Starting phenix.real_space_refine on Fri Jun 28 11:50:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/06_2024/7xmv_33306_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/06_2024/7xmv_33306.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/06_2024/7xmv_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_33306/06_2024/7xmv_33306_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/06_2024/7xmv_33306_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/06_2024/7xmv_33306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/06_2024/7xmv_33306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/06_2024/7xmv_33306_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmv_33306/06_2024/7xmv_33306_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 8.18, per 1000 atoms: 0.54 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: 6.17 Conformation dependent library (CDL) restraints added in 2.6 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: 2.78 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: 4.54 Time building geometry restraints manager: 6.74 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 - 17.31: 8136 17.31 - 34.63: 555 34.63 - 51.94: 141 51.94 - 69.25: 36 69.25 - 86.57: 48 Dihedral angle restraints: 8916 sinusoidal: 3618 harmonic: 5298 Sorted by residual: dihedral pdb=" CA GLU F 238 " pdb=" C GLU F 238 " pdb=" N ARG F 239 " pdb=" CA ARG F 239 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLU D 238 " pdb=" C GLU D 238 " pdb=" N ARG D 239 " pdb=" CA ARG D 239 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLU A 238 " pdb=" C GLU A 238 " pdb=" N ARG A 239 " pdb=" CA ARG A 239 " ideal model delta harmonic sigma weight residual 180.00 157.74 22.26 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 8913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 939 0.028 - 0.056: 765 0.056 - 0.084: 365 0.084 - 0.112: 167 0.112 - 0.140: 74 Chirality restraints: 2310 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 2307 not shown) Planarity restraints: 2568 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 2565 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 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: 0.010 Normalize map: mean=0, sd=1: 0.960 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: 3.740 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 41.640 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.015 0.309 14598 Z= 1.031 Angle : 0.958 11.961 19854 Z= 0.464 Chirality : 0.051 0.140 2310 Planarity : 0.044 0.579 2568 Dihedral : 15.358 86.566 5472 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.18 % Allowed : 1.57 % Favored : 97.25 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 131 PHE 0.016 0.002 PHE A 139 TYR 0.026 0.004 TYR D 247 ARG 0.005 0.001 ARG B 78 *********************** 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 : 1.794 Fit side-chains REVERT: A 312 MET cc_start: 0.8819 (mmm) cc_final: 0.8465 (mmm) REVERT: E 17 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8574 (mm-40) REVERT: C 312 MET cc_start: 0.8857 (mmm) cc_final: 0.8650 (mmp) REVERT: D 222 MET cc_start: 0.8890 (ptp) cc_final: 0.8654 (ptp) REVERT: B 17 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8581 (mm-40) REVERT: F 222 MET cc_start: 0.8897 (ptp) cc_final: 0.8686 (ptp) outliers start: 18 outliers final: 1 residues processed: 291 average time/residue: 1.7286 time to fit residues: 540.0323 Evaluate side-chains 177 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 306 GLU 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: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8235 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14598 Z= 0.179 Angle : 1.343 18.655 19854 Z= 0.589 Chirality : 0.046 0.135 2310 Planarity : 0.007 0.113 2568 Dihedral : 16.825 177.545 2193 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.31 % Allowed : 7.32 % Favored : 91.37 % 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: 0.14 (0.19), residues: 762 sheet: 0.43 (0.24), residues: 480 loop : -1.86 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 131 PHE 0.009 0.001 PHE F 139 TYR 0.005 0.001 TYR E 94 ARG 0.007 0.000 ARG F 239 *********************** 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 214 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 1.615 Fit side-chains REVERT: A 18 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7566 (mtm180) REVERT: A 78 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7483 (tmm-80) REVERT: A 205 MET cc_start: 0.8100 (mtp) cc_final: 0.7720 (mtt) REVERT: C 78 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7427 (tmm-80) REVERT: B 18 ARG cc_start: 0.7661 (mtm-85) cc_final: 0.7255 (mtm180) outliers start: 20 outliers final: 9 residues processed: 202 average time/residue: 1.5061 time to fit residues: 330.1887 Evaluate side-chains 193 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 279 ASP 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: 8.9990 chunk 136 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 145 optimal weight: 0.0270 chunk 162 optimal weight: 0.8980 chunk 55 optimal weight: 0.0060 chunk 131 optimal weight: 0.6980 overall best weight: 1.1256 ------------------------------------------------------------------------------- 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 B 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14598 Z= 0.175 Angle : 1.307 17.486 19854 Z= 0.574 Chirality : 0.045 0.130 2310 Planarity : 0.006 0.111 2568 Dihedral : 15.569 127.168 2190 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.63 % Allowed : 8.56 % Favored : 89.80 % 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: -0.25 (0.20), residues: 1818 helix: 0.42 (0.19), residues: 720 sheet: 0.68 (0.25), residues: 438 loop : -1.35 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 131 PHE 0.009 0.001 PHE D 139 TYR 0.006 0.001 TYR E 247 ARG 0.002 0.000 ARG A 78 *********************** 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 232 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 1.697 Fit side-chains REVERT: A 78 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7388 (tmm-80) REVERT: A 205 MET cc_start: 0.8109 (mtp) cc_final: 0.7705 (mtt) REVERT: E 116 PHE cc_start: 0.7881 (m-10) cc_final: 0.7656 (m-10) REVERT: C 78 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7409 (tmm-80) REVERT: B 18 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7434 (mtm180) REVERT: B 116 PHE cc_start: 0.7872 (m-10) cc_final: 0.7649 (m-10) outliers start: 25 outliers final: 10 residues processed: 215 average time/residue: 1.4376 time to fit residues: 337.1599 Evaluate side-chains 205 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 279 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 46 optimal weight: 0.0030 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 E 256 ASN B 57 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14598 Z= 0.127 Angle : 1.295 17.137 19854 Z= 0.567 Chirality : 0.044 0.167 2310 Planarity : 0.006 0.112 2568 Dihedral : 14.929 122.510 2190 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.98 % Allowed : 10.07 % Favored : 88.95 % 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: 0.07 (0.20), residues: 1818 helix: 0.61 (0.19), residues: 720 sheet: 0.86 (0.26), residues: 438 loop : -1.09 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 250 PHE 0.009 0.001 PHE F 139 TYR 0.006 0.001 TYR E 247 ARG 0.003 0.000 ARG B 18 *********************** 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 217 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 1.713 Fit side-chains REVERT: A 205 MET cc_start: 0.8110 (mtp) cc_final: 0.7747 (mtt) REVERT: A 312 MET cc_start: 0.8873 (mmm) cc_final: 0.8500 (mmm) REVERT: D 14 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: B 18 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7455 (mtm180) outliers start: 15 outliers final: 7 residues processed: 208 average time/residue: 1.4505 time to fit residues: 328.5863 Evaluate side-chains 198 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 279 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 158 GLN B 57 GLN B 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1542 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= 0.408 Angle : 1.350 18.461 19854 Z= 0.597 Chirality : 0.049 0.163 2310 Planarity : 0.007 0.113 2568 Dihedral : 15.622 131.758 2190 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.31 % Allowed : 10.92 % Favored : 87.78 % 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: -0.69 (0.19), residues: 1818 helix: -0.09 (0.18), residues: 768 sheet: 0.52 (0.25), residues: 420 loop : -1.48 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 131 PHE 0.014 0.002 PHE F 139 TYR 0.007 0.002 TYR A 91 ARG 0.005 0.001 ARG B 79 *********************** 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 206 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7420 (tmm-80) REVERT: A 312 MET cc_start: 0.8883 (mmm) cc_final: 0.8475 (mmm) REVERT: C 78 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7477 (tmm-80) REVERT: D 14 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: B 18 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7520 (mtm180) outliers start: 20 outliers final: 10 residues processed: 196 average time/residue: 1.5217 time to fit residues: 323.5028 Evaluate side-chains 192 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 179 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 279 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 34 optimal weight: 0.0370 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 0.0000 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.3466 ------------------------------------------------------------------------------- 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: 0.8236 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14598 Z= 0.204 Angle : 1.308 17.296 19854 Z= 0.574 Chirality : 0.046 0.161 2310 Planarity : 0.007 0.112 2568 Dihedral : 15.224 131.374 2190 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.18 % Allowed : 10.98 % Favored : 87.84 % 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: -0.20 (0.19), residues: 1818 helix: 0.45 (0.19), residues: 720 sheet: 0.66 (0.25), residues: 420 loop : -1.21 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 131 PHE 0.012 0.001 PHE F 139 TYR 0.005 0.001 TYR E 247 ARG 0.003 0.000 ARG F 18 *********************** 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 207 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.628 Fit side-chains REVERT: A 78 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7375 (tmm-80) REVERT: A 205 MET cc_start: 0.8144 (mtp) cc_final: 0.7651 (mtt) REVERT: A 312 MET cc_start: 0.8864 (mmm) cc_final: 0.8517 (mmm) REVERT: C 78 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7360 (tmm-80) REVERT: D 14 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: B 18 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7527 (mtm180) REVERT: F 205 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8050 (mtt) outliers start: 18 outliers final: 8 residues processed: 199 average time/residue: 1.5438 time to fit residues: 333.9864 Evaluate side-chains 196 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 279 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 158 GLN B 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14598 Z= 0.272 Angle : 1.324 17.565 19854 Z= 0.582 Chirality : 0.047 0.154 2310 Planarity : 0.007 0.112 2568 Dihedral : 15.370 133.524 2190 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.31 % Allowed : 11.63 % Favored : 87.06 % 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: -0.28 (0.19), residues: 1818 helix: 0.40 (0.19), residues: 720 sheet: 0.56 (0.25), residues: 420 loop : -1.24 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 131 PHE 0.012 0.001 PHE F 139 TYR 0.008 0.002 TYR B 247 ARG 0.003 0.000 ARG B 18 *********************** 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 206 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.770 Fit side-chains REVERT: A 78 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7360 (tmm-80) REVERT: A 312 MET cc_start: 0.8852 (mmm) cc_final: 0.8527 (mmm) REVERT: E 73 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7684 (mtm) REVERT: E 239 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7541 (ttm170) REVERT: C 78 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7355 (tmm-80) REVERT: D 14 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: B 18 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7529 (mtm180) REVERT: F 18 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7420 (mtm-85) outliers start: 20 outliers final: 9 residues processed: 195 average time/residue: 1.4859 time to fit residues: 315.0470 Evaluate side-chains 197 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 183 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 279 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.975 > 50: distance: 28 - 56: 4.457 distance: 31 - 53: 6.424 distance: 46 - 47: 3.307 distance: 47 - 50: 3.641 distance: 48 - 49: 3.118 distance: 48 - 53: 5.125 distance: 50 - 51: 8.685 distance: 50 - 52: 6.035 distance: 53 - 54: 4.335 distance: 54 - 55: 4.037 distance: 54 - 57: 3.930 distance: 55 - 56: 3.010 distance: 55 - 62: 4.614 distance: 57 - 58: 9.717 distance: 58 - 59: 4.874 distance: 59 - 60: 3.193 distance: 59 - 61: 4.890 distance: 62 - 63: 3.493 distance: 64 - 65: 11.808 distance: 64 - 70: 4.657 distance: 66 - 67: 6.151 distance: 66 - 68: 6.772 distance: 67 - 69: 7.224 distance: 71 - 72: 5.681 distance: 72 - 78: 5.077 distance: 75 - 76: 3.834 distance: 75 - 77: 16.182 distance: 78 - 79: 3.265 distance: 79 - 80: 5.303 distance: 79 - 82: 6.435 distance: 80 - 81: 10.713 distance: 80 - 87: 15.700 distance: 82 - 83: 12.035 distance: 83 - 84: 6.264 distance: 84 - 85: 6.484 distance: 84 - 86: 11.237 distance: 87 - 88: 13.319 distance: 88 - 89: 15.964 distance: 88 - 91: 10.035 distance: 89 - 90: 6.354 distance: 89 - 95: 11.308 distance: 91 - 92: 10.475 distance: 92 - 93: 12.162 distance: 92 - 94: 12.482 distance: 95 - 96: 15.702 distance: 96 - 97: 6.824 distance: 96 - 99: 20.463 distance: 97 - 98: 6.610 distance: 99 - 100: 20.078 distance: 99 - 101: 32.898 distance: 103 - 104: 6.835 distance: 103 - 106: 3.508 distance: 104 - 105: 6.446 distance: 104 - 113: 7.265 distance: 106 - 107: 4.845 distance: 107 - 108: 6.989 distance: 108 - 109: 6.787 distance: 109 - 110: 4.841 distance: 110 - 111: 7.749 distance: 110 - 112: 7.169 distance: 113 - 114: 4.549 distance: 114 - 115: 11.011 distance: 115 - 116: 9.158 distance: 115 - 117: 7.779 distance: 117 - 118: 5.822 distance: 118 - 119: 8.539 distance: 119 - 120: 7.207