Starting phenix.real_space_refine (version: dev) on Tue Dec 13 11:54:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/12_2022/7xmv_33306_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/12_2022/7xmv_33306.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/12_2022/7xmv_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_33306/12_2022/7xmv_33306_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/12_2022/7xmv_33306_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/12_2022/7xmv_33306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/12_2022/7xmv_33306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/12_2022/7xmv_33306_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/12_2022/7xmv_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 Convert atoms to be neutral 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 9.22, per 1000 atoms: 0.61 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: 6.81 Conformation dependent library (CDL) restraints added in 2.3 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: 1.53 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: 5.31 Time building geometry restraints manager: 7.20 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' ADP F 404 " pdb=" C2' ADP F 404 " ideal model delta sigma weight residual 1.267 1.513 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C1' ADP B 404 " pdb=" C2' ADP B 404 " ideal model delta sigma weight residual 1.267 1.513 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C1' ADP A 404 " pdb=" C2' ADP A 404 " ideal model delta sigma weight residual 1.267 1.513 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C1' ADP E 404 " pdb=" C2' ADP E 404 " ideal model delta sigma weight residual 1.267 1.513 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C1' ADP C 404 " pdb=" C2' ADP C 404 " ideal model delta sigma weight residual 1.267 1.512 -0.245 2.00e-02 2.50e+03 1.50e+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=" N1 ADP D 404 " pdb=" C6 ADP D 404 " pdb=" N6 ADP D 404 " ideal model delta sigma weight residual 106.84 121.56 -14.72 3.00e+00 1.11e-01 2.41e+01 angle pdb=" N1 ADP F 404 " pdb=" C6 ADP F 404 " pdb=" N6 ADP F 404 " ideal model delta sigma weight residual 106.84 121.54 -14.70 3.00e+00 1.11e-01 2.40e+01 angle pdb=" N1 ADP A 404 " pdb=" C6 ADP A 404 " pdb=" N6 ADP A 404 " ideal model delta sigma weight residual 106.84 121.54 -14.70 3.00e+00 1.11e-01 2.40e+01 angle pdb=" N1 ADP E 404 " pdb=" C6 ADP E 404 " pdb=" N6 ADP E 404 " ideal model delta sigma weight residual 106.84 121.53 -14.69 3.00e+00 1.11e-01 2.40e+01 angle pdb=" N1 ADP B 404 " pdb=" C6 ADP B 404 " pdb=" N6 ADP B 404 " ideal model delta sigma weight residual 106.84 121.51 -14.67 3.00e+00 1.11e-01 2.39e+01 ... (remaining 19849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.58: 8613 29.58 - 59.16: 234 59.16 - 88.74: 41 88.74 - 118.32: 16 118.32 - 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: 0.820 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: 5.180 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.120 Process input model: 42.660 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.500 ------------------------------------------------------------------------------- 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 0.246 14598 Z= 0.977 Angle : 0.925 14.721 19854 Z= 0.456 Chirality : 0.051 0.140 2334 Planarity : 0.035 0.579 2562 Dihedral : 15.936 147.906 5466 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.56 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 : 1.806 Fit side-chains outliers start: 18 outliers final: 1 residues processed: 291 average time/residue: 1.6085 time to fit residues: 504.7923 Evaluate side-chains 175 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.5260 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.8982 ------------------------------------------------------------------------------- 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: 0.8537 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 14598 Z= 0.172 Angle : 1.225 18.686 19854 Z= 0.454 Chirality : 0.045 0.130 2334 Planarity : 0.004 0.043 2562 Dihedral : 15.284 146.963 2184 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 1.24 % 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: -0.62 (0.20), residues: 1818 helix: 0.15 (0.19), residues: 762 sheet: 0.47 (0.24), residues: 480 loop : -1.84 (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 221 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 202 time to evaluate : 1.906 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 207 average time/residue: 1.4565 time to fit residues: 329.3928 Evaluate side-chains 186 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 179 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.5452 time to fit residues: 5.9273 ------------------------------------------------------------------------------- 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: 5.9990 chunk 136 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 162 optimal weight: 0.0170 chunk 55 optimal weight: 10.0000 chunk 131 optimal weight: 0.5980 overall best weight: 3.5224 ------------------------------------------------------------------------------- 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 57 GLN B 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 14598 Z= 0.421 Angle : 1.262 18.034 19854 Z= 0.479 Chirality : 0.049 0.164 2334 Planarity : 0.005 0.051 2562 Dihedral : 14.954 148.713 2184 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.54 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: -1.00 (0.19), residues: 1818 helix: -0.26 (0.18), residues: 768 sheet: 0.36 (0.24), residues: 456 loop : -1.90 (0.23), residues: 594 *********************** 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 200 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.919 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 191 average time/residue: 1.4239 time to fit residues: 297.3411 Evaluate side-chains 185 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 175 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.2779 time to fit residues: 4.4368 ------------------------------------------------------------------------------- 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: 0.9980 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 256 ASN B 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1492 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= 0.197 Angle : 1.204 17.313 19854 Z= 0.442 Chirality : 0.045 0.154 2334 Planarity : 0.004 0.045 2562 Dihedral : 14.690 147.673 2184 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: -0.39 (0.19), residues: 1818 helix: 0.29 (0.19), residues: 720 sheet: 0.58 (0.25), residues: 420 loop : -1.34 (0.22), 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 219 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 199 time to evaluate : 1.840 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 209 average time/residue: 1.3299 time to fit residues: 305.2057 Evaluate side-chains 196 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 185 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 6 average time/residue: 0.2567 time to fit residues: 4.5137 ------------------------------------------------------------------------------- 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: 0.6980 chunk 71 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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: 0.8546 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 14598 Z= 0.233 Angle : 1.215 17.321 19854 Z= 0.448 Chirality : 0.046 0.167 2334 Planarity : 0.004 0.046 2562 Dihedral : 14.612 147.561 2184 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: -0.33 (0.19), residues: 1818 helix: 0.36 (0.19), residues: 720 sheet: 0.55 (0.25), residues: 420 loop : -1.28 (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 212 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 1.920 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 201 average time/residue: 1.4157 time to fit residues: 312.2354 Evaluate side-chains 194 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 185 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 4 average time/residue: 0.2815 time to fit residues: 4.0967 ------------------------------------------------------------------------------- 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: 6.9990 chunk 156 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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: 0.8562 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 14598 Z= 0.333 Angle : 1.234 17.603 19854 Z= 0.461 Chirality : 0.047 0.183 2334 Planarity : 0.004 0.048 2562 Dihedral : 14.722 148.279 2184 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 1.44 % 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: -0.56 (0.19), residues: 1818 helix: 0.21 (0.19), residues: 720 sheet: 0.34 (0.24), residues: 456 loop : -1.49 (0.23), residues: 642 *********************** 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: 22 poor density : 190 time to evaluate : 1.877 Fit side-chains outliers start: 22 outliers final: 7 residues processed: 200 average time/residue: 1.4304 time to fit residues: 312.9095 Evaluate side-chains 194 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.2818 time to fit residues: 3.3903 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 158 GLN C 256 ASN B 57 GLN B 158 GLN B 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 14598 Z= 0.222 Angle : 1.208 17.309 19854 Z= 0.444 Chirality : 0.046 0.185 2334 Planarity : 0.004 0.046 2562 Dihedral : 14.574 147.875 2184 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 1.05 % 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: 0.35 (0.19), residues: 720 sheet: 0.50 (0.25), residues: 420 loop : -1.26 (0.23), residues: 678 *********************** 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 205 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 2.030 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 196 average time/residue: 1.4113 time to fit residues: 302.8099 Evaluate side-chains 194 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 1.872 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.2937 time to fit residues: 3.4498 ------------------------------------------------------------------------------- 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: 2.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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: 0.8556 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 14598 Z= 0.278 Angle : 1.222 17.369 19854 Z= 0.453 Chirality : 0.047 0.181 2334 Planarity : 0.004 0.047 2562 Dihedral : 14.619 147.905 2184 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: -0.46 (0.19), residues: 1818 helix: 0.31 (0.19), residues: 720 sheet: 0.38 (0.24), residues: 456 loop : -1.44 (0.24), residues: 642 *********************** 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 203 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 191 time to evaluate : 2.111 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 197 average time/residue: 1.4578 time to fit residues: 314.9617 Evaluate side-chains 197 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 1.724 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.3008 time to fit residues: 3.1619 ------------------------------------------------------------------------------- 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: 0.6980 chunk 166 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 106 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 14598 Z= 0.132 Angle : 1.191 17.247 19854 Z= 0.432 Chirality : 0.044 0.173 2334 Planarity : 0.003 0.044 2562 Dihedral : 14.279 145.751 2184 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: 0.62 (0.25), residues: 438 loop : -1.07 (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 217 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 1.871 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 212 average time/residue: 1.3658 time to fit residues: 318.6812 Evaluate side-chains 201 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 194 time to evaluate : 1.858 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.2520 time to fit residues: 3.8283 ------------------------------------------------------------------------------- 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: 9.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 0.2980 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 158 GLN C 57 GLN D 256 ASN B 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1891 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= 0.188 Angle : 1.203 17.288 19854 Z= 0.440 Chirality : 0.045 0.176 2334 Planarity : 0.004 0.044 2562 Dihedral : 14.214 145.578 2184 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.65 % 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: -0.02 (0.20), residues: 1818 helix: 0.58 (0.19), residues: 720 sheet: 0.74 (0.25), residues: 420 loop : -1.08 (0.23), 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 205 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 2.054 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 202 average time/residue: 1.4088 time to fit residues: 311.7338 Evaluate side-chains 193 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.2335 time to fit residues: 3.5821 ------------------------------------------------------------------------------- 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: 0.5980 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 125 optimal weight: 0.0970 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3461 r_free = 0.3461 target = 0.125789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.097518 restraints weight = 17152.139| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.85 r_work: 0.2872 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 14598 Z= 0.156 Angle : 1.195 17.255 19854 Z= 0.434 Chirality : 0.045 0.172 2334 Planarity : 0.003 0.043 2562 Dihedral : 14.094 144.991 2184 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.65 % 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: 0.08 (0.20), residues: 1818 helix: 0.63 (0.19), residues: 720 sheet: 0.84 (0.25), residues: 420 loop : -1.02 (0.24), residues: 678 =============================================================================== Job complete usr+sys time: 5321.39 seconds wall clock time: 94 minutes 54.77 seconds (5694.77 seconds total)