Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 18 23:39:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/08_2023/7lj3_23388.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/08_2023/7lj3_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_23388/08_2023/7lj3_23388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/08_2023/7lj3_23388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/08_2023/7lj3_23388.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj3_23388/08_2023/7lj3_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 16.57, per 1000 atoms: 0.64 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: 13.63 Conformation dependent library (CDL) restraints added in 3.3 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: 7.83 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: 8.14 Time building geometry restraints manager: 14.38 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.530 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 76.720 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.110 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:20.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.260 ------------------------------------------------------------------------------- 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 : 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 : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 11 residues processed: 601 average time/residue: 1.4387 time to fit residues: 987.3886 Evaluate side-chains 281 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 270 time to evaluate : 2.417 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 3.4451 ------------------------------------------------------------------------------- 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 252 ASN 0 22 HIS y 22 HIS y 105 HIS 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 7 170 ASN 7 193 ASN 7 260 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2709 moved from start: 0.6739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 26605 Z= 0.277 Angle : 0.772 10.699 37004 Z= 0.391 Chirality : 0.040 0.274 4397 Planarity : 0.006 0.068 3941 Dihedral : 16.730 173.924 5567 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.42 % Favored : 96.43 % Rotamer Outliers : 5.91 % 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: 1.58 (0.16), residues: 2546 helix: 1.65 (0.11), residues: 1773 sheet: None (None), residues: 0 loop : -0.29 (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 691 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 555 time to evaluate : 2.656 Fit side-chains revert: symmetry clash outliers start: 136 outliers final: 29 residues processed: 639 average time/residue: 1.6255 time to fit residues: 1172.7967 Evaluate side-chains 380 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 351 time to evaluate : 2.445 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 4 average time/residue: 0.2389 time to fit residues: 5.2484 ------------------------------------------------------------------------------- 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: 0.7980 chunk 76 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 168 optimal weight: 30.0000 chunk 68 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 268 optimal weight: 50.0000 chunk 221 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 chunk 199 optimal weight: 20.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- 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 0 34 HIS 0 47 HIS 0 256 HIS 5 69 HIS ** 4 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 8 177 ASN 9 25 GLN 7 105 HIS 7 165 GLN ** 7 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 260 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2947 moved from start: 0.9793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 26605 Z= 0.260 Angle : 0.656 7.719 37004 Z= 0.337 Chirality : 0.036 0.165 4397 Planarity : 0.005 0.073 3941 Dihedral : 16.416 158.718 5567 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.65 % Favored : 96.23 % Rotamer Outliers : 6.43 % 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: 2.17 (0.16), residues: 2546 helix: 2.16 (0.12), residues: 1775 sheet: None (None), residues: 0 loop : -0.25 (0.23), residues: 771 *********************** 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 641 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 493 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 46 residues processed: 598 average time/residue: 1.6400 time to fit residues: 1104.6217 Evaluate side-chains 393 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 347 time to evaluate : 2.618 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 11 average time/residue: 0.8488 time to fit residues: 14.7848 ------------------------------------------------------------------------------- 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: 30.0000 chunk 128 optimal weight: 6.9990 chunk 27 optimal weight: 0.0170 chunk 118 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 263 optimal weight: 50.0000 chunk 130 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 overall best weight: 3.5624 ------------------------------------------------------------------------------- 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 5 70 ASN 5 229 GLN 4 34 HIS ** 4 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 191 HIS 4 229 GLN 8 4 GLN 8 177 ASN 9 170 ASN 7 18 ASN 7 165 GLN ** 7 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2954 moved from start: 1.0566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 26605 Z= 0.171 Angle : 0.546 8.329 37004 Z= 0.280 Chirality : 0.033 0.183 4397 Planarity : 0.004 0.042 3941 Dihedral : 16.136 170.852 5567 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Rotamer Outliers : 5.64 % 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: 2.81 (0.16), residues: 2546 helix: 2.71 (0.12), residues: 1778 sheet: None (None), residues: 0 loop : -0.20 (0.22), residues: 768 *********************** 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 499 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 369 time to evaluate : 2.531 Fit side-chains outliers start: 130 outliers final: 61 residues processed: 461 average time/residue: 1.6258 time to fit residues: 846.2736 Evaluate side-chains 393 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 332 time to evaluate : 2.597 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 52 residues processed: 9 average time/residue: 0.5741 time to fit residues: 10.4528 ------------------------------------------------------------------------------- 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: 8.9990 chunk 149 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 196 optimal weight: 30.0000 chunk 108 optimal weight: 2.9990 chunk 225 optimal weight: 20.0000 chunk 182 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 191 HIS 4 229 GLN 8 170 ASN 7 165 GLN ** 7 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3032 moved from start: 1.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 26605 Z= 0.229 Angle : 0.592 7.784 37004 Z= 0.303 Chirality : 0.034 0.166 4397 Planarity : 0.004 0.044 3941 Dihedral : 16.083 177.191 5567 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.16 % Favored : 95.68 % 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: 2.46 (0.16), residues: 2546 helix: 2.48 (0.12), residues: 1801 sheet: None (None), residues: 0 loop : -0.53 (0.22), residues: 745 *********************** 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 506 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 374 time to evaluate : 2.767 Fit side-chains outliers start: 132 outliers final: 73 residues processed: 471 average time/residue: 1.6301 time to fit residues: 865.8980 Evaluate side-chains 398 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 325 time to evaluate : 2.590 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 64 residues processed: 11 average time/residue: 0.7001 time to fit residues: 13.3171 ------------------------------------------------------------------------------- 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: 4.9990 chunk 237 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 264 optimal weight: 50.0000 chunk 219 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS y 158 HIS ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 193 ASN ** 4 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 191 HIS 4 229 GLN 9 25 GLN 7 165 GLN 7 187 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3036 moved from start: 1.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 26605 Z= 0.195 Angle : 0.550 9.118 37004 Z= 0.281 Chirality : 0.033 0.344 4397 Planarity : 0.004 0.041 3941 Dihedral : 15.890 173.989 5567 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.89 % Favored : 95.95 % Rotamer Outliers : 5.86 % 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: 2.63 (0.16), residues: 2546 helix: 2.62 (0.12), residues: 1801 sheet: None (None), residues: 0 loop : -0.53 (0.22), residues: 745 *********************** 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 501 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 366 time to evaluate : 2.582 Fit side-chains outliers start: 135 outliers final: 94 residues processed: 467 average time/residue: 1.6490 time to fit residues: 871.7988 Evaluate side-chains 425 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 331 time to evaluate : 2.514 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 81 residues processed: 17 average time/residue: 0.6282 time to fit residues: 17.6296 ------------------------------------------------------------------------------- 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: 6.9990 chunk 150 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 263 optimal weight: 50.0000 chunk 164 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 121 optimal weight: 0.1980 overall best weight: 5.6388 ------------------------------------------------------------------------------- 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 0 229 GLN y 47 HIS y 165 GLN ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 177 ASN 4 191 HIS 4 229 GLN 9 22 HIS 9 25 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3066 moved from start: 1.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 26605 Z= 0.208 Angle : 0.566 9.447 37004 Z= 0.289 Chirality : 0.033 0.242 4397 Planarity : 0.004 0.044 3941 Dihedral : 15.800 172.008 5567 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.40 % 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: 2.56 (0.16), residues: 2546 helix: 2.58 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -0.56 (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 494 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 355 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 94 residues processed: 465 average time/residue: 1.6637 time to fit residues: 871.7590 Evaluate side-chains 421 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 327 time to evaluate : 2.822 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 82 residues processed: 13 average time/residue: 0.5859 time to fit residues: 13.9372 ------------------------------------------------------------------------------- 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: 20.0000 chunk 105 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 179 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 256 HIS y 47 HIS y 165 GLN ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 177 ASN 4 191 HIS 4 229 GLN 9 25 GLN 7 165 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3054 moved from start: 1.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 26605 Z= 0.172 Angle : 0.530 8.905 37004 Z= 0.270 Chirality : 0.032 0.276 4397 Planarity : 0.003 0.041 3941 Dihedral : 15.633 171.067 5567 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.08 % Favored : 95.76 % Rotamer Outliers : 4.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.76 (0.16), residues: 2546 helix: 2.73 (0.12), residues: 1798 sheet: None (None), residues: 0 loop : -0.48 (0.22), residues: 748 *********************** 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 453 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 342 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 87 residues processed: 435 average time/residue: 1.6600 time to fit residues: 815.3043 Evaluate side-chains 406 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 319 time to evaluate : 2.811 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 79 residues processed: 9 average time/residue: 0.8610 time to fit residues: 13.2191 ------------------------------------------------------------------------------- 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: 7.9990 chunk 252 optimal weight: 50.0000 chunk 229 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 70 ASN 0 25 GLN 0 47 HIS 0 256 HIS y 47 HIS y 165 GLN ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 9 25 GLN 9 191 HIS 7 165 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3051 moved from start: 1.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 26605 Z= 0.160 Angle : 0.520 8.600 37004 Z= 0.264 Chirality : 0.031 0.240 4397 Planarity : 0.003 0.040 3941 Dihedral : 15.418 169.807 5567 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.20 % Favored : 95.64 % Rotamer Outliers : 4.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.91 (0.17), residues: 2546 helix: 2.82 (0.12), residues: 1794 sheet: None (None), residues: 0 loop : -0.34 (0.23), residues: 752 *********************** 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 451 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 344 time to evaluate : 2.482 Fit side-chains revert: symmetry clash outliers start: 107 outliers final: 84 residues processed: 432 average time/residue: 1.6574 time to fit residues: 807.0295 Evaluate side-chains 403 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 319 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 78 residues processed: 7 average time/residue: 0.5057 time to fit residues: 8.4376 ------------------------------------------------------------------------------- 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: 20.0000 chunk 259 optimal weight: 50.0000 chunk 158 optimal weight: 0.3980 chunk 123 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 271 optimal weight: 50.0000 chunk 250 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 overall best weight: 6.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 70 ASN z 158 HIS 0 25 GLN 0 47 HIS 0 256 HIS y 47 HIS y 165 GLN ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 8 158 HIS 9 25 GLN 7 165 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3097 moved from start: 1.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 26605 Z= 0.239 Angle : 0.591 8.304 37004 Z= 0.301 Chirality : 0.034 0.256 4397 Planarity : 0.004 0.046 3941 Dihedral : 15.475 171.613 5567 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.60 % Favored : 95.25 % 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: 2.47 (0.16), residues: 2546 helix: 2.50 (0.12), residues: 1796 sheet: None (None), residues: 0 loop : -0.55 (0.22), residues: 750 ********************** 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 422 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 333 time to evaluate : 2.703 Fit side-chains outliers start: 89 outliers final: 78 residues processed: 416 average time/residue: 1.6461 time to fit residues: 775.7513 Evaluate side-chains 396 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 318 time to evaluate : 2.572 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 76 residues processed: 3 average time/residue: 1.3063 time to fit residues: 7.9984 ------------------------------------------------------------------------------- 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: 1.9990 chunk 230 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 199 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 47 HIS 0 256 HIS y 47 HIS y 165 GLN ** y 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 229 GLN 9 25 GLN 7 165 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.220571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.172860 restraints weight = 30673.328| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.30 r_work: 0.3758 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 1.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 26605 Z= 0.195 Angle : 0.548 8.265 37004 Z= 0.278 Chirality : 0.032 0.245 4397 Planarity : 0.003 0.044 3941 Dihedral : 15.312 171.170 5567 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.37 % 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: 2.58 (0.16), residues: 2546 helix: 2.61 (0.12), residues: 1790 sheet: None (None), residues: 0 loop : -0.56 (0.22), residues: 756 =============================================================================== Job complete usr+sys time: 12390.24 seconds wall clock time: 219 minutes 3.35 seconds (13143.35 seconds total)