Starting phenix.real_space_refine (version: dev) on Tue Feb 21 17:28:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/02_2023/7xmv_33306_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/02_2023/7xmv_33306.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/02_2023/7xmv_33306_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/02_2023/7xmv_33306_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/02_2023/7xmv_33306_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/02_2023/7xmv_33306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/02_2023/7xmv_33306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/02_2023/7xmv_33306_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/02_2023/7xmv_33306_updated.pdb" } resolution = 2.6 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= 0.011 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 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 29": "OD1" <-> "OD2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "E TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E ARG 195": "NH1" <-> "NH2" Residue "E TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 298": "OE1" <-> "OE2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "F TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F ASP 65": "OD1" <-> "OD2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 298": "OE1" <-> "OE2" Residue "F ARG 302": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15228 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "E" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "C" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "D" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "B" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "F" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "E" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "C" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "D" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "F" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 133 Classifications: {'water': 133} Link IDs: {None: 132} Time building chain proxies: 8.59, per 1000 atoms: 0.56 Number of scatterers: 15228 At special positions: 0 Unit cell: (120.84, 126.14, 83.74, 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 78 16.00 P 24 15.00 Mg 12 11.99 O 3642 8.00 N 2574 7.00 C 8898 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: 5.99 Conformation dependent library (CDL) restraints added in 2.2 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3444 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 18 sheets defined 35.8% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 109 through 120 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.977A pdb=" N GLN A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 removed outlier: 3.714A pdb=" N VAL A 174 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL A 175 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 109 through 120 Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 149 through 158 removed outlier: 3.979A pdb=" N GLN E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 183 removed outlier: 3.714A pdb=" N VAL E 174 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL E 175 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 279 through 283 Processing helix chain 'E' and resid 293 through 304 Processing helix chain 'E' and resid 310 through 313 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 109 through 120 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.978A pdb=" N GLN C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 183 removed outlier: 3.714A pdb=" N VAL C 174 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL C 175 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 293 through 304 Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 109 through 120 Processing helix chain 'D' and resid 133 through 138 Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.977A pdb=" N GLN D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 183 removed outlier: 3.714A pdb=" N VAL D 174 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL D 175 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 293 through 304 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 109 through 120 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.978A pdb=" N GLN B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 183 removed outlier: 3.714A pdb=" N VAL B 174 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL B 175 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'F' and resid 13 through 22 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 109 through 120 Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 149 through 158 removed outlier: 3.977A pdb=" N GLN F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 183 removed outlier: 3.714A pdb=" N VAL F 174 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL F 175 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 293 through 304 Processing helix chain 'F' and resid 310 through 313 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.517A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG A 84 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG A 124 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE A 89 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU A 126 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N THR A 127 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP A 144 " --> pdb=" O THR A 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 287 through 289 removed outlier: 6.303A pdb=" N VAL A 269 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS A 216 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N TYR A 247 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 218 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 165 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL A 219 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 167 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP A 188 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N SER A 168 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA A 190 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.515A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG E 84 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG E 124 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE E 89 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU E 126 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N THR E 127 " --> pdb=" O PRO E 142 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP E 144 " --> pdb=" O THR E 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= F, first strand: chain 'E' and resid 287 through 289 removed outlier: 6.304A pdb=" N VAL E 269 " --> pdb=" O ARG E 288 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS E 216 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N TYR E 247 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU E 218 " --> pdb=" O TYR E 247 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE E 165 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL E 219 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL E 167 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP E 188 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N SER E 168 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA E 190 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.516A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG C 84 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG C 124 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE C 89 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU C 126 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR C 127 " --> pdb=" O PRO C 142 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP C 144 " --> pdb=" O THR C 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= I, first strand: chain 'C' and resid 287 through 289 removed outlier: 6.304A pdb=" N VAL C 269 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS C 216 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N TYR C 247 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 218 " --> pdb=" O TYR C 247 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE C 165 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL C 219 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 167 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP C 188 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N SER C 168 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA C 190 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.516A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG D 84 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG D 124 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE D 89 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU D 126 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR D 127 " --> pdb=" O PRO D 142 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP D 144 " --> pdb=" O THR D 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= L, first strand: chain 'D' and resid 287 through 289 removed outlier: 6.304A pdb=" N VAL D 269 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS D 216 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N TYR D 247 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU D 218 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE D 165 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL D 219 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 167 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP D 188 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N SER D 168 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA D 190 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.516A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG B 84 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG B 124 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 89 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU B 126 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N THR B 127 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP B 144 " --> pdb=" O THR B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.304A pdb=" N VAL B 269 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS B 216 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N TYR B 247 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 218 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE B 165 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL B 219 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 167 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASP B 188 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N SER B 168 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA B 190 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.516A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG F 84 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG F 124 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE F 89 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU F 126 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N THR F 127 " --> pdb=" O PRO F 142 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP F 144 " --> pdb=" O THR F 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= R, first strand: chain 'F' and resid 287 through 289 removed outlier: 6.304A pdb=" N VAL F 269 " --> pdb=" O ARG F 288 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS F 216 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N TYR F 247 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU F 218 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE F 165 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL F 219 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 167 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP F 188 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N SER F 168 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA F 190 " --> pdb=" O SER F 168 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.40 Time building geometry restraints manager: 6.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4821 1.33 - 1.45: 1298 1.45 - 1.57: 8299 1.57 - 1.69: 48 1.69 - 1.80: 132 Bond restraints: 14598 Sorted by residual: bond pdb=" C1 HSX B 401 " pdb=" O4 HSX B 401 " ideal model delta sigma weight residual 1.293 1.602 -0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" C1 HSX A 401 " pdb=" O4 HSX A 401 " ideal model delta sigma weight residual 1.293 1.602 -0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" C1 HSX E 401 " pdb=" O4 HSX E 401 " ideal model delta sigma weight residual 1.293 1.602 -0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" C1 HSX C 401 " pdb=" O4 HSX C 401 " ideal model delta sigma weight residual 1.293 1.602 -0.309 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C1 HSX F 401 " pdb=" O4 HSX F 401 " ideal model delta sigma weight residual 1.293 1.601 -0.308 2.00e-02 2.50e+03 2.38e+02 ... (remaining 14593 not shown) Histogram of bond angle deviations from ideal: 98.77 - 106.17: 372 106.17 - 113.57: 8513 113.57 - 120.97: 6843 120.97 - 128.36: 4054 128.36 - 135.76: 72 Bond angle restraints: 19854 Sorted by residual: angle pdb=" CA GLY C 209 " pdb=" C GLY C 209 " pdb=" N ASP C 210 " ideal model delta sigma weight residual 114.23 117.89 -3.66 8.80e-01 1.29e+00 1.73e+01 angle pdb=" CA GLY F 209 " pdb=" C GLY F 209 " pdb=" N ASP F 210 " ideal model delta sigma weight residual 114.23 117.87 -3.64 8.80e-01 1.29e+00 1.71e+01 angle pdb=" CA GLY A 209 " pdb=" C GLY A 209 " pdb=" N ASP A 210 " ideal model delta sigma weight residual 114.23 117.85 -3.62 8.80e-01 1.29e+00 1.69e+01 angle pdb=" CA GLY B 209 " pdb=" C GLY B 209 " pdb=" N ASP B 210 " ideal model delta sigma weight residual 114.23 117.85 -3.62 8.80e-01 1.29e+00 1.69e+01 angle pdb=" CA GLY E 209 " pdb=" C GLY E 209 " pdb=" N ASP E 210 " ideal model delta sigma weight residual 114.23 117.85 -3.62 8.80e-01 1.29e+00 1.69e+01 ... (remaining 19849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.58: 8601 29.58 - 59.16: 240 59.16 - 88.74: 63 88.74 - 118.32: 0 118.32 - 147.91: 6 Dihedral angle restraints: 8910 sinusoidal: 3612 harmonic: 5298 Sorted by residual: dihedral pdb=" C2* AMP D 405 " pdb=" C1* AMP D 405 " pdb=" N9 AMP D 405 " pdb=" C4 AMP D 405 " ideal model delta sinusoidal sigma weight residual 91.55 -56.35 147.91 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C2* AMP C 405 " pdb=" C1* AMP C 405 " pdb=" N9 AMP C 405 " pdb=" C4 AMP C 405 " ideal model delta sinusoidal sigma weight residual 91.55 -56.34 147.89 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C2* AMP A 405 " pdb=" C1* AMP A 405 " pdb=" N9 AMP A 405 " pdb=" C4 AMP A 405 " ideal model delta sinusoidal sigma weight residual 91.55 -56.30 147.86 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 962 0.028 - 0.056: 766 0.056 - 0.084: 365 0.084 - 0.112: 167 0.112 - 0.140: 74 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CA ILE B 275 " pdb=" N ILE B 275 " pdb=" C ILE B 275 " pdb=" CB ILE B 275 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE F 275 " pdb=" N ILE F 275 " pdb=" C ILE F 275 " pdb=" CB ILE F 275 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE C 275 " pdb=" N ILE C 275 " pdb=" C ILE C 275 " pdb=" CB ILE C 275 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 2331 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 HSX F 401 " -0.257 2.00e-02 2.50e+03 5.79e-01 7.54e+03 pdb=" C2 HSX F 401 " -0.852 2.00e-02 2.50e+03 pdb=" C3 HSX F 401 " -0.177 2.00e-02 2.50e+03 pdb=" C4 HSX F 401 " 0.347 2.00e-02 2.50e+03 pdb=" C5 HSX F 401 " -0.361 2.00e-02 2.50e+03 pdb=" O1 HSX F 401 " 0.924 2.00e-02 2.50e+03 pdb=" O2 HSX F 401 " -0.588 2.00e-02 2.50e+03 pdb=" O3 HSX F 401 " 0.854 2.00e-02 2.50e+03 pdb=" O4 HSX F 401 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX B 401 " 0.257 2.00e-02 2.50e+03 5.79e-01 7.54e+03 pdb=" C2 HSX B 401 " 0.852 2.00e-02 2.50e+03 pdb=" C3 HSX B 401 " 0.177 2.00e-02 2.50e+03 pdb=" C4 HSX B 401 " -0.347 2.00e-02 2.50e+03 pdb=" C5 HSX B 401 " 0.361 2.00e-02 2.50e+03 pdb=" O1 HSX B 401 " -0.924 2.00e-02 2.50e+03 pdb=" O2 HSX B 401 " 0.588 2.00e-02 2.50e+03 pdb=" O3 HSX B 401 " -0.853 2.00e-02 2.50e+03 pdb=" O4 HSX B 401 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX C 401 " 0.257 2.00e-02 2.50e+03 5.79e-01 7.53e+03 pdb=" C2 HSX C 401 " 0.852 2.00e-02 2.50e+03 pdb=" C3 HSX C 401 " 0.177 2.00e-02 2.50e+03 pdb=" C4 HSX C 401 " -0.347 2.00e-02 2.50e+03 pdb=" C5 HSX C 401 " 0.362 2.00e-02 2.50e+03 pdb=" O1 HSX C 401 " -0.924 2.00e-02 2.50e+03 pdb=" O2 HSX C 401 " 0.587 2.00e-02 2.50e+03 pdb=" O3 HSX C 401 " -0.853 2.00e-02 2.50e+03 pdb=" O4 HSX C 401 " -0.110 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 279 2.46 - 3.07: 10234 3.07 - 3.68: 22867 3.68 - 4.29: 37901 4.29 - 4.90: 60106 Nonbonded interactions: 131387 Sorted by model distance: nonbonded pdb="MG MG F 403 " pdb=" O HOH F2606 " model vdw 1.853 2.170 nonbonded pdb="MG MG A 403 " pdb=" O HOH A2606 " model vdw 1.854 2.170 nonbonded pdb="MG MG C 403 " pdb=" O HOH C2604 " model vdw 1.856 2.170 nonbonded pdb="MG MG D 403 " pdb=" O HOH D2605 " model vdw 1.858 2.170 nonbonded pdb="MG MG E 403 " pdb=" O HOH E2605 " model vdw 1.864 2.170 ... (remaining 131382 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 24 5.49 5 Mg 12 5.21 5 S 78 5.16 5 C 8898 2.51 5 N 2574 2.21 5 O 3642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.010 Extract box with map and model: 4.870 Check model and map are aligned: 0.220 Process input model: 39.110 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:10.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 : 0.014 0.309 14598 Z= 0.983 Angle : 0.890 11.961 19854 Z= 0.448 Chirality : 0.051 0.140 2334 Planarity : 0.035 0.579 2562 Dihedral : 15.788 147.906 5466 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.87 (0.20), residues: 1818 helix: 0.03 (0.19), residues: 762 sheet: 0.21 (0.24), residues: 474 loop : -1.96 (0.23), residues: 582 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 291 time to evaluate : 1.884 Fit side-chains outliers start: 18 outliers final: 1 residues processed: 291 average time/residue: 1.7624 time to fit residues: 550.4938 Evaluate side-chains 175 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.689 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.2199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN D 57 GLN F 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 14598 Z= 0.182 Angle : 1.241 18.838 19854 Z= 0.460 Chirality : 0.045 0.133 2334 Planarity : 0.004 0.043 2562 Dihedral : 16.432 147.022 2184 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.65 (0.20), residues: 1818 helix: 0.12 (0.19), residues: 762 sheet: 0.46 (0.24), residues: 480 loop : -1.86 (0.24), residues: 576 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 1.815 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 198 average time/residue: 1.6077 time to fit residues: 346.1816 Evaluate side-chains 187 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 1.709 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.5348 time to fit residues: 5.7043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 0.0040 chunk 136 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 162 optimal weight: 0.0170 chunk 55 optimal weight: 10.0000 chunk 131 optimal weight: 0.5980 overall best weight: 2.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 GLN E 158 GLN C 57 GLN B 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 14598 Z= 0.287 Angle : 1.235 17.765 19854 Z= 0.460 Chirality : 0.047 0.135 2334 Planarity : 0.005 0.054 2562 Dihedral : 15.925 147.461 2184 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.78 (0.19), residues: 1818 helix: -0.11 (0.19), residues: 768 sheet: 0.58 (0.25), residues: 420 loop : -1.72 (0.22), residues: 630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 1.794 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 201 average time/residue: 1.5576 time to fit residues: 341.1464 Evaluate side-chains 190 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 181 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.2926 time to fit residues: 5.0825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 158 GLN E 256 ASN B 57 GLN B 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 14598 Z= 0.249 Angle : 1.219 17.381 19854 Z= 0.449 Chirality : 0.046 0.134 2334 Planarity : 0.004 0.046 2562 Dihedral : 15.753 147.829 2184 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.40 (0.19), residues: 1818 helix: 0.28 (0.19), residues: 720 sheet: 0.60 (0.25), residues: 420 loop : -1.36 (0.23), residues: 678 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 189 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 200 average time/residue: 1.6002 time to fit residues: 347.4829 Evaluate side-chains 194 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 185 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.2674 time to fit residues: 3.9839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 GLN E 158 GLN B 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 14598 Z= 0.314 Angle : 1.237 17.803 19854 Z= 0.460 Chirality : 0.047 0.140 2334 Planarity : 0.004 0.047 2562 Dihedral : 15.946 148.313 2184 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.51 (0.19), residues: 1818 helix: 0.20 (0.19), residues: 720 sheet: 0.49 (0.25), residues: 420 loop : -1.38 (0.23), residues: 678 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 190 average time/residue: 1.5890 time to fit residues: 328.3210 Evaluate side-chains 190 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 181 time to evaluate : 1.846 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.2945 time to fit residues: 3.5871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 0.0030 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 overall best weight: 1.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 GLN E 158 GLN B 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 14598 Z= 0.221 Angle : 1.213 17.402 19854 Z= 0.445 Chirality : 0.045 0.132 2334 Planarity : 0.004 0.046 2562 Dihedral : 15.741 147.898 2184 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.35 (0.19), residues: 1818 helix: 0.32 (0.19), residues: 720 sheet: 0.57 (0.25), residues: 420 loop : -1.30 (0.23), residues: 678 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 203 average time/residue: 1.5084 time to fit residues: 333.7936 Evaluate side-chains 198 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 1.795 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.2756 time to fit residues: 3.5533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 GLN E 158 GLN C 256 ASN B 158 GLN B 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 14598 Z= 0.139 Angle : 1.197 17.226 19854 Z= 0.434 Chirality : 0.044 0.131 2334 Planarity : 0.003 0.044 2562 Dihedral : 15.272 145.912 2184 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.06 (0.20), residues: 1818 helix: 0.54 (0.19), residues: 720 sheet: 0.66 (0.25), residues: 438 loop : -1.10 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 1.893 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 214 average time/residue: 1.4909 time to fit residues: 348.3010 Evaluate side-chains 205 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 1.794 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.2696 time to fit residues: 3.2001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 136 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 GLN E 158 GLN D 256 ASN B 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 14598 Z= 0.136 Angle : 1.198 17.224 19854 Z= 0.434 Chirality : 0.044 0.132 2334 Planarity : 0.003 0.043 2562 Dihedral : 14.975 144.706 2184 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.11 (0.20), residues: 1818 helix: 0.63 (0.19), residues: 720 sheet: 0.78 (0.25), residues: 438 loop : -0.96 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 205 time to evaluate : 1.849 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 211 average time/residue: 1.5343 time to fit residues: 353.8180 Evaluate side-chains 202 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 195 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.7381 time to fit residues: 4.1268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 106 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 158 GLN B 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 14598 Z= 0.157 Angle : 1.204 17.276 19854 Z= 0.439 Chirality : 0.044 0.130 2334 Planarity : 0.003 0.043 2562 Dihedral : 14.820 144.416 2184 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.16 (0.20), residues: 1818 helix: 0.66 (0.19), residues: 720 sheet: 0.82 (0.25), residues: 438 loop : -0.93 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 1.812 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 205 average time/residue: 1.5385 time to fit residues: 343.7290 Evaluate side-chains 202 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 1.799 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.8993 time to fit residues: 5.4760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 158 GLN B 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 14598 Z= 0.211 Angle : 1.212 17.441 19854 Z= 0.443 Chirality : 0.045 0.129 2334 Planarity : 0.004 0.044 2562 Dihedral : 14.975 145.359 2184 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.04 (0.20), residues: 1818 helix: 0.57 (0.19), residues: 720 sheet: 0.85 (0.25), residues: 420 loop : -1.02 (0.24), residues: 678 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 1.853 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 200 average time/residue: 1.5029 time to fit residues: 327.7754 Evaluate side-chains 194 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 1.749 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.1133 time to fit residues: 3.5004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 158 GLN B 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.095545 restraints weight = 17160.623| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.86 r_work: 0.2868 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14598 Z= 0.234 Angle : 1.221 17.472 19854 Z= 0.451 Chirality : 0.045 0.130 2334 Planarity : 0.004 0.044 2562 Dihedral : 15.150 146.157 2184 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.01 (0.20), residues: 1818 helix: 0.52 (0.19), residues: 720 sheet: 0.81 (0.25), residues: 420 loop : -1.04 (0.23), residues: 678 =============================================================================== Job complete usr+sys time: 5717.22 seconds wall clock time: 101 minutes 30.02 seconds (6090.02 seconds total)