Starting phenix.real_space_refine (version: dev) on Sun Feb 26 14:51:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/02_2023/7jqq_22441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/02_2023/7jqq_22441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/02_2023/7jqq_22441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/02_2023/7jqq_22441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/02_2023/7jqq_22441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/02_2023/7jqq_22441_updated.pdb" } resolution = 4.1 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= -0.000 sd= 0.005 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 Process input model Symmetric amino acids flipped Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ARG 200": "NH1" <-> "NH2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 282": "OD1" <-> "OD2" Residue "C TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D ASP 142": "OD1" <-> "OD2" Residue "D PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D ARG 330": "NH1" <-> "NH2" Residue "E TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 281": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 28416 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 43, 'rna3p_pyr': 55} Link IDs: {'rna2p': 17, 'rna3p': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 47, 'rna3p_pyr': 56} Link IDs: {'rna2p': 13, 'rna3p': 103} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 47, 'rna3p_pyr': 57} Link IDs: {'rna2p': 12, 'rna3p': 104} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 48, 'rna3p_pyr': 57} Link IDs: {'rna2p': 11, 'rna3p': 105} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "O" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 47, 'rna3p_pyr': 53} Link IDs: {'rna2p': 15, 'rna3p': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "G" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.17, per 1000 atoms: 0.57 Number of scatterers: 28416 At special positions: 0 Unit cell: (146.59, 150.87, 218.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 709 15.00 Mg 3 11.99 O 7351 8.00 N 4880 7.00 C 15415 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: 16.65 Conformation dependent library (CDL) restraints added in 2.0 seconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 16 sheets defined 33.1% alpha, 12.1% beta 251 base pairs and 313 stacking pairs defined. Time for finding SS restraints: 12.57 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 32 through 43 Proline residue: A 38 - end of helix Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 67 through 70 No H-bonds generated for 'chain 'A' and resid 67 through 70' Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 193 through 204 Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.892A pdb=" N TYR A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 removed outlier: 4.056A pdb=" N GLN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.759A pdb=" N HIS A 298 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 307 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'B' and resid 10 through 15 removed outlier: 4.527A pdb=" N TYR B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 Proline residue: B 38 - end of helix Processing helix chain 'B' and resid 60 through 64 removed outlier: 4.146A pdb=" N ASN B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 133 through 143 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 208 through 215 removed outlier: 4.122A pdb=" N GLY B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.774A pdb=" N ASN B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 307 Processing helix chain 'B' and resid 316 through 329 Processing helix chain 'C' and resid 10 through 15 removed outlier: 4.191A pdb=" N TYR C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.706A pdb=" N TYR C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Proline residue: C 38 - end of helix removed outlier: 3.939A pdb=" N LYS C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 69 removed outlier: 4.105A pdb=" N VAL C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL C 69 " --> pdb=" O TYR C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 133 through 146 removed outlier: 4.483A pdb=" N ARG C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 194 through 206 Processing helix chain 'C' and resid 208 through 215 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 300 through 307 Processing helix chain 'C' and resid 316 through 329 Processing helix chain 'D' and resid 9 through 15 removed outlier: 3.949A pdb=" N TYR D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Proline residue: D 38 - end of helix Processing helix chain 'D' and resid 57 through 60 removed outlier: 4.001A pdb=" N ALA D 60 " --> pdb=" O PRO D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 69 through 72 No H-bonds generated for 'chain 'D' and resid 69 through 72' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 99 through 103 Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 197 through 206 removed outlier: 4.622A pdb=" N LYS D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 292 through 298 removed outlier: 3.920A pdb=" N ASN D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 307 Processing helix chain 'D' and resid 318 through 329 Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 28 through 45 removed outlier: 4.269A pdb=" N TYR E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Proline residue: E 38 - end of helix Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.564A pdb=" N ALA E 60 " --> pdb=" O PRO E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.955A pdb=" N ALA E 70 " --> pdb=" O PHE E 66 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLN E 71 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLU E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 105 No H-bonds generated for 'chain 'E' and resid 102 through 105' Processing helix chain 'E' and resid 133 through 144 removed outlier: 4.355A pdb=" N ASN E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 193 through 206 removed outlier: 4.163A pdb=" N THR E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG E 204 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 Processing helix chain 'E' and resid 217 through 221 Processing helix chain 'E' and resid 258 through 260 No H-bonds generated for 'chain 'E' and resid 258 through 260' Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 294 through 298 Processing helix chain 'E' and resid 300 through 307 Processing helix chain 'E' and resid 317 through 327 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 23 removed outlier: 5.487A pdb=" N CYS A 153 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 22 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N CYS A 155 " --> pdb=" O VAL A 22 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 49 through 53 removed outlier: 6.707A pdb=" N PHE A 85 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 275 through 277 removed outlier: 8.504A pdb=" N TYR A 276 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER A 243 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS A 239 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 255 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 253 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 180 through 182 removed outlier: 3.744A pdb=" N ILE B 23 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS B 153 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL B 22 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N CYS B 155 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.671A pdb=" N TRP B 94 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 78 through 81 Processing sheet with id= G, first strand: chain 'B' and resid 311 through 313 removed outlier: 7.031A pdb=" N MET B 262 " --> pdb=" O ARG B 312 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL B 255 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE B 240 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 180 through 182 removed outlier: 7.199A pdb=" N LEU C 19 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLU C 189 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE C 21 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS C 153 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL C 22 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N CYS C 155 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 50 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASP C 118 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL C 52 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG C 53 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE C 85 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= J, first strand: chain 'D' and resid 180 through 182 removed outlier: 7.395A pdb=" N LEU D 19 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N GLU D 189 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE D 21 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS D 153 " --> pdb=" O ASN D 20 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL D 22 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS D 155 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE D 50 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP D 118 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TRP D 94 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG D 53 " --> pdb=" O TRP D 94 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE D 96 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 78 through 81 Processing sheet with id= L, first strand: chain 'D' and resid 261 through 263 removed outlier: 3.665A pdb=" N PHE D 242 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL D 255 " --> pdb=" O PHE D 240 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE D 240 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 152 through 155 removed outlier: 7.960A pdb=" N ILE E 50 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE E 85 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 180 through 182 Processing sheet with id= O, first strand: chain 'E' and resid 243 through 246 Processing sheet with id= P, first strand: chain 'E' and resid 262 through 264 332 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 622 hydrogen bonds 1132 hydrogen bond angles 0 basepair planarities 251 basepair parallelities 313 stacking parallelities Total time for adding SS restraints: 10.16 Time building geometry restraints manager: 17.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7557 1.35 - 1.50: 13166 1.50 - 1.65: 9646 1.65 - 1.80: 66 1.80 - 1.95: 37 Bond restraints: 30472 Sorted by residual: bond pdb=" CA LEU C 299 " pdb=" CB LEU C 299 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.51e-02 4.39e+03 5.88e+00 bond pdb=" CA ASP B 118 " pdb=" CB ASP B 118 " ideal model delta sigma weight residual 1.531 1.561 -0.030 1.48e-02 4.57e+03 4.22e+00 bond pdb=" C2 C N 65 " pdb=" O2 C N 65 " ideal model delta sigma weight residual 1.240 1.204 0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C3' DA G 23 " pdb=" O3' DA G 23 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.06e+00 bond pdb=" O1B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.481 1.516 -0.035 2.00e-02 2.50e+03 3.05e+00 ... (remaining 30467 not shown) Histogram of bond angle deviations from ideal: 97.34 - 105.15: 3344 105.15 - 112.96: 17090 112.96 - 120.76: 14346 120.76 - 128.57: 8922 128.57 - 136.38: 866 Bond angle restraints: 44568 Sorted by residual: angle pdb=" O4' A K 99 " pdb=" C1' A K 99 " pdb=" N9 A K 99 " ideal model delta sigma weight residual 108.20 114.58 -6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" C3' G K 11 " pdb=" O3' G K 11 " pdb=" P G K 12 " ideal model delta sigma weight residual 120.20 126.55 -6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" O3' G K 11 " pdb=" C3' G K 11 " pdb=" C2' G K 11 " ideal model delta sigma weight residual 109.50 115.85 -6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" N VAL C 162 " pdb=" CA VAL C 162 " pdb=" C VAL C 162 " ideal model delta sigma weight residual 112.98 107.90 5.08 1.25e+00 6.40e-01 1.65e+01 angle pdb=" C ARG D 200 " pdb=" N ARG D 201 " pdb=" CA ARG D 201 " ideal model delta sigma weight residual 122.06 114.66 7.40 1.86e+00 2.89e-01 1.58e+01 ... (remaining 44563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 14807 35.88 - 71.75: 1476 71.75 - 107.63: 153 107.63 - 143.51: 17 143.51 - 179.38: 13 Dihedral angle restraints: 16466 sinusoidal: 11616 harmonic: 4850 Sorted by residual: dihedral pdb=" O4' U O 69 " pdb=" C1' U O 69 " pdb=" N1 U O 69 " pdb=" C2 U O 69 " ideal model delta sinusoidal sigma weight residual -160.00 -26.11 -133.89 1 1.50e+01 4.44e-03 7.22e+01 dihedral pdb=" O4' U M 76 " pdb=" C1' U M 76 " pdb=" N1 U M 76 " pdb=" C2 U M 76 " ideal model delta sinusoidal sigma weight residual 232.00 88.30 143.70 1 1.70e+01 3.46e-03 6.00e+01 dihedral pdb=" O4' C K 18 " pdb=" C1' C K 18 " pdb=" N1 C K 18 " pdb=" C2 C K 18 " ideal model delta sinusoidal sigma weight residual -160.00 -61.46 -98.54 1 1.50e+01 4.44e-03 4.90e+01 ... (remaining 16463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4317 0.049 - 0.097: 823 0.097 - 0.146: 222 0.146 - 0.194: 35 0.194 - 0.243: 11 Chirality restraints: 5408 Sorted by residual: chirality pdb=" C1' U O 113 " pdb=" O4' U O 113 " pdb=" C2' U O 113 " pdb=" N1 U O 113 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1' A N 46 " pdb=" O4' A N 46 " pdb=" C2' A N 46 " pdb=" N9 A N 46 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE A 190 " pdb=" N ILE A 190 " pdb=" C ILE A 190 " pdb=" CB ILE A 190 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5405 not shown) Planarity restraints: 3128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C N 65 " 0.018 2.00e-02 2.50e+03 3.93e-02 3.47e+01 pdb=" N1 C N 65 " -0.015 2.00e-02 2.50e+03 pdb=" C2 C N 65 " -0.095 2.00e-02 2.50e+03 pdb=" O2 C N 65 " 0.060 2.00e-02 2.50e+03 pdb=" N3 C N 65 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C N 65 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C N 65 " 0.017 2.00e-02 2.50e+03 pdb=" C5 C N 65 " 0.017 2.00e-02 2.50e+03 pdb=" C6 C N 65 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C L 65 " -0.010 2.00e-02 2.50e+03 3.73e-02 3.14e+01 pdb=" N1 C L 65 " 0.016 2.00e-02 2.50e+03 pdb=" C2 C L 65 " 0.088 2.00e-02 2.50e+03 pdb=" O2 C L 65 " -0.061 2.00e-02 2.50e+03 pdb=" N3 C L 65 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C L 65 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C L 65 " -0.011 2.00e-02 2.50e+03 pdb=" C5 C L 65 " -0.020 2.00e-02 2.50e+03 pdb=" C6 C L 65 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C O 65 " -0.007 2.00e-02 2.50e+03 3.61e-02 2.92e+01 pdb=" N1 C O 65 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C O 65 " -0.081 2.00e-02 2.50e+03 pdb=" O2 C O 65 " 0.066 2.00e-02 2.50e+03 pdb=" N3 C O 65 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C O 65 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C O 65 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C O 65 " 0.020 2.00e-02 2.50e+03 pdb=" C6 C O 65 " 0.016 2.00e-02 2.50e+03 ... (remaining 3125 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 11 2.08 - 2.79: 7078 2.79 - 3.49: 42401 3.49 - 4.20: 81640 4.20 - 4.90: 112357 Nonbonded interactions: 243487 Sorted by model distance: nonbonded pdb=" OG SER B 31 " pdb=" O1B AGS B 401 " model vdw 1.379 2.440 nonbonded pdb=" CB SER A 31 " pdb="MG MG A 402 " model vdw 1.888 2.570 nonbonded pdb=" O1B AGS A 401 " pdb=" O3G AGS A 401 " model vdw 1.940 2.440 nonbonded pdb=" CB SER C 31 " pdb="MG MG C 402 " model vdw 1.962 2.570 nonbonded pdb=" O6 G N 6 " pdb=" O4 U N 113 " model vdw 2.031 2.432 ... (remaining 243482 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 'A' and resid 4 through 330) selection = (chain 'B' and resid 4 through 330) selection = (chain 'C' and resid 4 through 330) selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 6 Type Number sf(0) Gaussians P 709 5.49 5 Mg 3 5.21 5 S 58 5.16 5 C 15415 2.51 5 N 4880 2.21 5 O 7351 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 group one per residue 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: 1.560 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: 9.980 Check model and map are aligned: 0.440 Process input model: 82.240 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.260 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 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 : 0.004 0.052 30472 Z= 0.237 Angle : 0.879 9.692 44568 Z= 0.449 Chirality : 0.044 0.243 5408 Planarity : 0.005 0.076 3128 Dihedral : 23.121 179.385 13346 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 26.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.20), residues: 1625 helix: -0.81 (0.22), residues: 514 sheet: -2.23 (0.33), residues: 229 loop : -1.77 (0.20), residues: 882 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3847 time to fit residues: 125.4256 Evaluate side-chains 153 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 50.0000 chunk 172 optimal weight: 50.0000 chunk 95 optimal weight: 30.0000 chunk 58 optimal weight: 40.0000 chunk 116 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 177 optimal weight: 40.0000 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 50.0000 chunk 132 optimal weight: 0.8980 chunk 206 optimal weight: 50.0000 overall best weight: 10.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 268 HIS C 107 ASN C 132 ASN C 139 ASN C 259 GLN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 30472 Z= 0.245 Angle : 0.830 9.118 44568 Z= 0.416 Chirality : 0.043 0.250 5408 Planarity : 0.005 0.052 3128 Dihedral : 24.826 178.630 10061 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 26.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer Outliers : 0.14 % 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 (0.20), residues: 1625 helix: -0.66 (0.22), residues: 515 sheet: -2.15 (0.32), residues: 232 loop : -1.78 (0.20), residues: 878 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.3736 time to fit residues: 120.2551 Evaluate side-chains 151 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 0.4980 chunk 63 optimal weight: 20.0000 chunk 171 optimal weight: 50.0000 chunk 140 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 206 optimal weight: 50.0000 chunk 223 optimal weight: 30.0000 chunk 183 optimal weight: 50.0000 chunk 204 optimal weight: 50.0000 chunk 70 optimal weight: 0.1980 chunk 165 optimal weight: 20.0000 overall best weight: 7.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN B 171 ASN B 268 HIS C 107 ASN C 132 ASN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN E 221 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 30472 Z= 0.211 Angle : 0.786 8.349 44568 Z= 0.394 Chirality : 0.042 0.260 5408 Planarity : 0.005 0.072 3128 Dihedral : 24.669 179.206 10061 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.20), residues: 1625 helix: -0.47 (0.23), residues: 507 sheet: -2.02 (0.32), residues: 239 loop : -1.73 (0.20), residues: 879 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3945 time to fit residues: 128.4120 Evaluate side-chains 151 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 50.0000 chunk 155 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 40.0000 chunk 138 optimal weight: 30.0000 chunk 207 optimal weight: 40.0000 chunk 219 optimal weight: 40.0000 chunk 108 optimal weight: 8.9990 chunk 196 optimal weight: 50.0000 chunk 59 optimal weight: 8.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 259 GLN B 268 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5681 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 30472 Z= 0.191 Angle : 0.760 8.285 44568 Z= 0.381 Chirality : 0.041 0.267 5408 Planarity : 0.004 0.058 3128 Dihedral : 24.529 178.438 10061 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.20), residues: 1625 helix: -0.42 (0.23), residues: 505 sheet: -1.91 (0.33), residues: 217 loop : -1.66 (0.20), residues: 903 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3783 time to fit residues: 126.1464 Evaluate side-chains 155 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.069 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 50.0000 chunk 124 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 chunk 163 optimal weight: 40.0000 chunk 90 optimal weight: 30.0000 chunk 187 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 112 optimal weight: 30.0000 chunk 196 optimal weight: 50.0000 chunk 55 optimal weight: 40.0000 overall best weight: 25.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN B 132 ASN B 259 GLN B 268 HIS ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 ASN ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.096 30472 Z= 0.460 Angle : 1.073 11.316 44568 Z= 0.535 Chirality : 0.052 0.327 5408 Planarity : 0.007 0.066 3128 Dihedral : 25.204 178.186 10061 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 39.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.88 % Favored : 88.00 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.93 (0.19), residues: 1625 helix: -1.37 (0.21), residues: 524 sheet: -2.19 (0.36), residues: 190 loop : -2.29 (0.18), residues: 911 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 176 average time/residue: 0.3762 time to fit residues: 108.8215 Evaluate side-chains 144 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 2.044 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2324 time to fit residues: 2.9290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 8.9990 chunk 197 optimal weight: 50.0000 chunk 43 optimal weight: 30.0000 chunk 128 optimal weight: 40.0000 chunk 54 optimal weight: 0.1980 chunk 219 optimal weight: 20.0000 chunk 182 optimal weight: 40.0000 chunk 101 optimal weight: 5.9990 chunk 18 optimal weight: 50.0000 chunk 72 optimal weight: 8.9990 chunk 115 optimal weight: 40.0000 overall best weight: 8.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS C 107 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 30472 Z= 0.226 Angle : 0.834 8.691 44568 Z= 0.420 Chirality : 0.044 0.364 5408 Planarity : 0.005 0.062 3128 Dihedral : 24.859 179.744 10061 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 26.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer Outliers : 0.07 % 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: -2.54 (0.19), residues: 1625 helix: -0.99 (0.22), residues: 519 sheet: -2.26 (0.34), residues: 208 loop : -1.98 (0.19), residues: 898 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 198 average time/residue: 0.3867 time to fit residues: 124.9464 Evaluate side-chains 147 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 2.204 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2525 time to fit residues: 3.1069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 50.0000 chunk 24 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 160 optimal weight: 50.0000 chunk 124 optimal weight: 7.9990 chunk 184 optimal weight: 50.0000 chunk 122 optimal weight: 20.0000 chunk 218 optimal weight: 30.0000 chunk 136 optimal weight: 40.0000 chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS C 259 GLN C 298 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 30472 Z= 0.227 Angle : 0.817 10.024 44568 Z= 0.409 Chirality : 0.043 0.255 5408 Planarity : 0.005 0.071 3128 Dihedral : 24.742 179.166 10061 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.20), residues: 1625 helix: -0.82 (0.22), residues: 515 sheet: -2.16 (0.37), residues: 185 loop : -2.00 (0.19), residues: 925 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.3757 time to fit residues: 124.0298 Evaluate side-chains 152 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 30.0000 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 139 optimal weight: 30.0000 chunk 149 optimal weight: 40.0000 chunk 108 optimal weight: 0.0670 chunk 20 optimal weight: 20.0000 chunk 171 optimal weight: 50.0000 chunk 199 optimal weight: 50.0000 overall best weight: 7.8130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 30472 Z= 0.206 Angle : 0.793 9.187 44568 Z= 0.398 Chirality : 0.042 0.251 5408 Planarity : 0.005 0.064 3128 Dihedral : 24.625 178.858 10061 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.20), residues: 1625 helix: -0.74 (0.22), residues: 516 sheet: -2.03 (0.37), residues: 188 loop : -1.91 (0.19), residues: 921 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.3999 time to fit residues: 124.2663 Evaluate side-chains 154 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 20.0000 chunk 191 optimal weight: 50.0000 chunk 203 optimal weight: 50.0000 chunk 122 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 160 optimal weight: 50.0000 chunk 62 optimal weight: 7.9990 chunk 184 optimal weight: 40.0000 chunk 192 optimal weight: 50.0000 chunk 133 optimal weight: 0.8980 chunk 215 optimal weight: 30.0000 overall best weight: 7.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 30472 Z= 0.206 Angle : 0.786 9.184 44568 Z= 0.393 Chirality : 0.041 0.247 5408 Planarity : 0.005 0.061 3128 Dihedral : 24.562 178.133 10061 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.20), residues: 1625 helix: -0.73 (0.23), residues: 512 sheet: -1.77 (0.41), residues: 164 loop : -1.92 (0.19), residues: 949 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3974 time to fit residues: 122.6102 Evaluate side-chains 150 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.252 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 149 optimal weight: 40.0000 chunk 226 optimal weight: 40.0000 chunk 208 optimal weight: 50.0000 chunk 180 optimal weight: 50.0000 chunk 18 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 110 optimal weight: 40.0000 chunk 143 optimal weight: 10.0000 chunk 191 optimal weight: 50.0000 overall best weight: 6.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30472 Z= 0.195 Angle : 0.770 8.808 44568 Z= 0.386 Chirality : 0.041 0.243 5408 Planarity : 0.005 0.060 3128 Dihedral : 24.483 177.804 10061 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.20), residues: 1625 helix: -0.71 (0.22), residues: 510 sheet: -1.73 (0.40), residues: 164 loop : -1.90 (0.19), residues: 951 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3864 time to fit residues: 114.5519 Evaluate side-chains 147 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.249 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 20.0000 chunk 166 optimal weight: 50.0000 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 180 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 185 optimal weight: 40.0000 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 30.0000 chunk 158 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS C 284 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.100958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.096377 restraints weight = 189705.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.096488 restraints weight = 223831.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.096017 restraints weight = 141858.807| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 30472 Z= 0.193 Angle : 0.765 8.621 44568 Z= 0.384 Chirality : 0.041 0.240 5408 Planarity : 0.005 0.070 3128 Dihedral : 24.416 177.327 10061 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.20), residues: 1625 helix: -0.68 (0.23), residues: 515 sheet: -1.72 (0.41), residues: 164 loop : -1.89 (0.19), residues: 946 =============================================================================== Job complete usr+sys time: 3548.62 seconds wall clock time: 68 minutes 4.38 seconds (4084.38 seconds total)