Starting phenix.real_space_refine on Fri Feb 16 10:30:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/02_2024/7ouh_13077_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/02_2024/7ouh_13077.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/02_2024/7ouh_13077_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/02_2024/7ouh_13077_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/02_2024/7ouh_13077_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/02_2024/7ouh_13077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/02_2024/7ouh_13077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/02_2024/7ouh_13077_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/02_2024/7ouh_13077_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.024 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 76 5.49 5 Mg 4 5.21 5 S 46 5.16 5 C 9426 2.51 5 N 2704 2.21 5 O 2822 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "E ASP 174": "OD1" <-> "OD2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15088 Number of models: 1 Model: "" Number of chains: 18 Chain: "D" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2057 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 2 Chain: "E" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2212 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 257} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2423 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2057 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 2 Chain: "B" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2212 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 257} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2423 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "K" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "L" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 239 SG CYS D 35 103.581 121.200 24.861 1.00 69.67 S ATOM 260 SG CYS D 38 101.163 123.339 26.815 1.00 63.60 S ATOM 2296 SG CYS E 35 72.912 56.350 37.343 1.00 19.02 S ATOM 2317 SG CYS E 38 70.277 57.163 37.546 1.00 18.08 S ATOM 7744 SG CYS A 35 21.978 43.874 24.439 1.00 67.21 S ATOM 7765 SG CYS A 38 24.387 41.730 26.399 1.00 61.93 S ATOM 9801 SG CYS B 35 52.386 108.733 37.500 1.00 20.30 S ATOM 9822 SG CYS B 38 55.022 107.925 37.718 1.00 18.60 S Time building chain proxies: 8.10, per 1000 atoms: 0.54 Number of scatterers: 15088 At special positions: 0 Unit cell: (126.5, 166.1, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 46 16.00 P 76 15.00 Mg 4 11.99 F 6 9.00 O 2822 8.00 N 2704 7.00 C 9426 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: 6.22 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" ND1 HIS A 12 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 8 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 35 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 38 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 8 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 35 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 38 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" ND1 HIS D 12 " pdb="ZN ZN D1000 " - pdb=" NE2 HIS D 8 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 35 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 38 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 8 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 35 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 38 " Number of angles added : 8 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 14 sheets defined 45.2% alpha, 9.9% beta 8 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 6.79 Creating SS restraints... Processing helix chain 'D' and resid 4 through 11 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 158 through 174 Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 204 through 208 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'E' and resid 4 through 11 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 25 through 34 Processing helix chain 'E' and resid 37 through 40 No H-bonds generated for 'chain 'E' and resid 37 through 40' Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 151 through 174 removed outlier: 5.887A pdb=" N LEU E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 193 Processing helix chain 'E' and resid 204 through 208 Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'F' and resid 38 through 50 removed outlier: 3.953A pdb=" N CYS F 49 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS F 50 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 80 Processing helix chain 'F' and resid 89 through 102 removed outlier: 3.630A pdb=" N TYR F 92 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Proline residue: F 93 - end of helix Processing helix chain 'F' and resid 131 through 146 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.744A pdb=" N LEU F 170 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 192 removed outlier: 3.954A pdb=" N ARG F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 213 Processing helix chain 'F' and resid 221 through 234 removed outlier: 3.851A pdb=" N GLY F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 250 Processing helix chain 'F' and resid 253 through 256 Processing helix chain 'F' and resid 260 through 274 removed outlier: 3.791A pdb=" N HIS F 264 " --> pdb=" O SER F 261 " (cutoff:3.500A) Proline residue: F 265 - end of helix Processing helix chain 'F' and resid 279 through 291 removed outlier: 3.652A pdb=" N THR F 282 " --> pdb=" O SER F 279 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU F 283 " --> pdb=" O THR F 280 " (cutoff:3.500A) Proline residue: F 284 - end of helix Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.754A pdb=" N VAL F 302 " --> pdb=" O PRO F 299 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET F 303 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 158 through 174 Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 37 through 40 No H-bonds generated for 'chain 'B' and resid 37 through 40' Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 151 through 174 removed outlier: 5.887A pdb=" N LEU B 156 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.953A pdb=" N CYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 80 Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.630A pdb=" N TYR C 92 " --> pdb=" O GLU C 89 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 131 through 146 Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 161 through 172 removed outlier: 3.743A pdb=" N LEU C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 3.954A pdb=" N ARG C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 Processing helix chain 'C' and resid 221 through 234 removed outlier: 3.852A pdb=" N GLY C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 260 through 274 removed outlier: 3.792A pdb=" N HIS C 264 " --> pdb=" O SER C 261 " (cutoff:3.500A) Proline residue: C 265 - end of helix Processing helix chain 'C' and resid 279 through 291 removed outlier: 3.653A pdb=" N THR C 282 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU C 283 " --> pdb=" O THR C 280 " (cutoff:3.500A) Proline residue: C 284 - end of helix Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.754A pdb=" N VAL C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET C 303 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 324 through 332 Processing sheet with id= A, first strand: chain 'D' and resid 62 through 70 Processing sheet with id= B, first strand: chain 'D' and resid 118 through 122 removed outlier: 6.330A pdb=" N ARG D 142 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR D 121 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR D 144 " --> pdb=" O THR D 121 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'D' and resid 230 through 232 Processing sheet with id= D, first strand: chain 'D' and resid 255 through 258 Processing sheet with id= E, first strand: chain 'E' and resid 89 through 94 removed outlier: 7.023A pdb=" N HIS E 118 " --> pdb=" O TRP E 62 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N GLY E 64 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN E 120 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N ILE E 66 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG E 142 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR E 121 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR E 144 " --> pdb=" O THR E 121 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 230 through 232 Processing sheet with id= G, first strand: chain 'E' and resid 266 through 269 removed outlier: 4.075A pdb=" N GLN E 250 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 62 through 70 Processing sheet with id= I, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.331A pdb=" N ARG A 142 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR A 121 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR A 144 " --> pdb=" O THR A 121 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 230 through 232 Processing sheet with id= K, first strand: chain 'A' and resid 255 through 258 Processing sheet with id= L, first strand: chain 'B' and resid 89 through 94 removed outlier: 7.023A pdb=" N HIS B 118 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N GLY B 64 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN B 120 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N ILE B 66 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG B 142 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR B 121 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR B 144 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 230 through 232 Processing sheet with id= N, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.075A pdb=" N GLN B 250 " --> pdb=" O LEU B 257 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 6.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2176 1.31 - 1.43: 4825 1.43 - 1.56: 8451 1.56 - 1.68: 162 1.68 - 1.81: 62 Bond restraints: 15676 Sorted by residual: bond pdb=" CAJ KLQ B 304 " pdb=" CAX KLQ B 304 " ideal model delta sigma weight residual 2.011 1.303 0.708 2.00e-02 2.50e+03 1.25e+03 bond pdb=" CAJ KLQ E 304 " pdb=" CAX KLQ E 304 " ideal model delta sigma weight residual 2.011 1.303 0.708 2.00e-02 2.50e+03 1.25e+03 bond pdb=" CAW KLQ B 304 " pdb=" CBA KLQ B 304 " ideal model delta sigma weight residual 0.990 1.488 -0.498 2.00e-02 2.50e+03 6.19e+02 bond pdb=" CAW KLQ E 304 " pdb=" CBA KLQ E 304 " ideal model delta sigma weight residual 0.990 1.487 -0.497 2.00e-02 2.50e+03 6.19e+02 bond pdb=" CAW KLQ B 304 " pdb=" CAZ KLQ B 304 " ideal model delta sigma weight residual 1.723 1.336 0.387 2.00e-02 2.50e+03 3.74e+02 ... (remaining 15671 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.17: 1014 106.17 - 113.13: 8565 113.13 - 120.10: 5366 120.10 - 127.06: 6298 127.06 - 134.03: 445 Bond angle restraints: 21688 Sorted by residual: angle pdb=" CAY KLQ B 304 " pdb=" CAV KLQ B 304 " pdb=" FAG KLQ B 304 " ideal model delta sigma weight residual 142.84 115.88 26.96 3.00e+00 1.11e-01 8.08e+01 angle pdb=" CAY KLQ E 304 " pdb=" CAV KLQ E 304 " pdb=" FAG KLQ E 304 " ideal model delta sigma weight residual 142.84 115.94 26.90 3.00e+00 1.11e-01 8.04e+01 angle pdb=" CAI KLQ E 304 " pdb=" CAV KLQ E 304 " pdb=" FAG KLQ E 304 " ideal model delta sigma weight residual 97.12 116.37 -19.25 3.00e+00 1.11e-01 4.12e+01 angle pdb=" CAI KLQ B 304 " pdb=" CAV KLQ B 304 " pdb=" FAG KLQ B 304 " ideal model delta sigma weight residual 97.12 116.36 -19.24 3.00e+00 1.11e-01 4.11e+01 angle pdb=" CA PRO C 93 " pdb=" N PRO C 93 " pdb=" CD PRO C 93 " ideal model delta sigma weight residual 112.00 104.52 7.48 1.40e+00 5.10e-01 2.86e+01 ... (remaining 21683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 7753 16.87 - 33.74: 871 33.74 - 50.60: 374 50.60 - 67.47: 96 67.47 - 84.34: 18 Dihedral angle restraints: 9112 sinusoidal: 4196 harmonic: 4916 Sorted by residual: dihedral pdb=" CA PRO F 93 " pdb=" C PRO F 93 " pdb=" N GLU F 94 " pdb=" CA GLU F 94 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA PRO C 93 " pdb=" C PRO C 93 " pdb=" N GLU C 94 " pdb=" CA GLU C 94 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR A 230 " pdb=" C TYR A 230 " pdb=" N TYR A 231 " pdb=" CA TYR A 231 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 9109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1806 0.035 - 0.071: 426 0.071 - 0.106: 134 0.106 - 0.141: 44 0.141 - 0.176: 2 Chirality restraints: 2412 Sorted by residual: chirality pdb=" CB THR D 11 " pdb=" CA THR D 11 " pdb=" OG1 THR D 11 " pdb=" CG2 THR D 11 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CB THR A 11 " pdb=" CA THR A 11 " pdb=" OG1 THR A 11 " pdb=" CG2 THR A 11 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CBD KLQ B 304 " pdb=" CAO KLQ B 304 " pdb=" NBE KLQ B 304 " pdb=" OAQ KLQ B 304 " both_signs ideal model delta sigma weight residual False 2.53 2.67 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 2409 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 92 " -0.099 5.00e-02 4.00e+02 1.47e-01 3.46e+01 pdb=" N PRO C 93 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 92 " 0.098 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO F 93 " -0.254 5.00e-02 4.00e+02 pdb=" CA PRO F 93 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO F 93 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 124 " 0.047 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO C 125 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.038 5.00e-02 4.00e+02 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 32 2.31 - 2.96: 6475 2.96 - 3.61: 21768 3.61 - 4.25: 34586 4.25 - 4.90: 56331 Nonbonded interactions: 119192 Sorted by model distance: nonbonded pdb="MG MG E 302 " pdb=" OAB KLQ E 304 " model vdw 1.666 2.170 nonbonded pdb="MG MG B 302 " pdb=" OAB KLQ B 304 " model vdw 1.667 2.170 nonbonded pdb=" OE2 GLU B 158 " pdb="MG MG B 303 " model vdw 1.785 2.170 nonbonded pdb=" OE2 GLU E 158 " pdb="MG MG E 303 " model vdw 1.786 2.170 nonbonded pdb=" OE1 GLU E 158 " pdb="MG MG E 303 " model vdw 1.874 2.170 ... (remaining 119187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 280 or resid 1000)) selection = (chain 'B' and (resid 3 through 39 or resid 52 through 148 or resid 157 through \ 280 or resid 301)) selection = (chain 'D' and (resid 3 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 280 or resid 1000)) selection = (chain 'E' and (resid 3 through 39 or resid 52 through 148 or resid 157 through \ 280 or resid 301)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 6.440 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 49.150 Find NCS groups from input model: 0.990 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 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 0.708 15676 Z= 0.623 Angle : 0.739 26.961 21688 Z= 0.332 Chirality : 0.038 0.176 2412 Planarity : 0.006 0.147 2464 Dihedral : 17.444 84.340 5900 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1640 helix: 1.33 (0.20), residues: 748 sheet: -0.18 (0.33), residues: 220 loop : -0.74 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 65 HIS 0.009 0.001 HIS A 209 PHE 0.014 0.001 PHE C 274 TYR 0.011 0.001 TYR C 158 ARG 0.002 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 LEU cc_start: 0.7796 (tp) cc_final: 0.7483 (tt) REVERT: D 36 HIS cc_start: 0.6613 (t70) cc_final: 0.6275 (t70) REVERT: D 165 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6824 (mmmt) REVERT: D 167 LEU cc_start: 0.8451 (mt) cc_final: 0.8061 (mt) REVERT: E 26 THR cc_start: 0.8081 (p) cc_final: 0.7740 (p) REVERT: E 39 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7722 (mmm160) REVERT: E 53 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7968 (ttm-80) REVERT: E 90 SER cc_start: 0.8020 (t) cc_final: 0.7714 (p) REVERT: E 164 LEU cc_start: 0.8516 (tp) cc_final: 0.8280 (tp) REVERT: E 172 PHE cc_start: 0.8457 (m-10) cc_final: 0.8199 (m-80) REVERT: F 32 ASP cc_start: 0.6853 (m-30) cc_final: 0.6589 (m-30) REVERT: F 48 GLN cc_start: 0.7602 (tt0) cc_final: 0.7358 (tt0) REVERT: F 67 GLU cc_start: 0.6723 (tp30) cc_final: 0.5222 (tp30) REVERT: F 69 LYS cc_start: 0.7800 (tttt) cc_final: 0.7581 (tttp) REVERT: F 159 ILE cc_start: 0.6539 (mm) cc_final: 0.5906 (tt) REVERT: F 168 LEU cc_start: 0.8188 (tp) cc_final: 0.7880 (tp) REVERT: F 228 LEU cc_start: 0.8312 (mt) cc_final: 0.8029 (mt) REVERT: F 241 GLU cc_start: 0.5500 (tm-30) cc_final: 0.5054 (tm-30) REVERT: F 245 ILE cc_start: 0.7406 (mt) cc_final: 0.7119 (mt) REVERT: F 256 LYS cc_start: 0.7803 (ptpt) cc_final: 0.7452 (ptpt) REVERT: A 119 ILE cc_start: 0.7445 (tt) cc_final: 0.7219 (tt) REVERT: A 165 LYS cc_start: 0.6669 (mmmt) cc_final: 0.6276 (mmmt) REVERT: A 168 LEU cc_start: 0.7336 (mt) cc_final: 0.6948 (mt) REVERT: A 200 CYS cc_start: 0.6948 (p) cc_final: 0.6706 (p) REVERT: B 99 SER cc_start: 0.7288 (m) cc_final: 0.6957 (p) REVERT: B 130 GLN cc_start: 0.6414 (tp-100) cc_final: 0.6182 (tp-100) REVERT: B 150 ASN cc_start: 0.8088 (t0) cc_final: 0.7855 (t0) REVERT: C 134 LEU cc_start: 0.7094 (mp) cc_final: 0.6881 (mm) REVERT: C 149 ASP cc_start: 0.7215 (m-30) cc_final: 0.6967 (m-30) REVERT: C 196 LEU cc_start: 0.7562 (mp) cc_final: 0.7321 (mt) REVERT: C 204 ILE cc_start: 0.8413 (tp) cc_final: 0.7682 (tp) REVERT: C 208 PHE cc_start: 0.6614 (m-10) cc_final: 0.6338 (m-80) REVERT: C 256 LYS cc_start: 0.7895 (ptpt) cc_final: 0.7642 (ptpt) REVERT: C 263 TYR cc_start: 0.5717 (p90) cc_final: 0.5332 (p90) outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.3414 time to fit residues: 260.0813 Evaluate side-chains 516 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.1980 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 131 optimal weight: 0.0070 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 161 ASN E 123 ASN E 195 ASN F 102 ASN ** F 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS A 161 ASN B 41 ASN B 79 HIS B 192 ASN B 195 ASN B 201 GLN C 44 GLN C 133 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15676 Z= 0.198 Angle : 0.613 11.683 21688 Z= 0.301 Chirality : 0.040 0.171 2412 Planarity : 0.005 0.071 2464 Dihedral : 19.002 78.967 2674 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.99 % Allowed : 12.43 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1640 helix: 0.91 (0.19), residues: 754 sheet: -0.00 (0.33), residues: 220 loop : -0.71 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 270 HIS 0.016 0.001 HIS E 33 PHE 0.027 0.002 PHE F 246 TYR 0.025 0.002 TYR F 263 ARG 0.007 0.001 ARG F 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 523 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 165 LYS cc_start: 0.7257 (mmmt) cc_final: 0.6972 (mmmt) REVERT: D 167 LEU cc_start: 0.8446 (mt) cc_final: 0.8072 (mt) REVERT: D 171 TYR cc_start: 0.7966 (m-80) cc_final: 0.7755 (m-80) REVERT: D 216 ILE cc_start: 0.7897 (mt) cc_final: 0.7451 (mp) REVERT: E 53 ARG cc_start: 0.8366 (tpp80) cc_final: 0.7958 (ttm-80) REVERT: E 90 SER cc_start: 0.8009 (t) cc_final: 0.7705 (p) REVERT: E 180 MET cc_start: 0.6647 (tpp) cc_final: 0.6443 (tpp) REVERT: F 32 ASP cc_start: 0.6974 (m-30) cc_final: 0.6701 (m-30) REVERT: F 159 ILE cc_start: 0.6743 (mm) cc_final: 0.6041 (tt) REVERT: F 168 LEU cc_start: 0.8274 (tp) cc_final: 0.7937 (tp) REVERT: F 202 LYS cc_start: 0.7007 (mttt) cc_final: 0.6789 (mttt) REVERT: F 226 GLU cc_start: 0.6231 (mm-30) cc_final: 0.5945 (mm-30) REVERT: F 228 LEU cc_start: 0.8325 (mt) cc_final: 0.8050 (mt) REVERT: F 241 GLU cc_start: 0.5764 (tm-30) cc_final: 0.5222 (tm-30) REVERT: F 245 ILE cc_start: 0.7470 (mt) cc_final: 0.7186 (mt) REVERT: F 256 LYS cc_start: 0.7776 (ptpt) cc_final: 0.7380 (ptpt) REVERT: A 7 LEU cc_start: 0.7848 (tp) cc_final: 0.7506 (tt) REVERT: A 165 LYS cc_start: 0.6848 (mmmt) cc_final: 0.6520 (mmmt) REVERT: B 31 ILE cc_start: 0.8750 (mt) cc_final: 0.8493 (tt) REVERT: B 70 LYS cc_start: 0.7643 (ttmm) cc_final: 0.7415 (ttmm) REVERT: B 266 GLN cc_start: 0.7461 (tt0) cc_final: 0.7239 (tt0) REVERT: C 48 GLN cc_start: 0.7613 (tt0) cc_final: 0.7324 (tt0) REVERT: C 69 LYS cc_start: 0.7901 (tptm) cc_final: 0.7394 (tptt) REVERT: C 131 TRP cc_start: 0.7177 (t-100) cc_final: 0.6702 (t-100) REVERT: C 134 LEU cc_start: 0.7013 (mp) cc_final: 0.6739 (mm) REVERT: C 204 ILE cc_start: 0.8447 (tp) cc_final: 0.8008 (tp) REVERT: C 241 GLU cc_start: 0.5515 (tm-30) cc_final: 0.5247 (tm-30) REVERT: C 256 LYS cc_start: 0.7948 (ptpt) cc_final: 0.7649 (ptpt) outliers start: 29 outliers final: 18 residues processed: 528 average time/residue: 0.3334 time to fit residues: 241.3209 Evaluate side-chains 510 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 492 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 302 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 0.0970 chunk 152 optimal weight: 0.0980 chunk 165 optimal weight: 0.9990 chunk 136 optimal weight: 0.3980 chunk 151 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 122 optimal weight: 0.0050 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 161 ASN E 30 ASN E 59 ASN E 118 HIS E 175 ASN E 208 HIS F 44 GLN F 218 HIS A 161 ASN A 238 ASN B 59 ASN B 123 ASN B 130 GLN B 208 HIS ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15676 Z= 0.163 Angle : 0.601 11.629 21688 Z= 0.290 Chirality : 0.039 0.151 2412 Planarity : 0.005 0.054 2464 Dihedral : 18.926 78.869 2674 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.13 % Allowed : 16.83 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.09 (0.21), residues: 1640 helix: 0.78 (0.19), residues: 750 sheet: 0.12 (0.33), residues: 220 loop : -0.69 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 131 HIS 0.017 0.001 HIS E 33 PHE 0.023 0.002 PHE C 150 TYR 0.025 0.002 TYR C 263 ARG 0.008 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 502 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 165 LYS cc_start: 0.7129 (mmmt) cc_final: 0.6859 (mmmt) REVERT: D 167 LEU cc_start: 0.8435 (mt) cc_final: 0.8171 (mt) REVERT: D 216 ILE cc_start: 0.7576 (mt) cc_final: 0.7299 (mm) REVERT: E 53 ARG cc_start: 0.8362 (tpp80) cc_final: 0.7943 (ttm-80) REVERT: E 90 SER cc_start: 0.7993 (t) cc_final: 0.7701 (p) REVERT: F 32 ASP cc_start: 0.6963 (m-30) cc_final: 0.6716 (m-30) REVERT: F 159 ILE cc_start: 0.6653 (mm) cc_final: 0.5826 (tt) REVERT: F 168 LEU cc_start: 0.8231 (tp) cc_final: 0.7904 (tp) REVERT: F 171 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7156 (t80) REVERT: F 202 LYS cc_start: 0.7053 (mttt) cc_final: 0.6785 (mttt) REVERT: F 203 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7913 (tm-30) REVERT: F 226 GLU cc_start: 0.6218 (mm-30) cc_final: 0.5981 (mm-30) REVERT: F 241 GLU cc_start: 0.5705 (tm-30) cc_final: 0.5163 (tm-30) REVERT: F 245 ILE cc_start: 0.7387 (mt) cc_final: 0.7053 (mt) REVERT: F 256 LYS cc_start: 0.7741 (ptpt) cc_final: 0.7450 (ptpt) REVERT: A 7 LEU cc_start: 0.7840 (tp) cc_final: 0.7520 (tt) REVERT: A 165 LYS cc_start: 0.6757 (mmmt) cc_final: 0.6482 (mmmt) REVERT: A 167 LEU cc_start: 0.8677 (mt) cc_final: 0.8273 (mt) REVERT: C 48 GLN cc_start: 0.7522 (tt0) cc_final: 0.7292 (tm-30) REVERT: C 69 LYS cc_start: 0.7953 (tptm) cc_final: 0.7336 (tptt) REVERT: C 131 TRP cc_start: 0.7263 (t-100) cc_final: 0.6558 (t-100) REVERT: C 165 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6211 (mm) REVERT: C 203 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7631 (tm-30) REVERT: C 204 ILE cc_start: 0.8383 (tp) cc_final: 0.8097 (tp) REVERT: C 206 ASN cc_start: 0.6389 (t0) cc_final: 0.6172 (t0) REVERT: C 241 GLU cc_start: 0.5704 (tm-30) cc_final: 0.5320 (tm-30) outliers start: 31 outliers final: 23 residues processed: 512 average time/residue: 0.3306 time to fit residues: 230.3279 Evaluate side-chains 517 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 492 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 171 PHE Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 246 PHE Chi-restraints excluded: chain C residue 287 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 162 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 HIS D 161 ASN D 193 HIS E 118 HIS E 123 ASN A 161 ASN A 209 HIS A 238 ASN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15676 Z= 0.241 Angle : 0.619 11.557 21688 Z= 0.304 Chirality : 0.041 0.204 2412 Planarity : 0.005 0.039 2464 Dihedral : 18.991 78.494 2674 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.68 % Allowed : 18.89 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.00 (0.21), residues: 1640 helix: 0.65 (0.19), residues: 756 sheet: 0.20 (0.32), residues: 240 loop : -0.75 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 205 HIS 0.015 0.001 HIS E 33 PHE 0.026 0.002 PHE C 150 TYR 0.020 0.002 TYR C 158 ARG 0.009 0.000 ARG F 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 510 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 165 LYS cc_start: 0.7197 (mmmt) cc_final: 0.6952 (mmmt) REVERT: D 167 LEU cc_start: 0.8429 (mt) cc_final: 0.8077 (mt) REVERT: D 171 TYR cc_start: 0.7970 (m-80) cc_final: 0.7766 (m-80) REVERT: D 216 ILE cc_start: 0.7721 (mt) cc_final: 0.7412 (mm) REVERT: E 53 ARG cc_start: 0.8359 (tpp80) cc_final: 0.7926 (ttm-80) REVERT: E 90 SER cc_start: 0.8018 (t) cc_final: 0.7744 (p) REVERT: F 70 ARG cc_start: 0.6948 (ttp80) cc_final: 0.6503 (ttp80) REVERT: F 134 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6399 (mm) REVERT: F 159 ILE cc_start: 0.6774 (mm) cc_final: 0.6128 (tt) REVERT: F 168 LEU cc_start: 0.8374 (tp) cc_final: 0.8087 (tp) REVERT: F 202 LYS cc_start: 0.7154 (mttt) cc_final: 0.6880 (mttt) REVERT: F 203 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7923 (tm-30) REVERT: F 241 GLU cc_start: 0.5809 (tm-30) cc_final: 0.5293 (tm-30) REVERT: F 245 ILE cc_start: 0.7450 (mt) cc_final: 0.7056 (mt) REVERT: F 259 SER cc_start: 0.8323 (m) cc_final: 0.8112 (t) REVERT: A 7 LEU cc_start: 0.7843 (tp) cc_final: 0.7531 (tt) REVERT: A 165 LYS cc_start: 0.6793 (mmmt) cc_final: 0.6492 (mmmt) REVERT: A 167 LEU cc_start: 0.8719 (mt) cc_final: 0.8435 (mt) REVERT: C 44 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7605 (tm-30) REVERT: C 48 GLN cc_start: 0.7608 (tt0) cc_final: 0.7375 (tm-30) REVERT: C 69 LYS cc_start: 0.7963 (tptm) cc_final: 0.7324 (tptt) REVERT: C 165 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6849 (mm) REVERT: C 203 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7554 (tm-30) REVERT: C 204 ILE cc_start: 0.8436 (tp) cc_final: 0.8059 (tp) REVERT: C 206 ASN cc_start: 0.6619 (t0) cc_final: 0.6380 (t0) REVERT: C 241 GLU cc_start: 0.5873 (tm-30) cc_final: 0.5380 (tm-30) outliers start: 39 outliers final: 25 residues processed: 523 average time/residue: 0.3315 time to fit residues: 236.2484 Evaluate side-chains 516 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 489 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 246 PHE Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 302 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.0030 chunk 92 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 118 HIS E 250 GLN A 161 ASN B 250 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15676 Z= 0.207 Angle : 0.606 11.497 21688 Z= 0.298 Chirality : 0.040 0.197 2412 Planarity : 0.004 0.033 2464 Dihedral : 19.000 78.455 2674 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.82 % Allowed : 20.67 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.21), residues: 1640 helix: 0.57 (0.19), residues: 764 sheet: 0.20 (0.32), residues: 240 loop : -0.72 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 131 HIS 0.013 0.001 HIS E 33 PHE 0.033 0.002 PHE C 99 TYR 0.022 0.002 TYR C 199 ARG 0.010 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 506 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 165 LYS cc_start: 0.7186 (mmmt) cc_final: 0.6932 (mmmt) REVERT: D 216 ILE cc_start: 0.7800 (mt) cc_final: 0.7476 (mm) REVERT: E 31 ILE cc_start: 0.8567 (mp) cc_final: 0.8332 (tp) REVERT: E 53 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7689 (ttm170) REVERT: E 90 SER cc_start: 0.8033 (t) cc_final: 0.7740 (p) REVERT: F 67 GLU cc_start: 0.6866 (tp30) cc_final: 0.5640 (tp30) REVERT: F 70 ARG cc_start: 0.6855 (ttp80) cc_final: 0.6476 (ttp80) REVERT: F 202 LYS cc_start: 0.7078 (mttt) cc_final: 0.6831 (mttt) REVERT: F 203 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7971 (tm-30) REVERT: F 226 GLU cc_start: 0.6374 (mm-30) cc_final: 0.6156 (mm-30) REVERT: F 241 GLU cc_start: 0.5850 (tm-30) cc_final: 0.5207 (tm-30) REVERT: F 245 ILE cc_start: 0.7350 (mt) cc_final: 0.6968 (mt) REVERT: F 259 SER cc_start: 0.8359 (m) cc_final: 0.8119 (t) REVERT: F 287 MET cc_start: 0.5879 (ptp) cc_final: 0.5465 (ptp) REVERT: A 7 LEU cc_start: 0.7856 (tp) cc_final: 0.7534 (tt) REVERT: A 165 LYS cc_start: 0.6785 (mmmt) cc_final: 0.6524 (mmmt) REVERT: A 167 LEU cc_start: 0.8608 (mt) cc_final: 0.8363 (mt) REVERT: C 44 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7601 (tm-30) REVERT: C 48 GLN cc_start: 0.7593 (tt0) cc_final: 0.7324 (tm-30) REVERT: C 165 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6759 (mm) REVERT: C 206 ASN cc_start: 0.6763 (t0) cc_final: 0.6511 (t0) REVERT: C 241 GLU cc_start: 0.5899 (tm-30) cc_final: 0.5262 (tm-30) REVERT: C 259 SER cc_start: 0.8352 (m) cc_final: 0.8042 (p) outliers start: 41 outliers final: 27 residues processed: 524 average time/residue: 0.3464 time to fit residues: 251.6799 Evaluate side-chains 525 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 497 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 246 PHE Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 302 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 HIS E 118 HIS A 209 HIS B 133 GLN B 250 GLN C 218 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15676 Z= 0.205 Angle : 0.626 11.437 21688 Z= 0.306 Chirality : 0.041 0.275 2412 Planarity : 0.005 0.040 2464 Dihedral : 19.051 81.874 2674 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.95 % Allowed : 21.70 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1640 helix: 0.47 (0.19), residues: 766 sheet: 0.27 (0.32), residues: 240 loop : -0.68 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 205 HIS 0.022 0.001 HIS E 33 PHE 0.031 0.002 PHE C 99 TYR 0.015 0.001 TYR C 199 ARG 0.011 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 507 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 165 LYS cc_start: 0.7180 (mmmt) cc_final: 0.6941 (mmmt) REVERT: D 216 ILE cc_start: 0.7846 (mt) cc_final: 0.7507 (mm) REVERT: E 53 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7895 (ttm-80) REVERT: E 90 SER cc_start: 0.8020 (t) cc_final: 0.7720 (p) REVERT: F 67 GLU cc_start: 0.6947 (tp30) cc_final: 0.5557 (tp30) REVERT: F 70 ARG cc_start: 0.6746 (ttp80) cc_final: 0.6348 (ttp80) REVERT: F 202 LYS cc_start: 0.7185 (mttt) cc_final: 0.6920 (mttt) REVERT: F 203 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7988 (tm-30) REVERT: F 216 GLU cc_start: 0.6813 (mp0) cc_final: 0.6612 (mp0) REVERT: F 241 GLU cc_start: 0.5875 (tm-30) cc_final: 0.5099 (tm-30) REVERT: F 245 ILE cc_start: 0.7496 (mt) cc_final: 0.7074 (mt) REVERT: F 259 SER cc_start: 0.8438 (m) cc_final: 0.8137 (t) REVERT: F 287 MET cc_start: 0.5857 (ptp) cc_final: 0.5638 (ptp) REVERT: A 7 LEU cc_start: 0.7860 (tp) cc_final: 0.7534 (tt) REVERT: A 165 LYS cc_start: 0.6898 (mmmt) cc_final: 0.6617 (mmmt) REVERT: A 167 LEU cc_start: 0.8654 (mt) cc_final: 0.8392 (mt) REVERT: A 204 ARG cc_start: 0.8294 (mtt90) cc_final: 0.8059 (mtt90) REVERT: C 44 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7588 (tm-30) REVERT: C 48 GLN cc_start: 0.7670 (tt0) cc_final: 0.7468 (tm-30) REVERT: C 69 LYS cc_start: 0.7860 (tptm) cc_final: 0.7580 (tptt) REVERT: C 165 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6836 (mm) REVERT: C 206 ASN cc_start: 0.6799 (t0) cc_final: 0.6531 (t0) REVERT: C 241 GLU cc_start: 0.5971 (tm-30) cc_final: 0.5390 (tm-30) REVERT: C 259 SER cc_start: 0.8363 (m) cc_final: 0.8030 (p) outliers start: 43 outliers final: 31 residues processed: 522 average time/residue: 0.3301 time to fit residues: 234.7613 Evaluate side-chains 532 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 500 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 246 PHE Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 302 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.0370 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 0.0970 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 0.4980 chunk 101 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS F 102 ASN B 201 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15676 Z= 0.172 Angle : 0.632 11.963 21688 Z= 0.304 Chirality : 0.041 0.257 2412 Planarity : 0.004 0.032 2464 Dihedral : 18.989 83.281 2674 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.47 % Allowed : 23.49 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.21), residues: 1640 helix: 0.43 (0.19), residues: 762 sheet: 0.38 (0.32), residues: 240 loop : -0.67 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 131 HIS 0.022 0.001 HIS E 33 PHE 0.032 0.002 PHE C 141 TYR 0.017 0.001 TYR C 158 ARG 0.007 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 506 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 165 LYS cc_start: 0.7222 (mmmt) cc_final: 0.6934 (mmmt) REVERT: E 53 ARG cc_start: 0.8289 (tpp80) cc_final: 0.7891 (ttm-80) REVERT: E 90 SER cc_start: 0.7995 (t) cc_final: 0.7700 (p) REVERT: F 67 GLU cc_start: 0.7013 (tp30) cc_final: 0.5701 (tp30) REVERT: F 70 ARG cc_start: 0.6686 (ttp80) cc_final: 0.6252 (ttp80) REVERT: F 202 LYS cc_start: 0.7191 (mttt) cc_final: 0.6928 (mttt) REVERT: F 203 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7926 (tm-30) REVERT: F 216 GLU cc_start: 0.6839 (mp0) cc_final: 0.6616 (mp0) REVERT: F 226 GLU cc_start: 0.6410 (mm-30) cc_final: 0.6145 (mm-30) REVERT: F 241 GLU cc_start: 0.5773 (tm-30) cc_final: 0.5063 (tm-30) REVERT: F 245 ILE cc_start: 0.7491 (mt) cc_final: 0.7062 (mt) REVERT: F 259 SER cc_start: 0.8402 (m) cc_final: 0.8106 (t) REVERT: A 7 LEU cc_start: 0.7800 (tp) cc_final: 0.7513 (tt) REVERT: A 165 LYS cc_start: 0.6886 (mmmt) cc_final: 0.6623 (mmmt) REVERT: A 167 LEU cc_start: 0.8556 (mt) cc_final: 0.8354 (mt) REVERT: B 72 LYS cc_start: 0.7975 (mptt) cc_final: 0.7694 (mptt) REVERT: C 44 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7606 (tm-30) REVERT: C 48 GLN cc_start: 0.7655 (tt0) cc_final: 0.7430 (tm-30) REVERT: C 69 LYS cc_start: 0.7828 (tptm) cc_final: 0.7537 (tptt) REVERT: C 165 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6911 (mm) REVERT: C 206 ASN cc_start: 0.6707 (t0) cc_final: 0.6454 (t0) REVERT: C 241 GLU cc_start: 0.5939 (tm-30) cc_final: 0.5329 (tm-30) outliers start: 36 outliers final: 26 residues processed: 522 average time/residue: 0.3325 time to fit residues: 236.0503 Evaluate side-chains 534 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 507 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 246 PHE Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 302 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN E 118 HIS E 201 GLN ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15676 Z= 0.249 Angle : 0.660 11.479 21688 Z= 0.323 Chirality : 0.043 0.268 2412 Planarity : 0.005 0.037 2464 Dihedral : 19.123 84.598 2674 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.88 % Allowed : 24.18 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1640 helix: 0.38 (0.19), residues: 764 sheet: 0.42 (0.32), residues: 220 loop : -0.76 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 131 HIS 0.018 0.001 HIS E 33 PHE 0.035 0.002 PHE C 141 TYR 0.014 0.002 TYR C 158 ARG 0.011 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 520 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7683 (ttm170) REVERT: E 268 ILE cc_start: 0.8448 (mm) cc_final: 0.8170 (tp) REVERT: F 44 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7484 (tm-30) REVERT: F 67 GLU cc_start: 0.7134 (tp30) cc_final: 0.5462 (tp30) REVERT: F 70 ARG cc_start: 0.6790 (ttp80) cc_final: 0.6190 (ttp80) REVERT: F 73 LEU cc_start: 0.8069 (mt) cc_final: 0.7858 (mm) REVERT: F 91 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7111 (mt) REVERT: F 202 LYS cc_start: 0.7278 (mttt) cc_final: 0.7015 (mttt) REVERT: F 203 GLN cc_start: 0.8387 (mm-40) cc_final: 0.7986 (tm-30) REVERT: F 241 GLU cc_start: 0.5958 (tm-30) cc_final: 0.5209 (tm-30) REVERT: F 245 ILE cc_start: 0.7092 (mt) cc_final: 0.6715 (mt) REVERT: F 259 SER cc_start: 0.8480 (m) cc_final: 0.8125 (t) REVERT: A 7 LEU cc_start: 0.7891 (tp) cc_final: 0.7580 (tt) REVERT: A 165 LYS cc_start: 0.7009 (mmmt) cc_final: 0.6739 (mmmt) REVERT: A 167 LEU cc_start: 0.8615 (mt) cc_final: 0.8403 (mt) REVERT: A 204 ARG cc_start: 0.8298 (mtt90) cc_final: 0.8080 (mtt90) REVERT: C 44 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7625 (tm-30) REVERT: C 69 LYS cc_start: 0.7868 (tptm) cc_final: 0.7541 (tptt) REVERT: C 79 TYR cc_start: 0.7178 (t80) cc_final: 0.6422 (t80) REVERT: C 165 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6839 (mm) REVERT: C 206 ASN cc_start: 0.6979 (t0) cc_final: 0.6693 (t0) REVERT: C 241 GLU cc_start: 0.6060 (tm-30) cc_final: 0.5420 (tm-30) outliers start: 42 outliers final: 33 residues processed: 536 average time/residue: 0.3310 time to fit residues: 241.9124 Evaluate side-chains 548 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 513 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 246 PHE Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 303 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 136 optimal weight: 0.0050 chunk 142 optimal weight: 0.0470 chunk 99 optimal weight: 0.9980 chunk 159 optimal weight: 0.3980 overall best weight: 0.3092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 HIS D 250 GLN E 118 HIS F 206 ASN F 217 HIS A 30 ASN A 193 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 201 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 217 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15676 Z= 0.181 Angle : 0.669 12.234 21688 Z= 0.321 Chirality : 0.042 0.284 2412 Planarity : 0.004 0.039 2464 Dihedral : 19.008 84.407 2674 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.27 % Allowed : 25.27 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.14 (0.21), residues: 1640 helix: 0.34 (0.19), residues: 768 sheet: 0.58 (0.33), residues: 220 loop : -0.73 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 131 HIS 0.019 0.001 HIS E 33 PHE 0.030 0.002 PHE C 141 TYR 0.018 0.001 TYR C 158 ARG 0.011 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 514 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 ARG cc_start: 0.8268 (tpp80) cc_final: 0.7773 (ttm-80) REVERT: E 90 SER cc_start: 0.7988 (t) cc_final: 0.7691 (p) REVERT: E 268 ILE cc_start: 0.8483 (mm) cc_final: 0.8189 (tp) REVERT: F 67 GLU cc_start: 0.7110 (tp30) cc_final: 0.5649 (tp30) REVERT: F 70 ARG cc_start: 0.6671 (ttp80) cc_final: 0.6092 (ttp80) REVERT: F 73 LEU cc_start: 0.8071 (mt) cc_final: 0.7866 (mm) REVERT: F 202 LYS cc_start: 0.7086 (mttt) cc_final: 0.6857 (mttt) REVERT: F 203 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7954 (tm-30) REVERT: F 241 GLU cc_start: 0.5930 (tm-30) cc_final: 0.5211 (tm-30) REVERT: F 245 ILE cc_start: 0.7031 (mt) cc_final: 0.6646 (mt) REVERT: F 259 SER cc_start: 0.8469 (m) cc_final: 0.8129 (t) REVERT: F 263 TYR cc_start: 0.6113 (p90) cc_final: 0.5896 (p90) REVERT: A 165 LYS cc_start: 0.7068 (mmmt) cc_final: 0.6803 (mmmt) REVERT: B 178 LEU cc_start: 0.8333 (tt) cc_final: 0.8047 (tt) REVERT: C 44 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 69 LYS cc_start: 0.7785 (tptm) cc_final: 0.7527 (tptt) REVERT: C 79 TYR cc_start: 0.7138 (t80) cc_final: 0.6366 (t80) REVERT: C 177 ARG cc_start: 0.6670 (mtm110) cc_final: 0.6464 (mtm110) REVERT: C 241 GLU cc_start: 0.6007 (tm-30) cc_final: 0.5329 (tm-30) outliers start: 33 outliers final: 21 residues processed: 524 average time/residue: 0.3503 time to fit residues: 254.1442 Evaluate side-chains 537 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 516 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 246 PHE Chi-restraints excluded: chain C residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.0370 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 0.0070 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 HIS D 209 HIS D 250 GLN E 118 HIS E 266 GLN F 206 ASN A 161 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 123 ASN B 266 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15676 Z= 0.191 Angle : 0.682 12.996 21688 Z= 0.326 Chirality : 0.042 0.239 2412 Planarity : 0.005 0.048 2464 Dihedral : 19.008 84.315 2674 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.65 % Allowed : 26.79 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.13 (0.21), residues: 1640 helix: 0.33 (0.19), residues: 768 sheet: 0.60 (0.33), residues: 220 loop : -0.71 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 131 HIS 0.018 0.001 HIS E 33 PHE 0.029 0.002 PHE C 141 TYR 0.015 0.001 TYR C 158 ARG 0.011 0.000 ARG A 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 516 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 ARG cc_start: 0.8290 (tpp80) cc_final: 0.7789 (ttm-80) REVERT: E 268 ILE cc_start: 0.8494 (mm) cc_final: 0.8216 (tp) REVERT: F 67 GLU cc_start: 0.7129 (tp30) cc_final: 0.5624 (tp30) REVERT: F 70 ARG cc_start: 0.6696 (ttp80) cc_final: 0.6140 (ttp80) REVERT: F 202 LYS cc_start: 0.7070 (mttt) cc_final: 0.6691 (mttt) REVERT: F 203 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8018 (tm-30) REVERT: F 241 GLU cc_start: 0.5958 (tm-30) cc_final: 0.5217 (tm-30) REVERT: F 245 ILE cc_start: 0.7103 (mt) cc_final: 0.6704 (mt) REVERT: F 259 SER cc_start: 0.8473 (m) cc_final: 0.8119 (t) REVERT: B 178 LEU cc_start: 0.8429 (tt) cc_final: 0.8170 (tt) REVERT: C 44 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7601 (tm-30) REVERT: C 69 LYS cc_start: 0.7812 (tptm) cc_final: 0.7598 (tptp) REVERT: C 79 TYR cc_start: 0.7130 (t80) cc_final: 0.6355 (t80) REVERT: C 136 LEU cc_start: 0.7669 (mt) cc_final: 0.7456 (mm) REVERT: C 165 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6896 (mm) REVERT: C 241 GLU cc_start: 0.6053 (tm-30) cc_final: 0.5397 (tm-30) outliers start: 24 outliers final: 20 residues processed: 523 average time/residue: 0.3317 time to fit residues: 236.0007 Evaluate side-chains 539 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 518 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 246 PHE Chi-restraints excluded: chain C residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 0.0060 chunk 37 optimal weight: 0.0470 chunk 133 optimal weight: 0.7980 chunk 55 optimal weight: 0.0060 chunk 137 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.3110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 HIS D 250 GLN E 118 HIS ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 123 ASN B 201 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114127 restraints weight = 25839.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117911 restraints weight = 11850.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120283 restraints weight = 7129.436| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 15676 Z= 0.274 Angle : 0.906 59.196 21688 Z= 0.511 Chirality : 0.064 2.341 2412 Planarity : 0.006 0.211 2464 Dihedral : 19.008 84.314 2674 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.72 % Allowed : 27.06 % Favored : 71.22 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.51 % 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: -0.14 (0.21), residues: 1640 helix: 0.31 (0.19), residues: 768 sheet: 0.59 (0.33), residues: 220 loop : -0.70 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 131 HIS 0.344 0.003 HIS D 199 PHE 0.028 0.002 PHE C 150 TYR 0.022 0.001 TYR C 199 ARG 0.030 0.001 ARG C 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4479.25 seconds wall clock time: 80 minutes 56.87 seconds (4856.87 seconds total)