Starting phenix.real_space_refine (version: dev) on Thu Apr 7 06:36:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/04_2022/7lj3_23388.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/04_2022/7lj3_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_23388/04_2022/7lj3_23388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/04_2022/7lj3_23388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/04_2022/7lj3_23388.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/04_2022/7lj3_23388.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'rna3p_pyr': 35, 'rna2p_pur': 7, 'rna3p_pur': 27, 'rna2p_pyr': 6, '5*END': 1} Link IDs: {'rna3p': 61, 'rna2p': 13} Chain: "B" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1590 Classifications: {'RNA': 75} Modifications used: {'rna3p_pyr': 35, 'rna2p_pur': 7, 'rna3p_pur': 27, 'rna2p_pyr': 6, '5*END': 1} Link IDs: {'rna3p': 61, 'rna2p': 13} Chain: "C" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1590 Classifications: {'RNA': 75} Modifications used: {'rna3p_pyr': 35, 'rna2p_pur': 7, 'rna3p_pur': 27, 'rna2p_pyr': 6, '5*END': 1} Link IDs: {'rna3p': 61, 'rna2p': 13} Time building chain proxies: 15.79, per 1000 atoms: 0.61 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: 13.47 Conformation dependent library (CDL) restraints added in 3.4 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: 8.09 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: 8.67 Time building geometry restraints manager: 14.16 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: 15188 35.08 - 70.16: 525 70.16 - 105.24: 51 105.24 - 140.32: 18 140.32 - 175.41: 4 Dihedral angle restraints: 15786 sinusoidal: 8220 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 15783 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 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. 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 12.020 Check model and map are aligned: 0.520 Convert atoms to be neutral: 0.000 Process input model: 77.810 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2349 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 : 17.119 175.406 10838 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 % 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 *********************** 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 : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 11 residues processed: 601 average time/residue: 1.3797 time to fit residues: 953.1945 Evaluate side-chains 276 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 265 time to evaluate : 2.678 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 3.7260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 70 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 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: 3.7788 ------------------------------------------------------------------------------- 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 0 47 HIS y 22 HIS y 105 HIS y 165 GLN ** y 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 9 170 ASN 9 256 HIS 7 22 HIS ** 7 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 150 GLN 7 170 ASN 7 193 ASN 7 260 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2936 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 26605 Z= 0.277 Angle : 0.759 9.955 37004 Z= 0.384 Chirality : 0.039 0.196 4397 Planarity : 0.006 0.068 3941 Dihedral : 16.746 175.120 5567 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.65 % Favored : 96.19 % Rotamer Outliers : 5.73 % 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: 1.65 (0.16), residues: 2546 helix: 1.72 (0.11), residues: 1773 sheet: None (None), residues: 0 loop : -0.30 (0.23), residues: 773 *********************** 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 668 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 536 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 34 residues processed: 619 average time/residue: 1.4503 time to fit residues: 1025.2329 Evaluate side-chains 375 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 341 time to evaluate : 2.780 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 30 residues processed: 5 average time/residue: 0.4819 time to fit residues: 7.4971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 268 optimal weight: 50.0000 chunk 221 optimal weight: 6.9990 chunk 246 optimal weight: 20.0000 chunk 84 optimal weight: 30.0000 chunk 199 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 170 ASN 0 22 HIS 0 34 HIS ** y 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 69 HIS 6 70 ASN 4 158 HIS ** 4 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 9 25 GLN 7 105 HIS 7 170 ASN ** 7 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 260 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3219 moved from start: 0.9686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 26605 Z= 0.267 Angle : 0.677 10.480 37004 Z= 0.348 Chirality : 0.037 0.172 4397 Planarity : 0.005 0.058 3941 Dihedral : 16.447 159.198 5567 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % Rotamer Outliers : 6.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.16), residues: 2546 helix: 2.12 (0.12), residues: 1774 sheet: None (None), residues: 0 loop : -0.30 (0.23), residues: 772 *********************** 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 645 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 501 time to evaluate : 2.771 Fit side-chains revert: symmetry clash outliers start: 144 outliers final: 47 residues processed: 598 average time/residue: 1.6155 time to fit residues: 1095.7672 Evaluate side-chains 405 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 358 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 34 residues processed: 14 average time/residue: 0.5869 time to fit residues: 14.7392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 10.0000 chunk 186 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 249 optimal weight: 7.9990 chunk 263 optimal weight: 50.0000 chunk 130 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- 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 0 256 HIS y 193 ASN 5 70 ASN 5 229 GLN 4 34 HIS 4 158 HIS 4 191 HIS 4 229 GLN 8 4 GLN 9 170 ASN 7 18 ASN 7 34 HIS 7 165 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3281 moved from start: 1.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.121 26605 Z= 0.250 Angle : 0.626 9.136 37004 Z= 0.320 Chirality : 0.035 0.177 4397 Planarity : 0.004 0.045 3941 Dihedral : 16.303 162.487 5567 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.01 % Favored : 95.84 % Rotamer Outliers : 6.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.16), residues: 2546 helix: 2.39 (0.12), residues: 1777 sheet: None (None), residues: 0 loop : -0.39 (0.22), residues: 769 *********************** 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 540 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 398 time to evaluate : 3.145 Fit side-chains revert: symmetry clash outliers start: 142 outliers final: 74 residues processed: 497 average time/residue: 1.5028 time to fit residues: 847.5745 Evaluate side-chains 418 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 344 time to evaluate : 2.834 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 54 residues processed: 20 average time/residue: 0.6616 time to fit residues: 21.1660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 196 optimal weight: 30.0000 chunk 108 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 chunk 236 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 70 ASN 0 22 HIS 4 191 HIS 4 229 GLN 9 25 GLN 9 170 ASN 7 165 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3348 moved from start: 1.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 26605 Z= 0.266 Angle : 0.634 8.438 37004 Z= 0.324 Chirality : 0.035 0.172 4397 Planarity : 0.005 0.048 3941 Dihedral : 16.263 179.775 5567 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.52 % Favored : 95.33 % Rotamer Outliers : 6.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.16), residues: 2546 helix: 2.20 (0.12), residues: 1798 sheet: None (None), residues: 0 loop : -0.73 (0.22), residues: 748 *********************** 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 540 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 387 time to evaluate : 3.038 Fit side-chains revert: symmetry clash outliers start: 153 outliers final: 89 residues processed: 500 average time/residue: 1.5561 time to fit residues: 880.9730 Evaluate side-chains 426 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 337 time to evaluate : 2.839 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 74 residues processed: 16 average time/residue: 0.9577 time to fit residues: 22.3722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 7.9990 chunk 237 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 264 optimal weight: 50.0000 chunk 219 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 0 25 GLN 0 47 HIS y 165 GLN 4 191 HIS 8 170 ASN 9 22 HIS 9 25 GLN 9 165 GLN 9 170 ASN 7 18 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3352 moved from start: 1.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 26605 Z= 0.233 Angle : 0.600 10.980 37004 Z= 0.307 Chirality : 0.034 0.328 4397 Planarity : 0.004 0.047 3941 Dihedral : 16.080 177.088 5567 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.52 % Favored : 95.33 % Rotamer Outliers : 6.04 % 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: 2.22 (0.16), residues: 2546 helix: 2.32 (0.12), residues: 1798 sheet: None (None), residues: 0 loop : -0.69 (0.22), residues: 748 *********************** 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 495 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 356 time to evaluate : 2.862 Fit side-chains revert: symmetry clash outliers start: 139 outliers final: 97 residues processed: 462 average time/residue: 1.5574 time to fit residues: 815.2171 Evaluate side-chains 437 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 340 time to evaluate : 3.140 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 80 residues processed: 18 average time/residue: 0.9779 time to fit residues: 25.2492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 150 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 263 optimal weight: 50.0000 chunk 164 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 0 47 HIS 0 256 HIS y 165 GLN y 193 ASN 4 191 HIS 9 170 ASN 7 18 ASN 7 165 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3360 moved from start: 1.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.270 26605 Z= 0.235 Angle : 0.588 16.981 37004 Z= 0.304 Chirality : 0.033 0.269 4397 Planarity : 0.004 0.074 3941 Dihedral : 15.881 172.467 5567 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.75 % Favored : 95.09 % Rotamer Outliers : 5.78 % 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: 2.44 (0.16), residues: 2546 helix: 2.50 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -0.62 (0.22), residues: 751 *********************** 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 496 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 363 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 92 residues processed: 465 average time/residue: 1.5437 time to fit residues: 812.7649 Evaluate side-chains 430 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 338 time to evaluate : 2.763 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 79 residues processed: 13 average time/residue: 0.8507 time to fit residues: 17.2605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 158 HIS 0 22 HIS 0 47 HIS 0 256 HIS y 165 GLN y 212 ASN 4 191 HIS 8 34 HIS 9 170 ASN 7 18 ASN 7 165 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3406 moved from start: 1.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.314 26605 Z= 0.333 Angle : 0.660 21.053 37004 Z= 0.340 Chirality : 0.036 0.277 4397 Planarity : 0.005 0.117 3941 Dihedral : 15.987 176.393 5567 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.03 % Favored : 94.82 % Rotamer Outliers : 6.30 % 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: 2.05 (0.16), residues: 2546 helix: 2.21 (0.12), residues: 1792 sheet: None (None), residues: 0 loop : -0.76 (0.22), residues: 754 *********************** 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 496 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 351 time to evaluate : 2.862 Fit side-chains outliers start: 145 outliers final: 97 residues processed: 465 average time/residue: 1.5638 time to fit residues: 822.6995 Evaluate side-chains 435 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 338 time to evaluate : 2.820 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 84 residues processed: 13 average time/residue: 0.6983 time to fit residues: 16.0104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 2.9990 chunk 252 optimal weight: 50.0000 chunk 229 optimal weight: 8.9990 chunk 245 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 192 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 158 HIS ** 0 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 47 HIS 0 256 HIS y 165 GLN ** y 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 25 GLN 4 191 HIS 9 25 GLN 9 170 ASN 7 18 ASN 7 165 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3402 moved from start: 1.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.382 26605 Z= 0.316 Angle : 0.781 73.899 37004 Z= 0.375 Chirality : 0.035 0.258 4397 Planarity : 0.005 0.107 3941 Dihedral : 15.982 176.351 5567 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.99 % Favored : 94.85 % Rotamer Outliers : 4.78 % 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: 2.05 (0.16), residues: 2546 helix: 2.21 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -0.78 (0.22), residues: 751 *********************** 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 453 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 343 time to evaluate : 2.794 Fit side-chains outliers start: 110 outliers final: 94 residues processed: 440 average time/residue: 1.6083 time to fit residues: 800.5306 Evaluate side-chains 430 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 336 time to evaluate : 2.818 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 87 residues processed: 7 average time/residue: 0.9931 time to fit residues: 11.8869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 7.9990 chunk 259 optimal weight: 50.0000 chunk 158 optimal weight: 0.0050 chunk 123 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 271 optimal weight: 50.0000 chunk 250 optimal weight: 0.2980 chunk 216 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 overall best weight: 4.8600 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 0 47 HIS 0 256 HIS y 165 GLN ** y 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 191 HIS 4 229 GLN 9 170 ASN ** 7 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 165 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3401 moved from start: 1.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.439 26605 Z= 0.753 Angle : 0.856 73.899 37004 Z= 0.441 Chirality : 0.035 0.258 4397 Planarity : 0.005 0.146 3941 Dihedral : 15.982 176.351 5567 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.99 % Favored : 94.85 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.05 (0.16), residues: 2546 helix: 2.21 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -0.78 (0.22), residues: 751 ********************** 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 425 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 336 time to evaluate : 2.759 Fit side-chains outliers start: 89 outliers final: 87 residues processed: 425 average time/residue: 1.6348 time to fit residues: 782.1601 Evaluate side-chains 420 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 333 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 87 residues processed: 0 time to fit residues: 3.6350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 199 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 216 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 47 HIS 0 256 HIS y 165 GLN ** y 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 191 HIS 4 229 GLN 9 170 ASN 7 18 ASN ** 7 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 165 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.217085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.169272 restraints weight = 30505.302| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.23 r_work: 0.3833 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 1.12 restraints_weight: 0.2500 r_work: 0.3806 rms_B_bonded: 1.28 restraints_weight: 0.1250 r_work: 0.3788 rms_B_bonded: 1.54 restraints_weight: 0.0625 r_work: 0.3766 rms_B_bonded: 1.94 restraints_weight: 0.0312 r_work: 0.3736 rms_B_bonded: 2.51 restraints_weight: 0.0156 r_work: 0.3696 rms_B_bonded: 3.33 restraints_weight: 0.0078 r_work: 0.3640 rms_B_bonded: 4.59 restraints_weight: 0.0039 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 1.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.439 26605 Z= 0.753 Angle : 0.856 73.899 37004 Z= 0.441 Chirality : 0.035 0.258 4397 Planarity : 0.005 0.146 3941 Dihedral : 15.982 176.351 5567 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.99 % Favored : 94.85 % Rotamer Outliers : 3.91 % 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: 2.05 (0.16), residues: 2546 helix: 2.21 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -0.78 (0.22), residues: 751 =============================================================================== Job complete usr+sys time: 11235.89 seconds wall clock time: 198 minutes 50.48 seconds (11930.48 seconds total)