OUTLIER) cc_final: 0.5387 (pt0) REVERT: 0 1 MET cc_start: 0.4240 (mmm) cc_final: 0.3923 (mmm) REVERT: 0 28 ASP cc_start: 0.4926 (t0) cc_final: 0.4541 (t70) REVERT: 0 121 ASP cc_start: 0.5466 (OUTLIER) cc_final: 0.4949 (m-30) REVERT: 0 127 ARG cc_start: 0.5962 (ttt180) cc_final: 0.5143 (ttm-80) REVERT: 0 135 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6538 (mt) REVERT: 0 150 GLN cc_start: 0.6506 (mt0) cc_final: 0.5719 (mm-40) REVERT: 0 170 ASN cc_start: 0.5980 (OUTLIER) cc_final: 0.5571 (t0) REVERT: 0 175 ARG cc_start: 0.6316 (ttp-170) cc_final: 0.5553 (ttm-80) REVERT: 0 194 THR cc_start: 0.4786 (OUTLIER) cc_final: 0.4558 (p) REVERT: 0 218 GLU cc_start: 0.4822 (tp30) cc_final: 0.4530 (mt-10) REVERT: 0 219 GLU cc_start: 0.5872 (tt0) cc_final: 0.5644 (tt0) REVERT: 0 273 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7061 (tp30) REVERT: 0 274 ASP cc_start: 0.6696 (m-30) cc_final: 0.6401 (m-30) REVERT: y 1 MET cc_start: 0.1955 (mtm) cc_final: 0.0951 (mtt) REVERT: y 32 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7020 (mp0) REVERT: y 55 GLU cc_start: 0.5311 (OUTLIER) cc_final: 0.4970 (mt-10) REVERT: y 64 ARG cc_start: 0.5824 (tmm160) cc_final: 0.5547 (tpm170) REVERT: y 165 GLN cc_start: 0.5567 (OUTLIER) cc_final: 0.5117 (pp30) REVERT: y 175 ARG cc_start: 0.6645 (ttm170) cc_final: 0.6289 (ttt-90) REVERT: y 233 LYS cc_start: 0.6599 (mttp) cc_final: 0.6299 (mttp) REVERT: y 234 LEU cc_start: 0.7176 (mt) cc_final: 0.6948 (mp) REVERT: y 237 LYS cc_start: 0.5784 (ptmt) cc_final: 0.5186 (ptpt) REVERT: y 265 ASP cc_start: 0.4907 (t0) cc_final: 0.4345 (m-30) REVERT: y 269 GLU cc_start: 0.6425 (tp30) cc_final: 0.6003 (tp30) REVERT: y 276 ASP cc_start: 0.7215 (m-30) cc_final: 0.6916 (p0) REVERT: y 280 ASP cc_start: 0.6848 (m-30) cc_final: 0.6432 (m-30) REVERT: 5 43 GLU cc_start: 0.6277 (tt0) cc_final: 0.5726 (tp30) REVERT: 5 115 ASP cc_start: 0.6026 (t0) cc_final: 0.5738 (t0) REVERT: 5 187 ASN cc_start: 0.6831 (OUTLIER) cc_final: 0.5732 (t0) REVERT: 5 218 GLU cc_start: 0.5611 (mt-10) cc_final: 0.5146 (mt-10) REVERT: 5 241 MET cc_start: 0.7112 (mtt) cc_final: 0.6900 (mtm) REVERT: 5 282 PHE cc_start: 0.5795 (m-80) cc_final: 0.5501 (m-80) REVERT: 6 1 MET cc_start: 0.4294 (OUTLIER) cc_final: 0.3565 (tmt) REVERT: 6 63 TYR cc_start: 0.7417 (t80) cc_final: 0.7052 (t80) REVERT: 6 67 ARG cc_start: 0.6367 (ptp90) cc_final: 0.5723 (mtm110) REVERT: 6 98 ASP cc_start: 0.6334 (m-30) cc_final: 0.6034 (t0) REVERT: 6 166 ARG cc_start: 0.5239 (tpp80) cc_final: 0.4980 (mtm180) REVERT: 6 215 ARG cc_start: 0.7491 (mtp180) cc_final: 0.6982 (mpp80) REVERT: 6 219 GLU cc_start: 0.7174 (tt0) cc_final: 0.6408 (tp30) REVERT: 4 4 GLN cc_start: 0.5135 (OUTLIER) cc_final: 0.4034 (tp40) REVERT: 4 22 HIS cc_start: 0.5224 (m90) cc_final: 0.4994 (m170) REVERT: 4 40 LYS cc_start: 0.3325 (ttmt) cc_final: 0.2978 (ttpp) REVERT: 4 81 GLU cc_start: 0.6419 (mm-30) cc_final: 0.6185 (mp0) REVERT: 4 113 GLU cc_start: 0.5506 (mt-10) cc_final: 0.4807 (mp0) REVERT: 4 163 GLU cc_start: 0.6310 (tp30) cc_final: 0.4992 (mt-10) REVERT: 4 165 GLN cc_start: 0.6410 (tp40) cc_final: 0.5350 (pt0) REVERT: 4 169 GLU cc_start: 0.6816 (tp30) cc_final: 0.5999 (mt-10) REVERT: 4 191 HIS cc_start: 0.6016 (m-70) cc_final: 0.5678 (p90) REVERT: 4 219 GLU cc_start: 0.6283 (tm-30) cc_final: 0.5956 (tt0) REVERT: 4 229 GLN cc_start: 0.5610 (mt0) cc_final: 0.5132 (pt0) REVERT: 4 237 LYS cc_start: 0.4980 (tptp) cc_final: 0.4751 (ttmt) REVERT: 4 269 GLU cc_start: 0.6315 (mt-10) cc_final: 0.6031 (mt-10) REVERT: 8 21 ARG cc_start: 0.5348 (ttp-110) cc_final: 0.4959 (mmt-90) REVERT: 8 73 LEU cc_start: 0.5368 (mp) cc_final: 0.5111 (mt) REVERT: 8 111 ARG cc_start: 0.5457 (mmt180) cc_final: 0.5117 (mtm110) REVERT: 8 119 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6406 (mtt-85) REVERT: 8 123 GLU cc_start: 0.6901 (pt0) cc_final: 0.6331 (pm20) REVERT: 8 172 GLU cc_start: 0.6165 (tp30) cc_final: 0.5662 (tp30) REVERT: 8 191 HIS cc_start: 0.5659 (t70) cc_final: 0.5303 (t-170) REVERT: 8 237 LYS cc_start: 0.6997 (mttt) cc_final: 0.6758 (pttp) REVERT: 8 241 MET cc_start: 0.7149 (mtp) cc_final: 0.6729 (mtt) REVERT: 8 263 SER cc_start: 0.6534 (OUTLIER) cc_final: 0.6256 (p) REVERT: 9 28 ASP cc_start: 0.6596 (t0) cc_final: 0.6293 (t0) REVERT: 9 47 HIS cc_start: 0.4616 (OUTLIER) cc_final: 0.4304 (t-170) REVERT: 9 123 GLU cc_start: 0.7003 (tp30) cc_final: 0.6284 (mp0) REVERT: 9 161 ASP cc_start: 0.6806 (t0) cc_final: 0.6464 (p0) REVERT: 9 169 GLU cc_start: 0.6784 (tt0) cc_final: 0.6365 (pt0) REVERT: 9 211 MET cc_start: 0.5931 (mtp) cc_final: 0.5697 (mtm) REVERT: 9 215 ARG cc_start: 0.6471 (mmm-85) cc_final: 0.5794 (mpt-90) REVERT: 9 217 TRP cc_start: 0.5793 (t-100) cc_final: 0.5589 (t-100) REVERT: 9 219 GLU cc_start: 0.6910 (tt0) cc_final: 0.6268 (tm-30) REVERT: 9 241 MET cc_start: 0.5431 (mmm) cc_final: 0.4747 (mmm) REVERT: 7 46 LEU cc_start: 0.5748 (mt) cc_final: 0.5393 (mt) REVERT: 7 57 MET cc_start: 0.5720 (mmm) cc_final: 0.5503 (mmt) REVERT: 7 165 GLN cc_start: 0.6518 (tp40) cc_final: 0.5268 (mt0) REVERT: 7 166 ARG cc_start: 0.5807 (ttp80) cc_final: 0.5572 (ttp80) REVERT: 7 170 ASN cc_start: 0.6280 (t0) cc_final: 0.5843 (t0) REVERT: 7 218 GLU cc_start: 0.5412 (tp30) cc_final: 0.4661 (mt-10) REVERT: 7 219 GLU cc_start: 0.5396 (tp30) cc_final: 0.5164 (tp30) REVERT: 7 222 ARG cc_start: 0.6177 (ttm-80) cc_final: 0.5971 (ttp-110) REVERT: 7 229 GLN cc_start: 0.6207 (mt0) cc_final: 0.5760 (mt0) REVERT: 7 230 GLU cc_start: 0.6262 (tp30) cc_final: 0.6029 (tp30) REVERT: 7 237 LYS cc_start: 0.5646 (tptp) cc_final: 0.5092 (ttpt) REVERT: 7 258 VAL cc_start: 0.5873 (OUTLIER) cc_final: 0.5516 (t) REVERT: 7 259 GLU cc_start: 0.5577 (pt0) cc_final: 0.5111 (pp20) REVERT: 7 260 ASN cc_start: 0.6349 (t0) cc_final: 0.6115 (t0) REVERT: 7 265 ASP cc_start: 0.6840 (m-30) cc_final: 0.6479 (m-30) REVERT: 7 269 GLU cc_start: 0.5613 (tt0) cc_final: 0.5360 (mt-10) outliers start: 125 outliers final: 22 residues processed: 658 average time/residue: 1.5770 time to fit residues: 1170.7150 Evaluate side-chains 441 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 402 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 154 ILE Chi-restraints excluded: chain z residue 161 ASP 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 z residue 259 GLU 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 194 THR Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 55 GLU Chi-restraints excluded: chain y residue 165 GLN Chi-restraints excluded: chain y residue 266 THR 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 24 THR Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 41 CYS Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 119 ARG Chi-restraints excluded: chain 8 residue 263 SER Chi-restraints excluded: chain 9 residue 47 HIS Chi-restraints excluded: chain 9 residue 181 VAL Chi-restraints excluded: chain 9 residue 186 LEU Chi-restraints excluded: chain 7 residue 76 VAL Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 258 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 268 optimal weight: 50.0000 chunk 221 optimal weight: 0.3980 chunk 246 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 199 optimal weight: 7.9990 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 70 ASN z 170 ASN 0 22 HIS 0 170 ASN 5 69 HIS 4 158 HIS ** 4 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 22 HIS 8 177 ASN 9 18 ASN 9 25 GLN ** 7 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 193 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2918 moved from start: 0.9279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26605 Z= 0.222 Angle : 0.596 7.336 37004 Z= 0.307 Chirality : 0.034 0.165 4397 Planarity : 0.004 0.053 3941 Dihedral : 22.116 173.490 6508 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.42 % Favored : 96.43 % Rotamer: Outliers : 5.73 % Allowed : 22.58 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.16), residues: 2546 helix: 2.26 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -0.33 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 7 217 HIS 0.007 0.001 HIS 7 158 PHE 0.023 0.002 PHE 6 114 TYR 0.022 0.002 TYR 4 205 ARG 0.010 0.001 ARG 4 45 *********************** 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 614 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 482 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: z 21 ARG cc_start: 0.6329 (mmt-90) cc_final: 0.6049 (mmp80) REVERT: z 63 TYR cc_start: 0.7615 (t80) cc_final: 0.7312 (t80) REVERT: z 70 ASN cc_start: 0.6947 (t0) cc_final: 0.6527 (t160) REVERT: z 119 ARG cc_start: 0.6528 (mtt90) cc_final: 0.6224 (mtm-85) REVERT: z 124 ILE cc_start: 0.6084 (mm) cc_final: 0.5860 (mt) REVERT: z 154 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6904 (mt) REVERT: z 160 LYS cc_start: 0.5039 (tptt) cc_final: 0.4580 (tppt) REVERT: z 166 ARG cc_start: 0.6773 (mtt180) cc_final: 0.6461 (mtm180) REVERT: z 176 ARG cc_start: 0.5473 (OUTLIER) cc_final: 0.5077 (mtp85) REVERT: z 193 ASN cc_start: 0.6236 (m-40) cc_final: 0.6013 (m110) REVERT: z 218 GLU cc_start: 0.6081 (tp30) cc_final: 0.5778 (tt0) REVERT: z 219 GLU cc_start: 0.6694 (tt0) cc_final: 0.6074 (tp30) REVERT: z 259 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5490 (pt0) REVERT: 0 121 ASP cc_start: 0.6040 (OUTLIER) cc_final: 0.5708 (m-30) REVERT: 0 126 GLU cc_start: 0.6068 (mm-30) cc_final: 0.5835 (mt-10) REVERT: 0 127 ARG cc_start: 0.5808 (ttt180) cc_final: 0.5246 (ttm-80) REVERT: 0 142 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: 0 175 ARG cc_start: 0.6657 (ttp-170) cc_final: 0.5914 (ttm-80) REVERT: 0 194 THR cc_start: 0.4955 (OUTLIER) cc_final: 0.4711 (p) REVERT: 0 218 GLU cc_start: 0.5383 (tp30) cc_final: 0.4859 (mt-10) REVERT: 0 273 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7401 (tp30) REVERT: y 1 MET cc_start: 0.0962 (mtm) cc_final: 0.0230 (mtm) REVERT: y 32 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7369 (mp0) REVERT: y 62 TYR cc_start: 0.6628 (t80) cc_final: 0.5994 (t80) REVERT: y 92 TYR cc_start: 0.7703 (m-80) cc_final: 0.7430 (m-80) REVERT: y 123 GLU cc_start: 0.6586 (tp30) cc_final: 0.6181 (tt0) REVERT: y 127 ARG cc_start: 0.6199 (mtm110) cc_final: 0.5856 (mtm-85) REVERT: y 143 THR cc_start: 0.6786 (m) cc_final: 0.6537 (t) REVERT: y 175 ARG cc_start: 0.6541 (ttm170) cc_final: 0.6144 (ttt-90) REVERT: y 233 LYS cc_start: 0.6670 (mttp) cc_final: 0.6439 (mttp) REVERT: y 237 LYS cc_start: 0.6362 (ptmt) cc_final: 0.5984 (mtmt) REVERT: y 259 GLU cc_start: 0.5923 (tt0) cc_final: 0.5384 (pm20) REVERT: y 269 GLU cc_start: 0.6465 (tp30) cc_final: 0.6064 (mp0) REVERT: y 276 ASP cc_start: 0.7068 (m-30) cc_final: 0.6844 (p0) REVERT: y 280 ASP cc_start: 0.6884 (m-30) cc_final: 0.6441 (m-30) REVERT: 5 43 GLU cc_start: 0.7246 (tt0) cc_final: 0.6325 (tp30) REVERT: 5 65 GLU cc_start: 0.5624 (OUTLIER) cc_final: 0.5414 (mm-30) REVERT: 5 69 HIS cc_start: 0.5818 (OUTLIER) cc_final: 0.5552 (m-70) REVERT: 5 98 ASP cc_start: 0.4941 (p0) cc_final: 0.4255 (p0) REVERT: 5 103 ARG cc_start: 0.6315 (tpp80) cc_final: 0.5664 (ptp-170) REVERT: 5 115 ASP cc_start: 0.6244 (t0) cc_final: 0.5895 (t0) REVERT: 5 187 ASN cc_start: 0.6872 (m110) cc_final: 0.5922 (t0) REVERT: 5 191 HIS cc_start: 0.6413 (t-90) cc_final: 0.6148 (t70) REVERT: 5 194 THR cc_start: 0.5838 (OUTLIER) cc_final: 0.5580 (p) REVERT: 6 39 LYS cc_start: 0.6651 (tmtt) cc_final: 0.6447 (tmtm) REVERT: 6 63 TYR cc_start: 0.7535 (t80) cc_final: 0.7009 (t80) REVERT: 6 98 ASP cc_start: 0.6813 (m-30) cc_final: 0.5846 (t70) REVERT: 6 166 ARG cc_start: 0.5547 (tpp80) cc_final: 0.5237 (mtm180) REVERT: 6 175 ARG cc_start: 0.5623 (ttm170) cc_final: 0.5122 (ttt-90) REVERT: 6 211 MET cc_start: 0.6179 (mtm) cc_final: 0.5873 (mtm) REVERT: 6 215 ARG cc_start: 0.7560 (mtp180) cc_final: 0.6897 (mpp80) REVERT: 6 218 GLU cc_start: 0.6354 (tp30) cc_final: 0.6091 (mm-30) REVERT: 6 219 GLU cc_start: 0.6695 (tt0) cc_final: 0.6225 (mp0) REVERT: 6 240 ARG cc_start: 0.5555 (ttm-80) cc_final: 0.5304 (ttt-90) REVERT: 6 273 GLU cc_start: 0.7169 (tp30) cc_final: 0.6941 (tm-30) REVERT: 6 281 SER cc_start: 0.7448 (t) cc_final: 0.6879 (p) REVERT: 4 4 GLN cc_start: 0.4951 (OUTLIER) cc_final: 0.4271 (tp40) REVERT: 4 79 GLU cc_start: 0.6825 (tt0) cc_final: 0.5810 (tp30) REVERT: 4 113 GLU cc_start: 0.5701 (mt-10) cc_final: 0.5003 (mp0) REVERT: 4 163 GLU cc_start: 0.6433 (tp30) cc_final: 0.5861 (tp30) REVERT: 4 165 GLN cc_start: 0.6383 (tp40) cc_final: 0.5509 (pt0) REVERT: 4 169 GLU cc_start: 0.6713 (tp30) cc_final: 0.6214 (mt-10) REVERT: 4 176 ARG cc_start: 0.5613 (tpp-160) cc_final: 0.4769 (tpp80) REVERT: 4 191 HIS cc_start: 0.6233 (m-70) cc_final: 0.5741 (p90) REVERT: 4 219 GLU cc_start: 0.6450 (tm-30) cc_final: 0.6236 (tt0) REVERT: 4 222 ARG cc_start: 0.5968 (mtm-85) cc_final: 0.5427 (ptp90) REVERT: 4 230 GLU cc_start: 0.6124 (tt0) cc_final: 0.5902 (tp30) REVERT: 8 36 LYS cc_start: 0.6378 (mptt) cc_final: 0.5980 (mttt) REVERT: 8 37 ILE cc_start: 0.5540 (mm) cc_final: 0.5274 (mm) REVERT: 8 40 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5557 (ttmp) REVERT: 8 48 ARG cc_start: 0.6237 (mtm180) cc_final: 0.5848 (ttp80) REVERT: 8 144 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6210 (pp) REVERT: 9 28 ASP cc_start: 0.6902 (t0) cc_final: 0.6411 (t0) REVERT: 9 47 HIS cc_start: 0.5753 (OUTLIER) cc_final: 0.5241 (t-170) REVERT: 9 123 GLU cc_start: 0.6683 (tp30) cc_final: 0.5817 (mt-10) REVERT: 9 161 ASP cc_start: 0.6507 (t0) cc_final: 0.6259 (p0) REVERT: 9 163 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5924 (tp30) REVERT: 9 169 GLU cc_start: 0.7369 (tt0) cc_final: 0.6863 (pt0) REVERT: 9 176 ARG cc_start: 0.5924 (OUTLIER) cc_final: 0.4907 (tpm-80) REVERT: 9 182 LYS cc_start: 0.5533 (mtmm) cc_final: 0.5189 (pttm) REVERT: 9 211 MET cc_start: 0.6555 (mtp) cc_final: 0.6264 (mtm) REVERT: 9 215 ARG cc_start: 0.6542 (mmm-85) cc_final: 0.5911 (mpt-90) REVERT: 9 219 GLU cc_start: 0.6592 (tt0) cc_final: 0.6088 (tm-30) REVERT: 9 233 LYS cc_start: 0.5286 (mttt) cc_final: 0.4920 (mtpm) REVERT: 9 241 MET cc_start: 0.6319 (mmm) cc_final: 0.6111 (mmt) REVERT: 7 18 ASN cc_start: 0.4029 (m-40) cc_final: 0.3738 (m-40) REVERT: 7 39 LYS cc_start: 0.5655 (OUTLIER) cc_final: 0.5357 (mmtp) REVERT: 7 141 ARG cc_start: 0.5776 (OUTLIER) cc_final: 0.5444 (mtm-85) REVERT: 7 165 GLN cc_start: 0.6539 (tp40) cc_final: 0.5382 (mt0) REVERT: 7 218 GLU cc_start: 0.5804 (tp30) cc_final: 0.4986 (mt-10) REVERT: 7 222 ARG cc_start: 0.6374 (ttm-80) cc_final: 0.6018 (mtm180) REVERT: 7 229 GLN cc_start: 0.6216 (mt0) cc_final: 0.5656 (mt0) outliers start: 132 outliers final: 41 residues processed: 564 average time/residue: 1.5781 time to fit residues: 1001.4500 Evaluate side-chains 455 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 397 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 41 CYS Chi-restraints excluded: chain z residue 46 LEU Chi-restraints excluded: chain z residue 76 VAL Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 154 ILE Chi-restraints excluded: chain z residue 161 ASP Chi-restraints excluded: chain z residue 176 ARG Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 216 SER Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 244 SER Chi-restraints excluded: chain z residue 259 GLU Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 121 ASP Chi-restraints excluded: chain 0 residue 142 GLU Chi-restraints excluded: chain 0 residue 194 THR Chi-restraints excluded: chain 0 residue 241 MET Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 110 ASP Chi-restraints excluded: chain 5 residue 30 ASP Chi-restraints excluded: chain 5 residue 65 GLU Chi-restraints excluded: chain 5 residue 69 HIS Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 134 ILE Chi-restraints excluded: chain 5 residue 159 LEU Chi-restraints excluded: chain 5 residue 194 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 41 CYS Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 116 THR Chi-restraints excluded: chain 8 residue 144 LEU Chi-restraints excluded: chain 8 residue 159 LEU Chi-restraints excluded: chain 8 residue 281 SER Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 47 HIS Chi-restraints excluded: chain 9 residue 50 THR Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 176 ARG Chi-restraints excluded: chain 9 residue 184 LEU Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 39 LYS Chi-restraints excluded: chain 7 residue 140 VAL Chi-restraints excluded: chain 7 residue 141 ARG Chi-restraints excluded: chain 7 residue 146 THR Chi-restraints excluded: chain 7 residue 241 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 2.9990 chunk 186 optimal weight: 30.0000 chunk 128 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 249 optimal weight: 0.5980 chunk 263 optimal weight: 50.0000 chunk 130 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 0 229 GLN 5 69 HIS 4 34 HIS ** 4 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 8 4 GLN 9 18 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2981 moved from start: 1.0447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26605 Z= 0.205 Angle : 0.574 8.025 37004 Z= 0.295 Chirality : 0.034 0.168 4397 Planarity : 0.004 0.046 3941 Dihedral : 21.921 174.084 6508 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.65 % Favored : 96.19 % Rotamer: Outliers : 5.60 % Allowed : 24.84 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.16), residues: 2546 helix: 2.58 (0.12), residues: 1774 sheet: None (None), residues: 0 loop : -0.31 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 5 217 HIS 0.022 0.001 HIS 5 69 PHE 0.034 0.002 PHE 5 68 TYR 0.020 0.002 TYR z 94 ARG 0.013 0.001 ARG 7 240 *********************** 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 554 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 425 time to evaluate : 2.667 Fit side-chains revert: symmetry clash REVERT: z 21 ARG cc_start: 0.6403 (mmt-90) cc_final: 0.6112 (mmp80) REVERT: z 44 LYS cc_start: 0.6192 (ttmt) cc_final: 0.5696 (mmmt) REVERT: z 50 THR cc_start: 0.6841 (m) cc_final: 0.6555 (p) REVERT: z 63 TYR cc_start: 0.7618 (t80) cc_final: 0.7351 (t80) REVERT: z 70 ASN cc_start: 0.6874 (t0) cc_final: 0.6653 (t160) REVERT: z 119 ARG cc_start: 0.6954 (mtt90) cc_final: 0.6421 (mtm-85) REVERT: z 143 THR cc_start: 0.6295 (p) cc_final: 0.6034 (m) REVERT: z 160 LYS cc_start: 0.4832 (tptt) cc_final: 0.4494 (tppt) REVERT: z 166 ARG cc_start: 0.6117 (mtt180) cc_final: 0.5735 (mtm180) REVERT: z 176 ARG cc_start: 0.5281 (tpp-160) cc_final: 0.4812 (mtp85) REVERT: z 193 ASN cc_start: 0.6353 (m-40) cc_final: 0.6110 (m110) REVERT: z 218 GLU cc_start: 0.6363 (tp30) cc_final: 0.6050 (tt0) REVERT: z 219 GLU cc_start: 0.5893 (tt0) cc_final: 0.5337 (tp30) REVERT: 0 39 LYS cc_start: 0.6325 (tppp) cc_final: 0.5494 (ttmt) REVERT: 0 127 ARG cc_start: 0.5445 (ttt180) cc_final: 0.4958 (ttm-80) REVERT: 0 175 ARG cc_start: 0.6602 (ttp-170) cc_final: 0.5905 (ttm-80) REVERT: 0 194 THR cc_start: 0.4979 (OUTLIER) cc_final: 0.4635 (t) REVERT: 0 218 GLU cc_start: 0.5433 (tp30) cc_final: 0.4921 (mt-10) REVERT: 0 273 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: y 62 TYR cc_start: 0.6569 (t80) cc_final: 0.6087 (t80) REVERT: y 92 TYR cc_start: 0.7501 (m-80) cc_final: 0.7100 (m-80) REVERT: y 123 GLU cc_start: 0.6380 (tp30) cc_final: 0.5941 (mt-10) REVERT: y 127 ARG cc_start: 0.6389 (mtm110) cc_final: 0.6043 (mtp180) REVERT: y 143 THR cc_start: 0.6906 (m) cc_final: 0.6599 (t) REVERT: y 161 ASP cc_start: 0.4872 (t0) cc_final: 0.4525 (t0) REVERT: y 219 GLU cc_start: 0.6715 (tp30) cc_final: 0.6354 (tp30) REVERT: y 237 LYS cc_start: 0.6381 (ptmt) cc_final: 0.6081 (mtmt) REVERT: y 269 GLU cc_start: 0.6657 (tp30) cc_final: 0.6412 (mp0) REVERT: y 276 ASP cc_start: 0.7051 (m-30) cc_final: 0.6839 (p0) REVERT: y 280 ASP cc_start: 0.6708 (m-30) cc_final: 0.6381 (m-30) REVERT: 5 43 GLU cc_start: 0.7088 (tt0) cc_final: 0.6352 (tp30) REVERT: 5 69 HIS cc_start: 0.6601 (OUTLIER) cc_final: 0.6376 (m-70) REVERT: 5 94 TYR cc_start: 0.3344 (t80) cc_final: 0.3120 (t80) REVERT: 5 103 ARG cc_start: 0.6537 (tpp80) cc_final: 0.5998 (ttm170) REVERT: 5 104 ASP cc_start: 0.6216 (m-30) cc_final: 0.5831 (m-30) REVERT: 5 166 ARG cc_start: 0.4754 (OUTLIER) cc_final: 0.4529 (mtm-85) REVERT: 5 187 ASN cc_start: 0.7060 (m110) cc_final: 0.6572 (t0) REVERT: 6 63 TYR cc_start: 0.7469 (t80) cc_final: 0.6965 (t80) REVERT: 6 150 GLN cc_start: 0.4713 (mm-40) cc_final: 0.4301 (tt0) REVERT: 6 161 ASP cc_start: 0.6824 (m-30) cc_final: 0.6486 (m-30) REVERT: 6 166 ARG cc_start: 0.5808 (tpp80) cc_final: 0.5535 (mmm-85) REVERT: 6 175 ARG cc_start: 0.5875 (ttm170) cc_final: 0.5236 (ttt-90) REVERT: 6 178 MET cc_start: 0.6553 (ptp) cc_final: 0.6119 (ptm) REVERT: 6 211 MET cc_start: 0.6346 (mtm) cc_final: 0.6082 (mtp) REVERT: 6 215 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7056 (mpp80) REVERT: 6 218 GLU cc_start: 0.6381 (tp30) cc_final: 0.6084 (mm-30) REVERT: 6 219 GLU cc_start: 0.6624 (tt0) cc_final: 0.6099 (mp0) REVERT: 6 240 ARG cc_start: 0.5898 (ttm-80) cc_final: 0.5664 (ttp80) REVERT: 6 281 SER cc_start: 0.6886 (t) cc_final: 0.6404 (p) REVERT: 4 4 GLN cc_start: 0.4917 (OUTLIER) cc_final: 0.4166 (tp40) REVERT: 4 25 GLN cc_start: 0.5977 (pt0) cc_final: 0.5578 (pm20) REVERT: 4 79 GLU cc_start: 0.6580 (tt0) cc_final: 0.5726 (tp30) REVERT: 4 113 GLU cc_start: 0.5839 (mt-10) cc_final: 0.5213 (mp0) REVERT: 4 115 ASP cc_start: 0.5854 (OUTLIER) cc_final: 0.5589 (p0) REVERT: 4 123 GLU cc_start: 0.4816 (OUTLIER) cc_final: 0.4501 (tm-30) REVERT: 4 163 GLU cc_start: 0.5850 (tp30) cc_final: 0.5500 (tp30) REVERT: 4 165 GLN cc_start: 0.6662 (tp40) cc_final: 0.5774 (pt0) REVERT: 4 169 GLU cc_start: 0.6474 (tp30) cc_final: 0.6126 (mt-10) REVERT: 4 176 ARG cc_start: 0.6094 (tpp-160) cc_final: 0.5295 (tpp80) REVERT: 4 191 HIS cc_start: 0.6377 (m-70) cc_final: 0.5703 (p90) REVERT: 4 278 TYR cc_start: 0.7429 (p90) cc_final: 0.7223 (p90) REVERT: 8 25 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6412 (mp10) REVERT: 8 36 LYS cc_start: 0.6312 (mptt) cc_final: 0.6010 (mttt) REVERT: 8 40 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6076 (ttmp) REVERT: 8 144 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6041 (pp) REVERT: 8 233 LYS cc_start: 0.7065 (mttp) cc_final: 0.6799 (tttp) REVERT: 8 269 GLU cc_start: 0.5443 (mt-10) cc_final: 0.5120 (mp0) REVERT: 9 28 ASP cc_start: 0.6803 (t0) cc_final: 0.6480 (t0) REVERT: 9 48 ARG cc_start: 0.6223 (pmt-80) cc_final: 0.5983 (pmt-80) REVERT: 9 123 GLU cc_start: 0.6468 (tp30) cc_final: 0.5727 (mt-10) REVERT: 9 161 ASP cc_start: 0.6676 (t0) cc_final: 0.6342 (p0) REVERT: 9 163 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5849 (tt0) REVERT: 9 169 GLU cc_start: 0.7418 (tt0) cc_final: 0.6888 (pt0) REVERT: 9 176 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5596 (tpm-80) REVERT: 9 211 MET cc_start: 0.6853 (mtp) cc_final: 0.6618 (mtm) REVERT: 9 215 ARG cc_start: 0.6736 (mmm-85) cc_final: 0.6048 (mpt-90) REVERT: 9 219 GLU cc_start: 0.6749 (tt0) cc_final: 0.6264 (tm-30) REVERT: 9 233 LYS cc_start: 0.4824 (mttt) cc_final: 0.4614 (mtpm) REVERT: 9 241 MET cc_start: 0.6421 (mmm) cc_final: 0.6180 (mmt) REVERT: 9 244 SER cc_start: 0.5397 (m) cc_final: 0.4971 (p) REVERT: 7 39 LYS cc_start: 0.5575 (OUTLIER) cc_final: 0.5220 (mmtp) REVERT: 7 98 ASP cc_start: 0.6265 (p0) cc_final: 0.5884 (p0) REVERT: 7 141 ARG cc_start: 0.5724 (tpp-160) cc_final: 0.5442 (mtm-85) REVERT: 7 165 GLN cc_start: 0.6634 (tp40) cc_final: 0.5496 (mt0) REVERT: 7 218 GLU cc_start: 0.5715 (tp30) cc_final: 0.4833 (mt-10) REVERT: 7 229 GLN cc_start: 0.5238 (mt0) cc_final: 0.4743 (mt0) REVERT: 7 241 MET cc_start: 0.5726 (mmm) cc_final: 0.5359 (mmt) REVERT: 7 262 ASP cc_start: 0.5743 (m-30) cc_final: 0.5498 (t0) REVERT: 7 277 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6863 (pp) outliers start: 129 outliers final: 57 residues processed: 514 average time/residue: 1.5536 time to fit residues: 900.7608 Evaluate side-chains 442 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 372 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 41 CYS Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 244 SER 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 194 THR Chi-restraints excluded: chain 0 residue 241 MET Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 231 ARG Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 30 ASP Chi-restraints excluded: chain 5 residue 31 LEU Chi-restraints excluded: chain 5 residue 57 MET Chi-restraints excluded: chain 5 residue 69 HIS Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 116 THR Chi-restraints excluded: chain 5 residue 129 LEU 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 5 residue 266 THR 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 6 residue 184 LEU Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 41 CYS Chi-restraints excluded: chain 4 residue 115 ASP Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 123 GLU Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 4 residue 241 MET Chi-restraints excluded: chain 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 30 ASP Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 144 LEU Chi-restraints excluded: chain 8 residue 276 ASP Chi-restraints excluded: chain 8 residue 277 ILE Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 58 LEU Chi-restraints excluded: chain 9 residue 93 THR Chi-restraints excluded: chain 9 residue 108 VAL Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 176 ARG Chi-restraints excluded: chain 9 residue 181 VAL Chi-restraints excluded: chain 9 residue 220 LEU Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 39 LYS 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 162 THR Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 246 ASP 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 219 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 3 optimal weight: 30.0000 chunk 196 optimal weight: 30.0000 chunk 108 optimal weight: 0.0870 chunk 225 optimal weight: 20.0000 chunk 182 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 0 47 HIS 0 229 GLN y 212 ASN 5 69 HIS 5 70 ASN ** 4 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 9 25 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2989 moved from start: 1.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26605 Z= 0.167 Angle : 0.525 7.803 37004 Z= 0.269 Chirality : 0.032 0.178 4397 Planarity : 0.003 0.040 3941 Dihedral : 21.736 169.421 6508 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.77 % Favored : 96.11 % Rotamer: Outliers : 5.17 % Allowed : 26.27 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.16), residues: 2546 helix: 2.81 (0.12), residues: 1773 sheet: None (None), residues: 0 loop : -0.28 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 5 217 HIS 0.009 0.001 HIS 5 69 PHE 0.024 0.001 PHE y 19 TYR 0.013 0.002 TYR 6 94 ARG 0.008 0.001 ARG 5 111 *********************** 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 516 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 397 time to evaluate : 2.499 Fit side-chains REVERT: z 21 ARG cc_start: 0.6435 (mmt-90) cc_final: 0.5754 (mmp80) REVERT: z 44 LYS cc_start: 0.6505 (ttmt) cc_final: 0.6195 (mmmt) REVERT: z 45 ARG cc_start: 0.5703 (tmm-80) cc_final: 0.5299 (ttp-170) REVERT: z 63 TYR cc_start: 0.7656 (t80) cc_final: 0.7308 (t80) REVERT: z 70 ASN cc_start: 0.6704 (t0) cc_final: 0.6432 (t160) REVERT: z 119 ARG cc_start: 0.6980 (mtt90) cc_final: 0.6490 (mtm-85) REVERT: z 166 ARG cc_start: 0.6057 (mtt180) cc_final: 0.5663 (mtm180) REVERT: z 176 ARG cc_start: 0.4920 (tpp-160) cc_final: 0.4444 (mtp85) REVERT: z 193 ASN cc_start: 0.6522 (m-40) cc_final: 0.6295 (m110) REVERT: z 218 GLU cc_start: 0.6391 (tp30) cc_final: 0.6055 (tt0) REVERT: z 219 GLU cc_start: 0.5845 (tt0) cc_final: 0.5285 (tp30) REVERT: z 240 ARG cc_start: 0.6167 (ttp-170) cc_final: 0.5524 (ttp80) REVERT: z 259 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.5118 (pt0) REVERT: 0 4 GLN cc_start: 0.6027 (OUTLIER) cc_final: 0.4925 (mp10) REVERT: 0 39 LYS cc_start: 0.6124 (tppp) cc_final: 0.5354 (ttmm) REVERT: 0 47 HIS cc_start: 0.7033 (t-170) cc_final: 0.6753 (t70) REVERT: 0 99 ARG cc_start: 0.5265 (mtp85) cc_final: 0.5001 (mtm-85) REVERT: 0 127 ARG cc_start: 0.5378 (ttt180) cc_final: 0.4988 (ttm-80) REVERT: 0 166 ARG cc_start: 0.5824 (mtm-85) cc_final: 0.5394 (mtm-85) REVERT: 0 175 ARG cc_start: 0.6632 (ttp-170) cc_final: 0.5912 (ttm-80) REVERT: 0 194 THR cc_start: 0.4911 (OUTLIER) cc_final: 0.4606 (p) REVERT: 0 218 GLU cc_start: 0.5232 (tp30) cc_final: 0.4723 (mt-10) REVERT: 0 222 ARG cc_start: 0.5993 (ttm110) cc_final: 0.5748 (mtm110) REVERT: 0 265 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6404 (m-30) REVERT: 0 273 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7206 (tp30) REVERT: y 62 TYR cc_start: 0.6755 (t80) cc_final: 0.6257 (t80) REVERT: y 92 TYR cc_start: 0.7520 (m-80) cc_final: 0.7137 (m-80) REVERT: y 123 GLU cc_start: 0.6381 (tp30) cc_final: 0.5941 (mt-10) REVERT: y 143 THR cc_start: 0.6896 (m) cc_final: 0.6594 (t) REVERT: y 175 ARG cc_start: 0.6485 (ttp80) cc_final: 0.6132 (ttp-110) REVERT: y 219 GLU cc_start: 0.7004 (tp30) cc_final: 0.6696 (tp30) REVERT: y 269 GLU cc_start: 0.6620 (tp30) cc_final: 0.6334 (mp0) REVERT: y 276 ASP cc_start: 0.7049 (m-30) cc_final: 0.6816 (p0) REVERT: y 280 ASP cc_start: 0.7325 (m-30) cc_final: 0.6989 (m-30) REVERT: 5 43 GLU cc_start: 0.7159 (tt0) cc_final: 0.6509 (tp30) REVERT: 5 69 HIS cc_start: 0.6598 (OUTLIER) cc_final: 0.6317 (m-70) REVERT: 5 94 TYR cc_start: 0.3334 (t80) cc_final: 0.3102 (t80) REVERT: 5 103 ARG cc_start: 0.6678 (tpp80) cc_final: 0.5998 (ptp-170) REVERT: 5 187 ASN cc_start: 0.7191 (m110) cc_final: 0.6398 (t0) REVERT: 5 194 THR cc_start: 0.5619 (OUTLIER) cc_final: 0.5271 (p) REVERT: 6 63 TYR cc_start: 0.7832 (t80) cc_final: 0.7375 (t80) REVERT: 6 150 GLN cc_start: 0.5010 (mm-40) cc_final: 0.4504 (tt0) REVERT: 6 161 ASP cc_start: 0.7070 (m-30) cc_final: 0.6762 (m-30) REVERT: 6 166 ARG cc_start: 0.5773 (ttp80) cc_final: 0.5429 (mmm-85) REVERT: 6 175 ARG cc_start: 0.6069 (ttm170) cc_final: 0.5422 (ttt-90) REVERT: 6 178 MET cc_start: 0.6582 (ptp) cc_final: 0.6122 (ptm) REVERT: 6 211 MET cc_start: 0.6387 (mtm) cc_final: 0.6124 (mtp) REVERT: 6 215 ARG cc_start: 0.7680 (mtp180) cc_final: 0.6816 (tpp80) REVERT: 6 218 GLU cc_start: 0.6258 (tp30) cc_final: 0.6032 (mm-30) REVERT: 6 219 GLU cc_start: 0.6671 (tt0) cc_final: 0.6146 (mp0) REVERT: 6 240 ARG cc_start: 0.5852 (ttm-80) cc_final: 0.5638 (ttp80) REVERT: 6 273 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6784 (tm-30) REVERT: 4 4 GLN cc_start: 0.5024 (OUTLIER) cc_final: 0.3980 (tp40) REVERT: 4 79 GLU cc_start: 0.6582 (tt0) cc_final: 0.5711 (tp30) REVERT: 4 113 GLU cc_start: 0.5919 (mt-10) cc_final: 0.5276 (mp0) REVERT: 4 115 ASP cc_start: 0.5834 (OUTLIER) cc_final: 0.5598 (p0) REVERT: 4 142 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6936 (mt-10) REVERT: 4 165 GLN cc_start: 0.6625 (tp40) cc_final: 0.5807 (pt0) REVERT: 4 169 GLU cc_start: 0.6572 (tp30) cc_final: 0.6131 (mt-10) REVERT: 4 176 ARG cc_start: 0.6364 (tpp-160) cc_final: 0.5616 (tpp80) REVERT: 4 191 HIS cc_start: 0.6599 (m-70) cc_final: 0.5807 (p90) REVERT: 4 278 TYR cc_start: 0.7464 (p90) cc_final: 0.6796 (p90) REVERT: 8 36 LYS cc_start: 0.6284 (mptt) cc_final: 0.5999 (mttt) REVERT: 8 89 ARG cc_start: 0.5787 (OUTLIER) cc_final: 0.5521 (mmm-85) REVERT: 8 233 LYS cc_start: 0.7111 (mttp) cc_final: 0.6818 (tttp) REVERT: 8 269 GLU cc_start: 0.5320 (mt-10) cc_final: 0.5004 (mp0) REVERT: 9 28 ASP cc_start: 0.6775 (t0) cc_final: 0.6460 (t0) REVERT: 9 123 GLU cc_start: 0.6493 (tp30) cc_final: 0.5791 (mt-10) REVERT: 9 161 ASP cc_start: 0.6645 (t0) cc_final: 0.6371 (p0) REVERT: 9 169 GLU cc_start: 0.7314 (tt0) cc_final: 0.6961 (pt0) REVERT: 9 176 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5663 (tpm-80) REVERT: 9 215 ARG cc_start: 0.6782 (mmm-85) cc_final: 0.6099 (mpt-90) REVERT: 9 219 GLU cc_start: 0.6747 (tt0) cc_final: 0.6250 (tm-30) REVERT: 9 233 LYS cc_start: 0.5104 (mttt) cc_final: 0.4866 (mtpm) REVERT: 9 241 MET cc_start: 0.6540 (mmm) cc_final: 0.6275 (mmt) REVERT: 9 244 SER cc_start: 0.5468 (m) cc_final: 0.5004 (p) REVERT: 9 258 VAL cc_start: 0.7223 (OUTLIER) cc_final: 0.6677 (p) REVERT: 9 284 GLN cc_start: 0.6076 (pt0) cc_final: 0.5778 (pt0) REVERT: 7 12 ASP cc_start: 0.5896 (m-30) cc_final: 0.5499 (m-30) REVERT: 7 39 LYS cc_start: 0.5653 (OUTLIER) cc_final: 0.5257 (mmmm) REVERT: 7 98 ASP cc_start: 0.6332 (p0) cc_final: 0.5966 (p0) REVERT: 7 165 GLN cc_start: 0.6720 (tp40) cc_final: 0.5572 (mt0) REVERT: 7 218 GLU cc_start: 0.5630 (tp30) cc_final: 0.4848 (mt-10) REVERT: 7 229 GLN cc_start: 0.4773 (mt0) cc_final: 0.4409 (mt0) REVERT: 7 262 ASP cc_start: 0.6333 (m-30) cc_final: 0.5975 (t0) REVERT: 7 277 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6796 (pp) outliers start: 119 outliers final: 55 residues processed: 479 average time/residue: 1.6118 time to fit residues: 868.5231 Evaluate side-chains 430 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 361 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 29 VAL Chi-restraints excluded: chain z residue 41 CYS Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 161 ASP Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 244 SER Chi-restraints excluded: chain z residue 259 GLU Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 25 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 194 THR Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 265 ASP Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 216 SER Chi-restraints excluded: chain y residue 231 ARG Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain 5 residue 30 ASP Chi-restraints excluded: chain 5 residue 57 MET Chi-restraints excluded: chain 5 residue 69 HIS Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 194 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 263 SER Chi-restraints excluded: chain 5 residue 284 GLN Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 273 GLU Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 41 CYS Chi-restraints excluded: chain 4 residue 115 ASP Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 241 MET Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 30 ASP Chi-restraints excluded: chain 8 residue 89 ARG Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 258 VAL Chi-restraints excluded: chain 8 residue 276 ASP Chi-restraints excluded: chain 8 residue 277 ILE Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 93 THR Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 176 ARG Chi-restraints excluded: chain 9 residue 181 VAL Chi-restraints excluded: chain 9 residue 220 LEU Chi-restraints excluded: chain 9 residue 258 VAL Chi-restraints excluded: chain 7 residue 2 SER 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 162 THR Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 241 MET Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 30.0000 chunk 237 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 264 optimal weight: 50.0000 chunk 219 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 ** y 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 69 HIS 4 25 GLN 4 229 GLN 8 170 ASN 9 25 GLN 7 18 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3069 moved from start: 1.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26605 Z= 0.274 Angle : 0.627 9.764 37004 Z= 0.320 Chirality : 0.036 0.208 4397 Planarity : 0.005 0.062 3941 Dihedral : 21.771 172.788 6508 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.52 % Rotamer: Outliers : 6.17 % Allowed : 25.10 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.16), residues: 2546 helix: 2.31 (0.12), residues: 1802 sheet: None (None), residues: 0 loop : -0.61 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP 8 217 HIS 0.022 0.002 HIS 5 69 PHE 0.035 0.002 PHE 5 68 TYR 0.021 0.002 TYR 6 94 ARG 0.009 0.001 ARG y 227 *********************** 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 533 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 391 time to evaluate : 2.676 Fit side-chains REVERT: z 21 ARG cc_start: 0.6325 (mmt-90) cc_final: 0.5612 (mmp80) REVERT: z 44 LYS cc_start: 0.6650 (ttmt) cc_final: 0.6311 (mmmt) REVERT: z 63 TYR cc_start: 0.7713 (t80) cc_final: 0.7353 (t80) REVERT: z 116 THR cc_start: 0.6586 (m) cc_final: 0.6189 (p) REVERT: z 119 ARG cc_start: 0.7112 (mtt90) cc_final: 0.6549 (mtm-85) REVERT: z 166 ARG cc_start: 0.6299 (mtt180) cc_final: 0.5934 (mtp85) REVERT: z 168 GLU cc_start: 0.4836 (tp30) cc_final: 0.4534 (mp0) REVERT: z 176 ARG cc_start: 0.5097 (tpp-160) cc_final: 0.4703 (mtp180) REVERT: z 190 ARG cc_start: 0.5840 (mpt90) cc_final: 0.5260 (mtp85) REVERT: z 218 GLU cc_start: 0.6388 (tp30) cc_final: 0.6055 (tt0) REVERT: z 219 GLU cc_start: 0.5918 (tt0) cc_final: 0.5377 (tp30) REVERT: z 259 GLU cc_start: 0.5664 (OUTLIER) cc_final: 0.5418 (pt0) REVERT: 0 1 MET cc_start: 0.4756 (tpp) cc_final: 0.4528 (tpt) REVERT: 0 39 LYS cc_start: 0.6049 (tppp) cc_final: 0.5241 (ttmp) REVERT: 0 47 HIS cc_start: 0.6764 (t-170) cc_final: 0.6551 (t70) REVERT: 0 115 ASP cc_start: 0.6712 (p0) cc_final: 0.6441 (p0) REVERT: 0 142 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: 0 169 GLU cc_start: 0.5128 (tm-30) cc_final: 0.4920 (mm-30) REVERT: 0 175 ARG cc_start: 0.6566 (ttp-170) cc_final: 0.5879 (ttm-80) REVERT: 0 194 THR cc_start: 0.5125 (OUTLIER) cc_final: 0.4840 (t) REVERT: 0 218 GLU cc_start: 0.5814 (tp30) cc_final: 0.5286 (mt-10) REVERT: 0 222 ARG cc_start: 0.6106 (ttm110) cc_final: 0.5902 (mtm110) REVERT: 0 263 SER cc_start: 0.5444 (m) cc_final: 0.5125 (p) REVERT: 0 273 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7223 (tp30) REVERT: y 62 TYR cc_start: 0.6194 (t80) cc_final: 0.5750 (t80) REVERT: y 92 TYR cc_start: 0.7485 (m-80) cc_final: 0.7028 (m-80) REVERT: y 113 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6452 (tt0) REVERT: y 123 GLU cc_start: 0.6519 (tp30) cc_final: 0.6067 (mt-10) REVERT: y 143 THR cc_start: 0.6916 (m) cc_final: 0.6623 (t) REVERT: y 151 THR cc_start: 0.6932 (m) cc_final: 0.6514 (p) REVERT: y 175 ARG cc_start: 0.6608 (ttp80) cc_final: 0.6216 (ttp-110) REVERT: y 218 GLU cc_start: 0.5451 (mm-30) cc_final: 0.5204 (mt-10) REVERT: y 219 GLU cc_start: 0.6969 (tp30) cc_final: 0.6661 (tp30) REVERT: y 265 ASP cc_start: 0.7005 (t70) cc_final: 0.6392 (t70) REVERT: y 269 GLU cc_start: 0.6593 (tp30) cc_final: 0.6345 (mp0) REVERT: y 276 ASP cc_start: 0.7118 (m-30) cc_final: 0.6852 (p0) REVERT: y 280 ASP cc_start: 0.7264 (m-30) cc_final: 0.6932 (m-30) REVERT: 5 43 GLU cc_start: 0.6963 (tt0) cc_final: 0.6382 (tp30) REVERT: 5 99 ARG cc_start: 0.5045 (mmm160) cc_final: 0.3882 (mtp180) REVERT: 5 103 ARG cc_start: 0.6646 (tpp80) cc_final: 0.6104 (ptp-170) REVERT: 5 111 ARG cc_start: 0.5870 (ttp-110) cc_final: 0.5379 (ptp-110) REVERT: 5 187 ASN cc_start: 0.7183 (m110) cc_final: 0.6251 (t0) REVERT: 6 63 TYR cc_start: 0.7615 (t80) cc_final: 0.7225 (t80) REVERT: 6 70 ASN cc_start: 0.6167 (t0) cc_final: 0.5786 (t0) REVERT: 6 150 GLN cc_start: 0.5049 (mm-40) cc_final: 0.4290 (tt0) REVERT: 6 166 ARG cc_start: 0.5770 (OUTLIER) cc_final: 0.5492 (mmm-85) REVERT: 6 175 ARG cc_start: 0.6507 (ttm170) cc_final: 0.5805 (ttt-90) REVERT: 6 211 MET cc_start: 0.6415 (mtm) cc_final: 0.6168 (mtp) REVERT: 6 215 ARG cc_start: 0.7685 (mtp180) cc_final: 0.7011 (mpp80) REVERT: 6 218 GLU cc_start: 0.6110 (tp30) cc_final: 0.5749 (mm-30) REVERT: 6 219 GLU cc_start: 0.6580 (tt0) cc_final: 0.6032 (mp0) REVERT: 6 240 ARG cc_start: 0.6239 (ttm-80) cc_final: 0.5876 (ttp80) REVERT: 6 281 SER cc_start: 0.7021 (t) cc_final: 0.6310 (p) REVERT: 4 4 GLN cc_start: 0.4862 (OUTLIER) cc_final: 0.4122 (tp40) REVERT: 4 21 ARG cc_start: 0.6559 (ttt-90) cc_final: 0.5535 (ttp80) REVERT: 4 36 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.5992 (ptpp) REVERT: 4 79 GLU cc_start: 0.6467 (tt0) cc_final: 0.5642 (tp30) REVERT: 4 123 GLU cc_start: 0.4749 (OUTLIER) cc_final: 0.4457 (tm-30) REVERT: 4 165 GLN cc_start: 0.7047 (tp40) cc_final: 0.6272 (pt0) REVERT: 4 169 GLU cc_start: 0.6543 (tp30) cc_final: 0.6107 (mt-10) REVERT: 4 176 ARG cc_start: 0.6295 (tpp-160) cc_final: 0.5737 (tpp80) REVERT: 4 191 HIS cc_start: 0.6502 (m-70) cc_final: 0.5563 (p90) REVERT: 4 278 TYR cc_start: 0.7729 (p90) cc_final: 0.7069 (p90) REVERT: 8 36 LYS cc_start: 0.6144 (mptt) cc_final: 0.5890 (mttt) REVERT: 8 44 LYS cc_start: 0.6461 (mptm) cc_final: 0.6178 (mmtm) REVERT: 8 89 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5593 (mmm-85) REVERT: 8 189 ASP cc_start: 0.4655 (p0) cc_final: 0.4275 (m-30) REVERT: 8 233 LYS cc_start: 0.7116 (mttp) cc_final: 0.6800 (tttp) REVERT: 9 18 ASN cc_start: 0.6645 (m-40) cc_final: 0.6433 (m-40) REVERT: 9 118 VAL cc_start: 0.4946 (m) cc_final: 0.4356 (t) REVERT: 9 169 GLU cc_start: 0.7318 (tt0) cc_final: 0.6830 (pt0) REVERT: 9 176 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.5806 (tpm-80) REVERT: 9 215 ARG cc_start: 0.6693 (mmm-85) cc_final: 0.5957 (mpt-90) REVERT: 9 219 GLU cc_start: 0.6967 (tt0) cc_final: 0.6457 (tm-30) REVERT: 9 233 LYS cc_start: 0.5272 (mttt) cc_final: 0.4901 (mtpm) REVERT: 9 240 ARG cc_start: 0.5905 (ttm-80) cc_final: 0.5663 (ttp80) REVERT: 9 241 MET cc_start: 0.6750 (mmm) cc_final: 0.6373 (mmt) REVERT: 9 244 SER cc_start: 0.5889 (m) cc_final: 0.5278 (p) REVERT: 9 258 VAL cc_start: 0.7287 (OUTLIER) cc_final: 0.6763 (p) REVERT: 9 259 GLU cc_start: 0.6854 (pt0) cc_final: 0.6487 (pp20) REVERT: 9 284 GLN cc_start: 0.6281 (pt0) cc_final: 0.5992 (pt0) REVERT: 7 12 ASP cc_start: 0.5889 (m-30) cc_final: 0.5392 (m-30) REVERT: 7 39 LYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5580 (mmtp) REVERT: 7 41 CYS cc_start: 0.3208 (m) cc_final: 0.2527 (m) REVERT: 7 48 ARG cc_start: 0.5839 (tpt170) cc_final: 0.5612 (tpt170) REVERT: 7 74 SER cc_start: 0.5661 (t) cc_final: 0.5330 (m) REVERT: 7 98 ASP cc_start: 0.5953 (p0) cc_final: 0.5338 (t0) REVERT: 7 161 ASP cc_start: 0.5622 (m-30) cc_final: 0.5308 (p0) REVERT: 7 165 GLN cc_start: 0.6706 (tp40) cc_final: 0.5809 (mt0) REVERT: 7 218 GLU cc_start: 0.5897 (tp30) cc_final: 0.5268 (mt-10) REVERT: 7 229 GLN cc_start: 0.5382 (mt0) cc_final: 0.5022 (mt0) REVERT: 7 241 MET cc_start: 0.5614 (mmm) cc_final: 0.5397 (mtt) REVERT: 7 262 ASP cc_start: 0.6332 (m-30) cc_final: 0.6111 (t0) outliers start: 142 outliers final: 83 residues processed: 497 average time/residue: 1.5556 time to fit residues: 872.3792 Evaluate side-chains 455 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 361 time to evaluate : 2.509 ------------------------------------------------------------------------------- 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 141 ARG Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 216 SER Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 236 VAL Chi-restraints excluded: chain z residue 239 LEU Chi-restraints excluded: chain z residue 242 CYS Chi-restraints excluded: chain z residue 244 SER Chi-restraints excluded: chain z residue 259 GLU Chi-restraints excluded: chain 0 residue 21 ARG Chi-restraints excluded: chain 0 residue 25 GLN Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 75 SER Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 116 THR Chi-restraints excluded: chain 0 residue 135 LEU Chi-restraints excluded: chain 0 residue 142 GLU Chi-restraints excluded: chain 0 residue 180 CYS Chi-restraints excluded: chain 0 residue 194 THR Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 216 SER Chi-restraints excluded: chain y residue 231 ARG Chi-restraints excluded: chain y residue 266 THR Chi-restraints excluded: chain 5 residue 52 LEU Chi-restraints excluded: chain 5 residue 57 MET Chi-restraints excluded: chain 5 residue 93 THR Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 194 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 263 SER Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 5 residue 284 GLN Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 166 ARG Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 36 LYS Chi-restraints excluded: chain 4 residue 41 CYS Chi-restraints excluded: chain 4 residue 116 THR Chi-restraints excluded: chain 4 residue 123 GLU Chi-restraints excluded: chain 4 residue 131 SER 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 241 MET Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 30 ASP Chi-restraints excluded: chain 8 residue 89 ARG Chi-restraints excluded: chain 8 residue 92 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 276 ASP 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 93 THR Chi-restraints excluded: chain 9 residue 108 VAL Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 176 ARG Chi-restraints excluded: chain 9 residue 181 VAL Chi-restraints excluded: chain 9 residue 206 THR Chi-restraints excluded: chain 9 residue 220 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 9 residue 272 ILE Chi-restraints excluded: chain 9 residue 276 ASP 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 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 230 GLU Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 50.0000 chunk 29 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 263 optimal weight: 50.0000 chunk 164 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 9 22 HIS 9 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3100 moved from start: 1.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26605 Z= 0.266 Angle : 0.608 9.491 37004 Z= 0.310 Chirality : 0.035 0.223 4397 Planarity : 0.004 0.047 3941 Dihedral : 21.768 171.317 6508 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.75 % Favored : 95.09 % Rotamer: Outliers : 5.34 % Allowed : 25.97 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.16), residues: 2546 helix: 2.25 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -0.63 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 6 217 HIS 0.019 0.002 HIS 5 69 PHE 0.025 0.002 PHE 4 275 TYR 0.022 0.002 TYR 6 94 ARG 0.008 0.001 ARG 5 48 *********************** 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 501 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 378 time to evaluate : 3.768 Fit side-chains revert: symmetry clash REVERT: z 21 ARG cc_start: 0.6216 (mmt-90) cc_final: 0.5698 (mmp80) REVERT: z 44 LYS cc_start: 0.6263 (ttmt) cc_final: 0.6027 (mmmt) REVERT: z 63 TYR cc_start: 0.7709 (t80) cc_final: 0.7366 (t80) REVERT: z 104 ASP cc_start: 0.6830 (t0) cc_final: 0.6452 (m-30) REVERT: z 116 THR cc_start: 0.6728 (m) cc_final: 0.6376 (p) REVERT: z 119 ARG cc_start: 0.7431 (mtt90) cc_final: 0.6787 (mtm-85) REVERT: z 166 ARG cc_start: 0.6519 (mtt180) cc_final: 0.6078 (mtp180) REVERT: z 168 GLU cc_start: 0.4854 (OUTLIER) cc_final: 0.4547 (mp0) REVERT: z 176 ARG cc_start: 0.4960 (tpp-160) cc_final: 0.4720 (mtp85) REVERT: z 190 ARG cc_start: 0.5416 (mpt90) cc_final: 0.5198 (mtp85) REVERT: z 218 GLU cc_start: 0.6367 (tp30) cc_final: 0.6058 (tt0) REVERT: z 219 GLU cc_start: 0.5896 (tt0) cc_final: 0.5366 (tp30) REVERT: z 259 GLU cc_start: 0.5628 (OUTLIER) cc_final: 0.5307 (pt0) REVERT: 0 1 MET cc_start: 0.4653 (tpp) cc_final: 0.4322 (tpt) REVERT: 0 39 LYS cc_start: 0.6046 (tppp) cc_final: 0.5306 (ttmm) REVERT: 0 47 HIS cc_start: 0.6856 (t-170) cc_final: 0.6577 (t70) REVERT: 0 98 ASP cc_start: 0.5762 (m-30) cc_final: 0.5514 (t70) REVERT: 0 115 ASP cc_start: 0.6746 (p0) cc_final: 0.6470 (p0) REVERT: 0 175 ARG cc_start: 0.6542 (ttp-170) cc_final: 0.5872 (ttm-80) REVERT: 0 194 THR cc_start: 0.5084 (OUTLIER) cc_final: 0.4785 (t) REVERT: 0 218 GLU cc_start: 0.5809 (tp30) cc_final: 0.5290 (mt-10) REVERT: 0 222 ARG cc_start: 0.6110 (ttm110) cc_final: 0.5876 (mtt90) REVERT: 0 246 ASP cc_start: 0.5432 (OUTLIER) cc_final: 0.5024 (p0) REVERT: 0 265 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6446 (m-30) REVERT: 0 273 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: y 28 ASP cc_start: 0.5860 (p0) cc_final: 0.5491 (t0) REVERT: y 62 TYR cc_start: 0.6200 (t80) cc_final: 0.5756 (t80) REVERT: y 113 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6208 (tt0) REVERT: y 143 THR cc_start: 0.6940 (m) cc_final: 0.6661 (t) REVERT: y 175 ARG cc_start: 0.6757 (ttp80) cc_final: 0.6378 (ttp-110) REVERT: y 211 MET cc_start: 0.5679 (mtp) cc_final: 0.5445 (mtm) REVERT: y 218 GLU cc_start: 0.5597 (mm-30) cc_final: 0.5225 (mt-10) REVERT: y 219 GLU cc_start: 0.7041 (tp30) cc_final: 0.6717 (tp30) REVERT: y 269 GLU cc_start: 0.6539 (tp30) cc_final: 0.6209 (mp0) REVERT: y 276 ASP cc_start: 0.7107 (m-30) cc_final: 0.6840 (p0) REVERT: y 280 ASP cc_start: 0.7210 (m-30) cc_final: 0.6917 (m-30) REVERT: 5 29 VAL cc_start: 0.7145 (t) cc_final: 0.6786 (m) REVERT: 5 43 GLU cc_start: 0.6941 (tt0) cc_final: 0.6450 (tm-30) REVERT: 5 99 ARG cc_start: 0.4567 (mmm160) cc_final: 0.3590 (mtp180) REVERT: 5 103 ARG cc_start: 0.6658 (tpp80) cc_final: 0.6113 (ptp-170) REVERT: 5 142 GLU cc_start: 0.5250 (mt-10) cc_final: 0.4979 (mt-10) REVERT: 5 187 ASN cc_start: 0.7099 (OUTLIER) cc_final: 0.6220 (t0) REVERT: 5 194 THR cc_start: 0.5796 (OUTLIER) cc_final: 0.5424 (p) REVERT: 6 25 GLN cc_start: 0.6358 (pt0) cc_final: 0.6114 (pt0) REVERT: 6 140 VAL cc_start: 0.6382 (OUTLIER) cc_final: 0.6132 (m) REVERT: 6 166 ARG cc_start: 0.5748 (ttp80) cc_final: 0.5482 (mmm-85) REVERT: 6 175 ARG cc_start: 0.6038 (ttm170) cc_final: 0.5351 (ttt-90) REVERT: 6 211 MET cc_start: 0.6408 (mtm) cc_final: 0.6139 (mtp) REVERT: 6 215 ARG cc_start: 0.7318 (mtp180) cc_final: 0.6630 (tpp80) REVERT: 6 218 GLU cc_start: 0.6192 (tp30) cc_final: 0.5821 (mm-30) REVERT: 6 219 GLU cc_start: 0.6878 (tt0) cc_final: 0.6215 (mp0) REVERT: 6 240 ARG cc_start: 0.6196 (ttm-80) cc_final: 0.5856 (ttp80) REVERT: 6 281 SER cc_start: 0.7181 (t) cc_final: 0.6562 (p) REVERT: 4 4 GLN cc_start: 0.5083 (OUTLIER) cc_final: 0.4062 (tp-100) REVERT: 4 21 ARG cc_start: 0.6513 (ttt-90) cc_final: 0.5474 (ttp80) REVERT: 4 36 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.5948 (pttt) REVERT: 4 79 GLU cc_start: 0.6471 (tt0) cc_final: 0.5649 (tp30) REVERT: 4 98 ASP cc_start: 0.6566 (p0) cc_final: 0.6134 (t0) REVERT: 4 123 GLU cc_start: 0.4767 (OUTLIER) cc_final: 0.4467 (tm-30) REVERT: 4 165 GLN cc_start: 0.7135 (tp40) cc_final: 0.6338 (pt0) REVERT: 4 169 GLU cc_start: 0.6703 (tp30) cc_final: 0.6217 (mt-10) REVERT: 4 176 ARG cc_start: 0.6341 (tpp-160) cc_final: 0.5446 (ttp80) REVERT: 4 191 HIS cc_start: 0.6006 (m-70) cc_final: 0.5329 (p90) REVERT: 4 280 ASP cc_start: 0.7918 (t0) cc_final: 0.7313 (m-30) REVERT: 8 44 LYS cc_start: 0.6463 (mptm) cc_final: 0.6161 (mmtm) REVERT: 8 89 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.5211 (mmm-85) REVERT: 8 189 ASP cc_start: 0.5133 (p0) cc_final: 0.4581 (m-30) REVERT: 8 233 LYS cc_start: 0.7179 (mttp) cc_final: 0.6860 (tttp) REVERT: 9 18 ASN cc_start: 0.6514 (m-40) cc_final: 0.6215 (m-40) REVERT: 9 26 LYS cc_start: 0.6742 (mttm) cc_final: 0.6310 (mttm) REVERT: 9 30 ASP cc_start: 0.7098 (t0) cc_final: 0.6807 (t70) REVERT: 9 99 ARG cc_start: 0.5968 (ttp-170) cc_final: 0.5643 (mtp180) REVERT: 9 118 VAL cc_start: 0.5232 (m) cc_final: 0.4529 (t) REVERT: 9 169 GLU cc_start: 0.7481 (tt0) cc_final: 0.6999 (pt0) REVERT: 9 176 ARG cc_start: 0.6237 (OUTLIER) cc_final: 0.5654 (tpm-80) REVERT: 9 215 ARG cc_start: 0.6491 (mmm-85) cc_final: 0.5763 (mpt-90) REVERT: 9 219 GLU cc_start: 0.7013 (tt0) cc_final: 0.6561 (tm-30) REVERT: 9 233 LYS cc_start: 0.5555 (mttt) cc_final: 0.5206 (mtpm) REVERT: 9 241 MET cc_start: 0.6553 (mmm) cc_final: 0.6218 (mmt) REVERT: 9 244 SER cc_start: 0.6141 (m) cc_final: 0.5556 (p) REVERT: 9 258 VAL cc_start: 0.7317 (OUTLIER) cc_final: 0.6720 (p) REVERT: 9 259 GLU cc_start: 0.6985 (pt0) cc_final: 0.6510 (pp20) REVERT: 9 284 GLN cc_start: 0.6061 (pt0) cc_final: 0.5630 (pt0) REVERT: 7 12 ASP cc_start: 0.6024 (m-30) cc_final: 0.5658 (m-30) REVERT: 7 39 LYS cc_start: 0.5811 (OUTLIER) cc_final: 0.5386 (mmmm) REVERT: 7 48 ARG cc_start: 0.5998 (tpt170) cc_final: 0.5779 (tpt170) REVERT: 7 98 ASP cc_start: 0.5975 (p0) cc_final: 0.5479 (t0) REVERT: 7 165 GLN cc_start: 0.7014 (tp40) cc_final: 0.6084 (mt0) REVERT: 7 176 ARG cc_start: 0.6276 (tpp-160) cc_final: 0.5897 (tpp80) REVERT: 7 218 GLU cc_start: 0.5885 (tp30) cc_final: 0.5266 (mt-10) REVERT: 7 229 GLN cc_start: 0.5034 (mt0) cc_final: 0.4736 (mt0) REVERT: 7 234 LEU cc_start: 0.6303 (mt) cc_final: 0.5953 (mt) REVERT: 7 277 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6501 (pp) outliers start: 123 outliers final: 77 residues processed: 466 average time/residue: 1.7021 time to fit residues: 888.9816 Evaluate side-chains 449 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 355 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 28 ASP 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 161 ASP Chi-restraints excluded: chain z residue 168 GLU Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 216 SER Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 236 VAL Chi-restraints excluded: chain z residue 244 SER Chi-restraints excluded: chain z residue 259 GLU 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 177 ASN Chi-restraints excluded: chain 0 residue 180 CYS Chi-restraints excluded: chain 0 residue 194 THR Chi-restraints excluded: chain 0 residue 240 ARG Chi-restraints excluded: chain 0 residue 243 LEU Chi-restraints excluded: chain 0 residue 246 ASP Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 265 ASP 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 216 SER Chi-restraints excluded: chain y residue 231 ARG Chi-restraints excluded: chain y residue 266 THR 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 73 LEU Chi-restraints excluded: chain 5 residue 93 THR Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 159 LEU Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 187 ASN Chi-restraints excluded: chain 5 residue 194 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 263 SER Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 5 residue 284 GLN Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 140 VAL Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 36 LYS Chi-restraints excluded: chain 4 residue 41 CYS 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 241 MET Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 89 ARG Chi-restraints excluded: chain 8 residue 92 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 225 LEU Chi-restraints excluded: chain 8 residue 276 ASP 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 93 THR Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 176 ARG Chi-restraints excluded: chain 9 residue 206 THR Chi-restraints excluded: chain 9 residue 220 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 23 LEU Chi-restraints excluded: chain 7 residue 39 LYS Chi-restraints excluded: chain 7 residue 76 VAL Chi-restraints excluded: chain 7 residue 93 THR 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 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 25 GLN 0 177 ASN ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 9 25 GLN 7 18 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3092 moved from start: 1.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26605 Z= 0.202 Angle : 0.551 9.166 37004 Z= 0.281 Chirality : 0.033 0.216 4397 Planarity : 0.004 0.045 3941 Dihedral : 21.561 170.553 6507 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 4.73 % Allowed : 26.75 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.16), residues: 2546 helix: 2.49 (0.12), residues: 1796 sheet: None (None), residues: 0 loop : -0.59 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 4 217 HIS 0.012 0.001 HIS 0 22 PHE 0.013 0.001 PHE 5 68 TYR 0.019 0.002 TYR 6 94 ARG 0.009 0.001 ARG 0 127 *********************** 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 486 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 377 time to evaluate : 2.557 Fit side-chains REVERT: z 21 ARG cc_start: 0.6364 (mmt-90) cc_final: 0.5719 (mmp80) REVERT: z 44 LYS cc_start: 0.6655 (ttmt) cc_final: 0.6337 (mmmt) REVERT: z 63 TYR cc_start: 0.7718 (t80) cc_final: 0.7323 (t80) REVERT: z 104 ASP cc_start: 0.6715 (t0) cc_final: 0.6356 (m-30) REVERT: z 116 THR cc_start: 0.6697 (m) cc_final: 0.6333 (p) REVERT: z 119 ARG cc_start: 0.7384 (mtt90) cc_final: 0.6707 (mtm-85) REVERT: z 166 ARG cc_start: 0.6544 (mtt180) cc_final: 0.6082 (mtp180) REVERT: z 168 GLU cc_start: 0.4692 (OUTLIER) cc_final: 0.4430 (mp0) REVERT: z 176 ARG cc_start: 0.5425 (tpp-160) cc_final: 0.5123 (mtp85) REVERT: z 218 GLU cc_start: 0.6168 (tp30) cc_final: 0.5898 (tt0) REVERT: z 219 GLU cc_start: 0.5791 (tt0) cc_final: 0.5265 (tp30) REVERT: z 259 GLU cc_start: 0.5302 (OUTLIER) cc_final: 0.4995 (pt0) REVERT: 0 1 MET cc_start: 0.4365 (tpp) cc_final: 0.4040 (tpt) REVERT: 0 39 LYS cc_start: 0.5840 (tppp) cc_final: 0.5347 (ttmp) REVERT: 0 47 HIS cc_start: 0.6834 (t-170) cc_final: 0.6581 (t70) REVERT: 0 115 ASP cc_start: 0.6779 (p0) cc_final: 0.6501 (p0) REVERT: 0 169 GLU cc_start: 0.5561 (mm-30) cc_final: 0.5117 (mt-10) REVERT: 0 175 ARG cc_start: 0.6511 (ttp-170) cc_final: 0.5718 (ttt180) REVERT: 0 194 THR cc_start: 0.5077 (OUTLIER) cc_final: 0.4756 (t) REVERT: 0 218 GLU cc_start: 0.5815 (tp30) cc_final: 0.5293 (mt-10) REVERT: 0 222 ARG cc_start: 0.6133 (ttm110) cc_final: 0.5863 (mtt90) REVERT: 0 265 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6422 (m-30) REVERT: 0 273 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7322 (tp30) REVERT: y 62 TYR cc_start: 0.6234 (t80) cc_final: 0.5737 (t80) REVERT: y 92 TYR cc_start: 0.7472 (m-80) cc_final: 0.7241 (m-80) REVERT: y 113 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6286 (tt0) REVERT: y 143 THR cc_start: 0.6881 (m) cc_final: 0.6597 (t) REVERT: y 186 LEU cc_start: 0.3847 (OUTLIER) cc_final: 0.3195 (mm) REVERT: y 211 MET cc_start: 0.5983 (mtp) cc_final: 0.5780 (mtm) REVERT: y 219 GLU cc_start: 0.6956 (tp30) cc_final: 0.6659 (tp30) REVERT: y 269 GLU cc_start: 0.6643 (tp30) cc_final: 0.6372 (mp0) REVERT: y 276 ASP cc_start: 0.7105 (m-30) cc_final: 0.6842 (p0) REVERT: y 280 ASP cc_start: 0.7194 (m-30) cc_final: 0.6883 (m-30) REVERT: 5 6 ILE cc_start: 0.7367 (mm) cc_final: 0.7061 (mt) REVERT: 5 43 GLU cc_start: 0.6934 (tt0) cc_final: 0.6474 (tm-30) REVERT: 5 48 ARG cc_start: 0.5225 (ttt90) cc_final: 0.5023 (ttt90) REVERT: 5 99 ARG cc_start: 0.4662 (mmm160) cc_final: 0.3524 (mtp180) REVERT: 5 103 ARG cc_start: 0.6604 (tpp80) cc_final: 0.6041 (ptp-170) REVERT: 5 104 ASP cc_start: 0.6231 (m-30) cc_final: 0.5832 (m-30) REVERT: 5 142 GLU cc_start: 0.4950 (mt-10) cc_final: 0.4729 (mt-10) REVERT: 5 187 ASN cc_start: 0.6963 (m110) cc_final: 0.5912 (t0) REVERT: 5 194 THR cc_start: 0.5489 (OUTLIER) cc_final: 0.5234 (m) REVERT: 6 21 ARG cc_start: 0.6455 (ptp-110) cc_final: 0.5729 (ppt170) REVERT: 6 25 GLN cc_start: 0.6394 (pt0) cc_final: 0.6145 (pt0) REVERT: 6 70 ASN cc_start: 0.6030 (t0) cc_final: 0.5634 (t0) REVERT: 6 175 ARG cc_start: 0.6082 (ttm170) cc_final: 0.5402 (ttt-90) REVERT: 6 211 MET cc_start: 0.6416 (mtm) cc_final: 0.6136 (mtp) REVERT: 6 215 ARG cc_start: 0.7661 (mtp180) cc_final: 0.6827 (mpp80) REVERT: 6 218 GLU cc_start: 0.6226 (tp30) cc_final: 0.5844 (mm-30) REVERT: 6 219 GLU cc_start: 0.6830 (tt0) cc_final: 0.6254 (mp0) REVERT: 6 240 ARG cc_start: 0.6078 (ttm-80) cc_final: 0.5843 (ttp80) REVERT: 6 281 SER cc_start: 0.6956 (t) cc_final: 0.6535 (p) REVERT: 4 4 GLN cc_start: 0.5012 (OUTLIER) cc_final: 0.3990 (tp40) REVERT: 4 21 ARG cc_start: 0.6593 (ttt-90) cc_final: 0.5597 (ttp80) REVERT: 4 36 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.5858 (ptpt) REVERT: 4 37 ILE cc_start: 0.6484 (mm) cc_final: 0.6271 (mp) REVERT: 4 79 GLU cc_start: 0.6431 (tt0) cc_final: 0.5574 (tp30) REVERT: 4 98 ASP cc_start: 0.6606 (p0) cc_final: 0.6214 (t0) REVERT: 4 123 GLU cc_start: 0.5018 (OUTLIER) cc_final: 0.4688 (tm-30) REVERT: 4 165 GLN cc_start: 0.7062 (tp40) cc_final: 0.6450 (pt0) REVERT: 4 169 GLU cc_start: 0.6524 (tp30) cc_final: 0.6135 (mt-10) REVERT: 4 176 ARG cc_start: 0.6403 (tpp-160) cc_final: 0.5555 (ttp80) REVERT: 4 185 ASP cc_start: 0.2492 (OUTLIER) cc_final: 0.2211 (m-30) REVERT: 4 191 HIS cc_start: 0.5983 (m-70) cc_final: 0.5299 (p90) REVERT: 4 241 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6704 (tpp) REVERT: 4 280 ASP cc_start: 0.7774 (t0) cc_final: 0.7363 (m-30) REVERT: 8 44 LYS cc_start: 0.6518 (mptm) cc_final: 0.6264 (mmtm) REVERT: 8 89 ARG cc_start: 0.5478 (OUTLIER) cc_final: 0.5190 (mmm-85) REVERT: 8 189 ASP cc_start: 0.5225 (p0) cc_final: 0.4563 (m-30) REVERT: 8 233 LYS cc_start: 0.7039 (mttp) cc_final: 0.6776 (tttp) REVERT: 9 18 ASN cc_start: 0.6529 (m-40) cc_final: 0.6256 (m-40) REVERT: 9 30 ASP cc_start: 0.7064 (t0) cc_final: 0.6749 (t70) REVERT: 9 99 ARG cc_start: 0.5962 (ttp-170) cc_final: 0.5549 (mtp180) REVERT: 9 118 VAL cc_start: 0.5100 (m) cc_final: 0.4374 (t) REVERT: 9 169 GLU cc_start: 0.7485 (tt0) cc_final: 0.7003 (pt0) REVERT: 9 176 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.5665 (tpm-80) REVERT: 9 215 ARG cc_start: 0.6811 (mmm-85) cc_final: 0.6106 (mpt-90) REVERT: 9 219 GLU cc_start: 0.6754 (tt0) cc_final: 0.6305 (tm-30) REVERT: 9 233 LYS cc_start: 0.5111 (mttt) cc_final: 0.4810 (mtpm) REVERT: 9 241 MET cc_start: 0.6523 (mmm) cc_final: 0.6162 (mmt) REVERT: 9 244 SER cc_start: 0.6108 (m) cc_final: 0.5509 (p) REVERT: 9 258 VAL cc_start: 0.7387 (OUTLIER) cc_final: 0.6839 (p) REVERT: 9 259 GLU cc_start: 0.6919 (pt0) cc_final: 0.6464 (pp20) REVERT: 9 284 GLN cc_start: 0.6343 (pt0) cc_final: 0.6075 (pt0) REVERT: 7 12 ASP cc_start: 0.6083 (m-30) cc_final: 0.5686 (m-30) REVERT: 7 21 ARG cc_start: 0.6295 (ttm-80) cc_final: 0.6026 (ttp80) REVERT: 7 39 LYS cc_start: 0.5932 (OUTLIER) cc_final: 0.5475 (mmmm) REVERT: 7 48 ARG cc_start: 0.5903 (tpt170) cc_final: 0.5591 (tpt170) REVERT: 7 98 ASP cc_start: 0.6296 (p0) cc_final: 0.5802 (t0) REVERT: 7 165 GLN cc_start: 0.7108 (tp40) cc_final: 0.6226 (mt0) REVERT: 7 176 ARG cc_start: 0.6203 (tpp-160) cc_final: 0.5867 (tpp80) REVERT: 7 218 GLU cc_start: 0.5850 (tp30) cc_final: 0.5246 (mt-10) REVERT: 7 229 GLN cc_start: 0.5158 (mt0) cc_final: 0.4821 (mt0) REVERT: 7 277 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6587 (pp) outliers start: 109 outliers final: 67 residues processed: 459 average time/residue: 1.7235 time to fit residues: 886.6476 Evaluate side-chains 436 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 353 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 28 ASP Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 168 GLU Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 216 SER Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 244 SER Chi-restraints excluded: chain z residue 259 GLU Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 75 SER Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 116 THR Chi-restraints excluded: chain 0 residue 135 LEU Chi-restraints excluded: chain 0 residue 180 CYS Chi-restraints excluded: chain 0 residue 194 THR Chi-restraints excluded: chain 0 residue 243 LEU Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 265 ASP Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 216 SER 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 5 residue 57 MET Chi-restraints excluded: chain 5 residue 73 LEU Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 194 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 263 SER Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 5 residue 284 GLN Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 36 LYS Chi-restraints excluded: chain 4 residue 41 CYS 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 241 MET Chi-restraints excluded: chain 4 residue 246 ASP Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 89 ARG Chi-restraints excluded: chain 8 residue 92 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 159 LEU Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 276 ASP 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 93 THR Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 176 ARG Chi-restraints excluded: chain 9 residue 206 THR Chi-restraints excluded: chain 9 residue 220 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 18 ASN 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 140 VAL Chi-restraints excluded: chain 7 residue 146 THR Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 168 GLU Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 20.0000 chunk 252 optimal weight: 50.0000 chunk 229 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 9 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3114 moved from start: 1.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26605 Z= 0.227 Angle : 0.580 8.823 37004 Z= 0.295 Chirality : 0.034 0.225 4397 Planarity : 0.004 0.046 3941 Dihedral : 21.540 171.595 6507 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.71 % Favored : 95.13 % Rotamer: Outliers : 4.65 % Allowed : 27.31 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.16), residues: 2546 helix: 2.40 (0.12), residues: 1794 sheet: None (None), residues: 0 loop : -0.63 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 4 217 HIS 0.008 0.001 HIS 5 69 PHE 0.047 0.002 PHE 4 275 TYR 0.024 0.002 TYR 6 94 ARG 0.008 0.001 ARG 5 48 *********************** 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 465 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 358 time to evaluate : 2.785 Fit side-chains REVERT: z 21 ARG cc_start: 0.6211 (mmt-90) cc_final: 0.5704 (mmp80) REVERT: z 44 LYS cc_start: 0.6636 (ttmt) cc_final: 0.6382 (mmpt) REVERT: z 63 TYR cc_start: 0.7720 (t80) cc_final: 0.7330 (t80) REVERT: z 104 ASP cc_start: 0.6720 (t0) cc_final: 0.6381 (m-30) REVERT: z 116 THR cc_start: 0.6663 (m) cc_final: 0.6303 (p) REVERT: z 119 ARG cc_start: 0.7406 (mtt90) cc_final: 0.6714 (mtm-85) REVERT: z 166 ARG cc_start: 0.6546 (mtt180) cc_final: 0.6082 (mtp180) REVERT: z 168 GLU cc_start: 0.4845 (OUTLIER) cc_final: 0.4561 (mp0) REVERT: z 190 ARG cc_start: 0.5681 (mmt-90) cc_final: 0.5328 (mmp80) REVERT: z 218 GLU cc_start: 0.6354 (tp30) cc_final: 0.6034 (tt0) REVERT: z 219 GLU cc_start: 0.5873 (tt0) cc_final: 0.5354 (tp30) REVERT: z 259 GLU cc_start: 0.5357 (OUTLIER) cc_final: 0.5012 (pt0) REVERT: 0 1 MET cc_start: 0.4393 (tpp) cc_final: 0.4075 (tpt) REVERT: 0 39 LYS cc_start: 0.5794 (tppp) cc_final: 0.5304 (ttmp) REVERT: 0 47 HIS cc_start: 0.6847 (t-170) cc_final: 0.6588 (t70) REVERT: 0 115 ASP cc_start: 0.6815 (p0) cc_final: 0.6526 (p0) REVERT: 0 169 GLU cc_start: 0.5565 (mm-30) cc_final: 0.5085 (mt-10) REVERT: 0 175 ARG cc_start: 0.6539 (ttp-170) cc_final: 0.5870 (ttm-80) REVERT: 0 194 THR cc_start: 0.5174 (OUTLIER) cc_final: 0.4855 (t) REVERT: 0 218 GLU cc_start: 0.5832 (tp30) cc_final: 0.5315 (mt-10) REVERT: 0 222 ARG cc_start: 0.6112 (ttm110) cc_final: 0.5867 (mtt90) REVERT: 0 265 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6438 (m-30) REVERT: 0 273 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: y 62 TYR cc_start: 0.6223 (t80) cc_final: 0.5776 (t80) REVERT: y 113 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6180 (tt0) REVERT: y 143 THR cc_start: 0.6907 (m) cc_final: 0.6616 (t) REVERT: y 175 ARG cc_start: 0.6723 (ttp80) cc_final: 0.6342 (ttp-110) REVERT: y 186 LEU cc_start: 0.3627 (OUTLIER) cc_final: 0.2972 (mm) REVERT: y 211 MET cc_start: 0.5964 (mtp) cc_final: 0.5743 (mtm) REVERT: y 218 GLU cc_start: 0.4877 (mt-10) cc_final: 0.4592 (mp0) REVERT: y 219 GLU cc_start: 0.6980 (tp30) cc_final: 0.6685 (tp30) REVERT: y 269 GLU cc_start: 0.6662 (tp30) cc_final: 0.6396 (mp0) REVERT: y 276 ASP cc_start: 0.7110 (m-30) cc_final: 0.6840 (p0) REVERT: y 280 ASP cc_start: 0.7257 (m-30) cc_final: 0.6952 (m-30) REVERT: 5 29 VAL cc_start: 0.7108 (t) cc_final: 0.6886 (m) REVERT: 5 43 GLU cc_start: 0.6916 (tt0) cc_final: 0.6460 (tm-30) REVERT: 5 99 ARG cc_start: 0.4501 (mmm160) cc_final: 0.3437 (mtp180) REVERT: 5 101 LYS cc_start: 0.5955 (tttt) cc_final: 0.5737 (tmtt) REVERT: 5 103 ARG cc_start: 0.6719 (tpp80) cc_final: 0.6148 (ptp-170) REVERT: 5 104 ASP cc_start: 0.6261 (m-30) cc_final: 0.5859 (m-30) REVERT: 5 142 GLU cc_start: 0.5048 (mt-10) cc_final: 0.4831 (mt-10) REVERT: 5 187 ASN cc_start: 0.6938 (m110) cc_final: 0.5893 (t0) REVERT: 5 194 THR cc_start: 0.5738 (OUTLIER) cc_final: 0.5373 (p) REVERT: 6 25 GLN cc_start: 0.6440 (OUTLIER) cc_final: 0.6201 (pt0) REVERT: 6 140 VAL cc_start: 0.6250 (OUTLIER) cc_final: 0.6025 (m) REVERT: 6 175 ARG cc_start: 0.6050 (ttm170) cc_final: 0.5399 (ttt-90) REVERT: 6 211 MET cc_start: 0.6406 (mtm) cc_final: 0.6115 (mtp) REVERT: 6 215 ARG cc_start: 0.7277 (mtp180) cc_final: 0.6487 (mpp80) REVERT: 6 218 GLU cc_start: 0.6176 (tp30) cc_final: 0.5790 (mm-30) REVERT: 6 219 GLU cc_start: 0.6832 (tt0) cc_final: 0.6257 (mp0) REVERT: 6 240 ARG cc_start: 0.6128 (ttm-80) cc_final: 0.5760 (ttp80) REVERT: 6 281 SER cc_start: 0.7209 (t) cc_final: 0.6598 (p) REVERT: 4 4 GLN cc_start: 0.5021 (OUTLIER) cc_final: 0.3916 (tp40) REVERT: 4 21 ARG cc_start: 0.6496 (ttt-90) cc_final: 0.5509 (ttm170) REVERT: 4 36 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.5885 (ptpt) REVERT: 4 79 GLU cc_start: 0.6458 (tt0) cc_final: 0.5675 (tp30) REVERT: 4 123 GLU cc_start: 0.5024 (OUTLIER) cc_final: 0.4692 (tm-30) REVERT: 4 161 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6708 (m-30) REVERT: 4 165 GLN cc_start: 0.7211 (tp40) cc_final: 0.6413 (pt0) REVERT: 4 169 GLU cc_start: 0.6898 (tp30) cc_final: 0.6482 (mt-10) REVERT: 4 176 ARG cc_start: 0.6405 (tpp-160) cc_final: 0.5545 (ttp80) REVERT: 4 191 HIS cc_start: 0.5951 (m-70) cc_final: 0.5335 (p90) REVERT: 4 280 ASP cc_start: 0.7883 (t0) cc_final: 0.7487 (m-30) REVERT: 8 40 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5837 (ttmm) REVERT: 8 44 LYS cc_start: 0.6636 (mptm) cc_final: 0.6302 (mmtm) REVERT: 8 89 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.5217 (mmm-85) REVERT: 8 189 ASP cc_start: 0.5216 (p0) cc_final: 0.4565 (m-30) REVERT: 8 233 LYS cc_start: 0.7141 (mttp) cc_final: 0.6838 (tttp) REVERT: 9 30 ASP cc_start: 0.7073 (t0) cc_final: 0.6806 (t70) REVERT: 9 99 ARG cc_start: 0.5913 (ttp-170) cc_final: 0.5613 (mtp180) REVERT: 9 118 VAL cc_start: 0.5192 (m) cc_final: 0.4450 (t) REVERT: 9 169 GLU cc_start: 0.7500 (tt0) cc_final: 0.7003 (pt0) REVERT: 9 176 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.5846 (ttm-80) REVERT: 9 215 ARG cc_start: 0.6822 (mmm-85) cc_final: 0.6099 (mpt-90) REVERT: 9 219 GLU cc_start: 0.6857 (tt0) cc_final: 0.6404 (tm-30) REVERT: 9 233 LYS cc_start: 0.5545 (mttt) cc_final: 0.5210 (mtpm) REVERT: 9 241 MET cc_start: 0.6652 (mmm) cc_final: 0.6295 (mmt) REVERT: 9 244 SER cc_start: 0.6151 (m) cc_final: 0.5539 (p) REVERT: 9 258 VAL cc_start: 0.7286 (OUTLIER) cc_final: 0.6719 (p) REVERT: 9 259 GLU cc_start: 0.6918 (pt0) cc_final: 0.6482 (pp20) REVERT: 9 284 GLN cc_start: 0.6084 (pt0) cc_final: 0.5738 (pt0) REVERT: 7 12 ASP cc_start: 0.6099 (m-30) cc_final: 0.5705 (m-30) REVERT: 7 21 ARG cc_start: 0.6440 (ttm-80) cc_final: 0.6086 (ttp80) REVERT: 7 39 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5465 (mmmm) REVERT: 7 48 ARG cc_start: 0.5865 (tpt170) cc_final: 0.5601 (tpt170) REVERT: 7 98 ASP cc_start: 0.6476 (p0) cc_final: 0.5990 (t0) REVERT: 7 165 GLN cc_start: 0.7247 (tp40) cc_final: 0.6361 (mt0) REVERT: 7 176 ARG cc_start: 0.6254 (tpp-160) cc_final: 0.5931 (tpp80) REVERT: 7 218 GLU cc_start: 0.5884 (tp30) cc_final: 0.5268 (mt-10) REVERT: 7 229 GLN cc_start: 0.5280 (mt0) cc_final: 0.4953 (mt0) outliers start: 107 outliers final: 77 residues processed: 442 average time/residue: 1.7324 time to fit residues: 857.0014 Evaluate side-chains 448 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 353 time to evaluate : 2.539 ------------------------------------------------------------------------------- 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 139 SER Chi-restraints excluded: chain z residue 168 GLU Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 216 SER Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 239 LEU Chi-restraints excluded: chain z residue 244 SER Chi-restraints excluded: chain z residue 259 GLU 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 194 THR Chi-restraints excluded: chain 0 residue 243 LEU Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 265 ASP Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain y residue 174 VAL Chi-restraints excluded: chain y residue 186 LEU Chi-restraints excluded: chain y residue 216 SER 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 5 residue 57 MET Chi-restraints excluded: chain 5 residue 73 LEU Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 194 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 263 SER Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 5 residue 284 GLN Chi-restraints excluded: chain 6 residue 25 GLN Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 140 VAL Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 36 LYS Chi-restraints excluded: chain 4 residue 41 CYS 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 161 ASP 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 241 MET Chi-restraints excluded: chain 4 residue 246 ASP Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 89 ARG Chi-restraints excluded: chain 8 residue 92 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 159 LEU Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 276 ASP 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 93 THR Chi-restraints excluded: chain 9 residue 112 THR Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 176 ARG Chi-restraints excluded: chain 9 residue 206 THR Chi-restraints excluded: chain 9 residue 220 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 9 residue 272 ILE Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 39 LYS Chi-restraints excluded: chain 7 residue 76 VAL Chi-restraints excluded: chain 7 residue 93 THR 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 162 THR Chi-restraints excluded: chain 7 residue 168 GLU Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 5.9990 chunk 259 optimal weight: 50.0000 chunk 158 optimal weight: 0.3980 chunk 123 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 271 optimal weight: 50.0000 chunk 250 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 9 25 GLN 7 18 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3096 moved from start: 1.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26605 Z= 0.182 Angle : 0.532 8.514 37004 Z= 0.271 Chirality : 0.032 0.217 4397 Planarity : 0.003 0.043 3941 Dihedral : 21.391 170.092 6507 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.52 % Favored : 95.33 % Rotamer: Outliers : 4.21 % Allowed : 27.79 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.16), residues: 2546 helix: 2.59 (0.12), residues: 1793 sheet: None (None), residues: 0 loop : -0.60 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 4 217 HIS 0.006 0.001 HIS 6 158 PHE 0.025 0.001 PHE y 19 TYR 0.027 0.002 TYR 5 94 ARG 0.008 0.000 ARG 0 127 ********************** 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 466 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 369 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: z 21 ARG cc_start: 0.6362 (mmt-90) cc_final: 0.5739 (mmp80) REVERT: z 44 LYS cc_start: 0.6673 (ttmt) cc_final: 0.6356 (mmmt) REVERT: z 63 TYR cc_start: 0.7714 (t80) cc_final: 0.7354 (t80) REVERT: z 70 ASN cc_start: 0.6932 (t0) cc_final: 0.6689 (t160) REVERT: z 104 ASP cc_start: 0.6682 (t0) cc_final: 0.6322 (m-30) REVERT: z 116 THR cc_start: 0.6682 (m) cc_final: 0.6348 (p) REVERT: z 119 ARG cc_start: 0.7396 (mtt90) cc_final: 0.6708 (mtm-85) REVERT: z 166 ARG cc_start: 0.6365 (mtt180) cc_final: 0.5914 (mtp180) REVERT: z 168 GLU cc_start: 0.4669 (OUTLIER) cc_final: 0.4416 (mp0) REVERT: z 218 GLU cc_start: 0.6151 (tp30) cc_final: 0.5890 (tt0) REVERT: z 219 GLU cc_start: 0.5894 (tt0) cc_final: 0.5392 (tp30) REVERT: z 259 GLU cc_start: 0.5121 (OUTLIER) cc_final: 0.4780 (pt0) REVERT: 0 1 MET cc_start: 0.4325 (tpp) cc_final: 0.3998 (tpt) REVERT: 0 39 LYS cc_start: 0.6554 (tppp) cc_final: 0.5995 (ttmm) REVERT: 0 47 HIS cc_start: 0.6875 (t-170) cc_final: 0.6566 (t70) REVERT: 0 115 ASP cc_start: 0.6789 (p0) cc_final: 0.6585 (p0) REVERT: 0 169 GLU cc_start: 0.5523 (mm-30) cc_final: 0.5057 (mt-10) REVERT: 0 175 ARG cc_start: 0.6507 (ttp-170) cc_final: 0.5718 (ttt180) REVERT: 0 194 THR cc_start: 0.5099 (OUTLIER) cc_final: 0.4750 (t) REVERT: 0 218 GLU cc_start: 0.5847 (tp30) cc_final: 0.5314 (mt-10) REVERT: 0 222 ARG cc_start: 0.6017 (ttm110) cc_final: 0.5752 (mtt90) REVERT: 0 265 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6428 (m-30) REVERT: 0 273 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: y 62 TYR cc_start: 0.6252 (t80) cc_final: 0.5753 (t80) REVERT: y 92 TYR cc_start: 0.7447 (m-80) cc_final: 0.7206 (m-80) REVERT: y 113 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6268 (tt0) REVERT: y 143 THR cc_start: 0.6908 (m) cc_final: 0.6630 (t) REVERT: y 186 LEU cc_start: 0.3671 (OUTLIER) cc_final: 0.3063 (mm) REVERT: y 211 MET cc_start: 0.5959 (mtp) cc_final: 0.5759 (mtm) REVERT: y 219 GLU cc_start: 0.6862 (tp30) cc_final: 0.6598 (tp30) REVERT: y 269 GLU cc_start: 0.6660 (tp30) cc_final: 0.6378 (mp0) REVERT: y 276 ASP cc_start: 0.7089 (m-30) cc_final: 0.6843 (p0) REVERT: y 280 ASP cc_start: 0.7234 (m-30) cc_final: 0.6930 (m-30) REVERT: 5 6 ILE cc_start: 0.7301 (mm) cc_final: 0.7004 (mt) REVERT: 5 43 GLU cc_start: 0.6891 (tt0) cc_final: 0.6449 (tm-30) REVERT: 5 99 ARG cc_start: 0.4866 (mmm160) cc_final: 0.3608 (mtp180) REVERT: 5 103 ARG cc_start: 0.6672 (tpp80) cc_final: 0.6054 (ptp-170) REVERT: 5 104 ASP cc_start: 0.6244 (m-30) cc_final: 0.5805 (m-30) REVERT: 5 142 GLU cc_start: 0.5116 (mt-10) cc_final: 0.4805 (mt-10) REVERT: 5 187 ASN cc_start: 0.6951 (m110) cc_final: 0.5920 (t0) REVERT: 5 194 THR cc_start: 0.5441 (OUTLIER) cc_final: 0.5085 (p) REVERT: 6 25 GLN cc_start: 0.6435 (OUTLIER) cc_final: 0.6204 (pt0) REVERT: 6 70 ASN cc_start: 0.5856 (t0) cc_final: 0.5436 (t0) REVERT: 6 140 VAL cc_start: 0.6175 (OUTLIER) cc_final: 0.5947 (m) REVERT: 6 175 ARG cc_start: 0.6071 (ttm170) cc_final: 0.5386 (ttt-90) REVERT: 6 211 MET cc_start: 0.6409 (mtm) cc_final: 0.6128 (mtp) REVERT: 6 215 ARG cc_start: 0.7662 (mtp180) cc_final: 0.6829 (mpp80) REVERT: 6 218 GLU cc_start: 0.6247 (tp30) cc_final: 0.5879 (mm-30) REVERT: 6 219 GLU cc_start: 0.6827 (tt0) cc_final: 0.6247 (mp0) REVERT: 6 240 ARG cc_start: 0.6045 (ttm-80) cc_final: 0.5820 (ttp80) REVERT: 6 281 SER cc_start: 0.6827 (t) cc_final: 0.6383 (p) REVERT: 4 4 GLN cc_start: 0.5026 (OUTLIER) cc_final: 0.3899 (tp40) REVERT: 4 21 ARG cc_start: 0.6472 (ttt-90) cc_final: 0.5540 (ttp80) REVERT: 4 36 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.5822 (ptpp) REVERT: 4 79 GLU cc_start: 0.6445 (tt0) cc_final: 0.5624 (tp30) REVERT: 4 123 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.4694 (tm-30) REVERT: 4 165 GLN cc_start: 0.7191 (tp40) cc_final: 0.6414 (pt0) REVERT: 4 169 GLU cc_start: 0.6881 (tp30) cc_final: 0.6464 (mt-10) REVERT: 4 176 ARG cc_start: 0.6317 (tpp-160) cc_final: 0.5438 (ttp80) REVERT: 4 185 ASP cc_start: 0.2476 (OUTLIER) cc_final: 0.2192 (m-30) REVERT: 4 191 HIS cc_start: 0.5971 (m-70) cc_final: 0.5328 (p90) REVERT: 4 280 ASP cc_start: 0.7785 (t0) cc_final: 0.7552 (m-30) REVERT: 8 44 LYS cc_start: 0.6642 (mptm) cc_final: 0.6310 (mmtm) REVERT: 8 68 PHE cc_start: 0.6500 (t80) cc_final: 0.6165 (t80) REVERT: 8 189 ASP cc_start: 0.5235 (p0) cc_final: 0.4557 (m-30) REVERT: 8 233 LYS cc_start: 0.7036 (mttp) cc_final: 0.6774 (tttp) REVERT: 9 30 ASP cc_start: 0.7056 (t0) cc_final: 0.6754 (t70) REVERT: 9 99 ARG cc_start: 0.5824 (ttp-170) cc_final: 0.5517 (mtp180) REVERT: 9 118 VAL cc_start: 0.5238 (m) cc_final: 0.4506 (t) REVERT: 9 169 GLU cc_start: 0.7444 (tt0) cc_final: 0.7059 (pt0) REVERT: 9 176 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5602 (tpm-80) REVERT: 9 182 LYS cc_start: 0.6298 (mtmm) cc_final: 0.5937 (pttm) REVERT: 9 215 ARG cc_start: 0.6795 (mmm-85) cc_final: 0.6087 (mpt-90) REVERT: 9 219 GLU cc_start: 0.6670 (tt0) cc_final: 0.6216 (tm-30) REVERT: 9 233 LYS cc_start: 0.5105 (mttt) cc_final: 0.4816 (mtpm) REVERT: 9 241 MET cc_start: 0.6587 (mmm) cc_final: 0.6314 (mmt) REVERT: 9 244 SER cc_start: 0.6126 (m) cc_final: 0.5486 (p) REVERT: 9 258 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.6855 (p) REVERT: 9 259 GLU cc_start: 0.6765 (pt0) cc_final: 0.6402 (pp20) REVERT: 9 284 GLN cc_start: 0.6327 (pt0) cc_final: 0.6062 (pt0) REVERT: 7 4 GLN cc_start: 0.6349 (tp40) cc_final: 0.6105 (mm-40) REVERT: 7 12 ASP cc_start: 0.6100 (m-30) cc_final: 0.5711 (m-30) REVERT: 7 21 ARG cc_start: 0.6126 (ttm-80) cc_final: 0.5918 (ttp80) REVERT: 7 28 ASP cc_start: 0.6712 (t0) cc_final: 0.6435 (t0) REVERT: 7 39 LYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5447 (mmmm) REVERT: 7 48 ARG cc_start: 0.5865 (tpt170) cc_final: 0.5544 (tpt170) REVERT: 7 98 ASP cc_start: 0.6268 (p0) cc_final: 0.5825 (t0) REVERT: 7 165 GLN cc_start: 0.7391 (tp40) cc_final: 0.6417 (mt0) REVERT: 7 218 GLU cc_start: 0.5854 (tp30) cc_final: 0.5247 (mt-10) REVERT: 7 229 GLN cc_start: 0.5127 (mt0) cc_final: 0.4794 (mt0) REVERT: 7 255 LYS cc_start: 0.6683 (mptt) cc_final: 0.6479 (ttmm) REVERT: 7 277 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6371 (pp) outliers start: 97 outliers final: 69 residues processed: 446 average time/residue: 1.6570 time to fit residues: 831.3255 Evaluate side-chains 447 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 361 time to evaluate : 2.403 ------------------------------------------------------------------------------- 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 139 SER Chi-restraints excluded: chain z residue 168 GLU Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 216 SER Chi-restraints excluded: chain z residue 224 CYS Chi-restraints excluded: chain z residue 244 SER Chi-restraints excluded: chain z residue 259 GLU Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 75 SER Chi-restraints excluded: chain 0 residue 108 VAL Chi-restraints excluded: chain 0 residue 116 THR Chi-restraints excluded: chain 0 residue 135 LEU Chi-restraints excluded: chain 0 residue 180 CYS Chi-restraints excluded: chain 0 residue 194 THR Chi-restraints excluded: chain 0 residue 250 CYS Chi-restraints excluded: chain 0 residue 265 ASP 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 216 SER 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 5 residue 57 MET Chi-restraints excluded: chain 5 residue 73 LEU Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 5 residue 194 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 263 SER Chi-restraints excluded: chain 5 residue 266 THR Chi-restraints excluded: chain 5 residue 284 GLN Chi-restraints excluded: chain 6 residue 25 GLN Chi-restraints excluded: chain 6 residue 131 SER Chi-restraints excluded: chain 6 residue 140 VAL Chi-restraints excluded: chain 4 residue 4 GLN Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 36 LYS Chi-restraints excluded: chain 4 residue 41 CYS 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 246 ASP Chi-restraints excluded: chain 8 residue 14 VAL Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 92 TYR Chi-restraints excluded: chain 8 residue 108 VAL Chi-restraints excluded: chain 8 residue 159 LEU 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 6 ILE Chi-restraints excluded: chain 9 residue 24 THR Chi-restraints excluded: chain 9 residue 93 THR Chi-restraints excluded: chain 9 residue 112 THR Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 176 ARG Chi-restraints excluded: chain 9 residue 206 THR Chi-restraints excluded: chain 9 residue 220 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 23 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 185 ASP Chi-restraints excluded: chain 7 residue 241 MET Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.0070 chunk 230 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 overall best weight: 6.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 9 25 GLN 7 18 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.218081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.170647 restraints weight = 30513.859| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.22 r_work: 0.3737 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 1.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26605 Z= 0.231 Angle : 0.581 8.712 37004 Z= 0.295 Chirality : 0.034 0.224 4397 Planarity : 0.004 0.047 3941 Dihedral : 21.433 170.964 6507 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.95 % Favored : 94.89 % Rotamer: Outliers : 4.08 % Allowed : 28.31 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.16), residues: 2546 helix: 2.46 (0.12), residues: 1790 sheet: None (None), residues: 0 loop : -0.70 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 4 217 HIS 0.008 0.001 HIS 5 69 PHE 0.013 0.002 PHE 9 179 TYR 0.025 0.002 TYR 6 94 ARG 0.007 0.001 ARG 0 127 =============================================================================== Job complete usr+sys time: 12728.93 seconds wall clock time: 227 minutes 16.22 seconds (13636.22 seconds total)