Starting phenix.real_space_refine (version: dev) on Tue Apr 5 18:14:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/04_2022/7ouh_13077_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/04_2022/7ouh_13077.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/04_2022/7ouh_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_13077/04_2022/7ouh_13077_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/04_2022/7ouh_13077_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/04_2022/7ouh_13077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/04_2022/7ouh_13077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/04_2022/7ouh_13077_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/04_2022/7ouh_13077_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 19, 'TRANS': 257, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 275, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 257, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 275, 'PCIS': 1} 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: {' ZN': 1, ' MG': 2, '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: {' ZN': 1, ' MG': 2, '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: 8.54, per 1000 atoms: 0.57 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: 6.12 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral 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: 4.81 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: 4.18 Time building geometry restraints manager: 6.55 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 1.987 1.303 0.684 2.00e-02 2.50e+03 1.17e+03 bond pdb=" CAJ KLQ E 304 " pdb=" CAX KLQ E 304 " ideal model delta sigma weight residual 1.987 1.303 0.684 2.00e-02 2.50e+03 1.17e+03 bond pdb=" CAW KLQ B 304 " pdb=" CBA KLQ B 304 " ideal model delta sigma weight residual 0.988 1.488 -0.500 2.00e-02 2.50e+03 6.24e+02 bond pdb=" CAW KLQ E 304 " pdb=" CBA KLQ E 304 " ideal model delta sigma weight residual 0.988 1.487 -0.499 2.00e-02 2.50e+03 6.24e+02 bond pdb=" CAZ KLQ B 304 " pdb=" NBF KLQ B 304 " ideal model delta sigma weight residual 1.079 1.454 -0.375 2.00e-02 2.50e+03 3.51e+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 144.65 115.88 28.77 3.00e+00 1.11e-01 9.20e+01 angle pdb=" CAY KLQ E 304 " pdb=" CAV KLQ E 304 " pdb=" FAG KLQ E 304 " ideal model delta sigma weight residual 144.65 115.94 28.71 3.00e+00 1.11e-01 9.16e+01 angle pdb=" CAI KLQ E 304 " pdb=" CAV KLQ E 304 " pdb=" FAG KLQ E 304 " ideal model delta sigma weight residual 94.22 116.37 -22.15 3.00e+00 1.11e-01 5.45e+01 angle pdb=" CAI KLQ B 304 " pdb=" CAV KLQ B 304 " pdb=" FAG KLQ B 304 " ideal model delta sigma weight residual 94.22 116.36 -22.14 3.00e+00 1.11e-01 5.45e+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: 7720 16.87 - 33.74: 820 33.74 - 50.60: 368 50.60 - 67.47: 92 67.47 - 84.34: 20 Dihedral angle restraints: 9020 sinusoidal: 4104 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 9017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1806 0.035 - 0.071: 426 0.071 - 0.106: 138 0.106 - 0.141: 40 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=" CA ILE D 268 " pdb=" N ILE D 268 " pdb=" C ILE D 268 " pdb=" CB ILE D 268 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-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 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. 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: 1.760 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: 6.930 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.130 Process input model: 45.810 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 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 : 0.013 0.684 15676 Z= 0.611 Angle : 0.740 28.771 21688 Z= 0.333 Chirality : 0.038 0.176 2412 Planarity : 0.006 0.147 2464 Dihedral : 17.338 84.340 5808 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 1.724 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 outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.3261 time to fit residues: 254.1425 Evaluate side-chains 501 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2026 ------------------------------------------------------------------------------- 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: 5.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 0.0070 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 overall best weight: 1.1404 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 175 ASN E 195 ASN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 HIS ** F 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 HIS ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN B 79 HIS B 192 ASN B 195 ASN B 208 HIS C 44 GLN C 133 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 15676 Z= 0.318 Angle : 0.698 14.531 21688 Z= 0.350 Chirality : 0.043 0.198 2412 Planarity : 0.006 0.085 2464 Dihedral : 18.995 78.363 2582 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 2.27 % 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 (0.20), residues: 1640 helix: 0.67 (0.19), residues: 762 sheet: -0.16 (0.32), residues: 220 loop : -0.77 (0.24), residues: 658 *********************** 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 554 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 521 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 531 average time/residue: 0.3180 time to fit residues: 231.4907 Evaluate side-chains 508 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 487 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1571 time to fit residues: 7.7234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 126 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 0.0980 chunk 165 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN E 59 ASN E 118 HIS E 208 HIS F 44 GLN F 218 HIS A 161 ASN B 123 ASN B 192 ASN B 266 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 15676 Z= 0.205 Angle : 0.644 12.223 21688 Z= 0.316 Chirality : 0.041 0.205 2412 Planarity : 0.006 0.087 2464 Dihedral : 18.966 78.879 2582 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 1.79 % 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: -0.15 (0.21), residues: 1640 helix: 0.55 (0.19), residues: 762 sheet: 0.02 (0.31), residues: 240 loop : -0.82 (0.24), residues: 638 *********************** 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 540 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 514 time to evaluate : 1.585 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 outliers start: 26 outliers final: 12 residues processed: 523 average time/residue: 0.3285 time to fit residues: 237.7705 Evaluate side-chains 501 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 489 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2388 time to fit residues: 6.4608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 0.1980 chunk 80 optimal weight: 0.8980 chunk 145 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 HIS E 118 HIS F 102 ASN A 209 HIS B 123 ASN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 15676 Z= 0.221 Angle : 0.653 14.918 21688 Z= 0.322 Chirality : 0.041 0.197 2412 Planarity : 0.006 0.102 2464 Dihedral : 18.987 81.855 2582 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 2.20 % 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: -0.20 (0.20), residues: 1640 helix: 0.49 (0.19), residues: 758 sheet: 0.01 (0.31), residues: 240 loop : -0.82 (0.24), residues: 642 *********************** 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 535 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 503 time to evaluate : 1.845 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 outliers start: 32 outliers final: 14 residues processed: 513 average time/residue: 0.3304 time to fit residues: 232.3238 Evaluate side-chains 518 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 504 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1642 time to fit residues: 6.2491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.0170 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 67 optimal weight: 0.0040 chunk 138 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 overall best weight: 0.1830 ------------------------------------------------------------------------------- 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 E 134 HIS ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 246 GLN B 146 HIS B 266 GLN C 218 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 15676 Z= 0.191 Angle : 0.665 14.938 21688 Z= 0.322 Chirality : 0.040 0.336 2412 Planarity : 0.005 0.071 2464 Dihedral : 18.918 84.957 2582 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 1.85 % 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: -0.19 (0.21), residues: 1640 helix: 0.41 (0.19), residues: 756 sheet: 0.13 (0.31), residues: 240 loop : -0.75 (0.24), residues: 644 *********************** 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 534 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 507 time to evaluate : 1.736 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 outliers start: 27 outliers final: 6 residues processed: 518 average time/residue: 0.3326 time to fit residues: 240.2977 Evaluate side-chains 502 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 496 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1560 time to fit residues: 3.9124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN D 161 ASN D 250 GLN E 118 HIS E 134 HIS E 266 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 133 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.171 15676 Z= 0.279 Angle : 0.689 18.054 21688 Z= 0.344 Chirality : 0.042 0.312 2412 Planarity : 0.006 0.106 2464 Dihedral : 19.008 85.915 2582 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.06 % 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: -0.21 (0.20), residues: 1640 helix: 0.37 (0.19), residues: 752 sheet: 0.36 (0.32), residues: 220 loop : -0.80 (0.24), residues: 668 *********************** 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 529 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 509 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 515 average time/residue: 0.3257 time to fit residues: 229.9932 Evaluate side-chains 521 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 509 time to evaluate : 1.634 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1825 time to fit residues: 5.7013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 0.0020 chunk 90 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 101 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 overall best weight: 0.2746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 250 GLN E 118 HIS E 134 HIS F 206 ASN F 217 HIS ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 209 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 177 ASN B 201 GLN B 266 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 15676 Z= 0.187 Angle : 0.654 11.618 21688 Z= 0.318 Chirality : 0.040 0.250 2412 Planarity : 0.005 0.080 2464 Dihedral : 18.950 84.841 2582 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 1.24 % 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: -0.17 (0.21), residues: 1640 helix: 0.34 (0.19), residues: 762 sheet: 0.49 (0.33), residues: 220 loop : -0.74 (0.24), residues: 658 *********************** 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 518 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 500 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 508 average time/residue: 0.3314 time to fit residues: 231.4131 Evaluate side-chains 506 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 498 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1386 time to fit residues: 4.1541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 161 ASN D 209 HIS D 250 GLN E 118 HIS E 134 HIS A 30 ASN A 193 HIS A 209 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS C 217 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 15676 Z= 0.230 Angle : 0.673 12.563 21688 Z= 0.330 Chirality : 0.042 0.235 2412 Planarity : 0.005 0.072 2464 Dihedral : 19.023 83.799 2582 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 1.51 % 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: -0.26 (0.21), residues: 1640 helix: 0.27 (0.19), residues: 764 sheet: 0.45 (0.33), residues: 220 loop : -0.80 (0.24), residues: 656 *********************** 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 529 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 507 time to evaluate : 1.625 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 outliers start: 22 outliers final: 11 residues processed: 514 average time/residue: 0.3291 time to fit residues: 230.8993 Evaluate side-chains 516 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 505 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1705 time to fit residues: 5.4332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 0.0070 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 0.0770 overall best weight: 1.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 250 GLN E 118 HIS E 201 GLN E 266 GLN F 206 ASN A 133 GLN A 161 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS B 118 HIS B 201 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 15676 Z= 0.356 Angle : 0.764 20.099 21688 Z= 0.376 Chirality : 0.047 0.324 2412 Planarity : 0.005 0.070 2464 Dihedral : 19.400 85.107 2582 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.96 % 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: -0.61 (0.20), residues: 1640 helix: 0.03 (0.19), residues: 772 sheet: -0.03 (0.32), residues: 224 loop : -0.93 (0.24), residues: 644 *********************** 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 538 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 524 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 527 average time/residue: 0.3239 time to fit residues: 234.5827 Evaluate side-chains 532 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 524 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2367 time to fit residues: 4.9978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 110 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 102 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 105 optimal weight: 0.0870 chunk 141 optimal weight: 0.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN E 118 HIS E 201 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 118 HIS C 306 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.186 15676 Z= 0.259 Angle : 0.757 16.761 21688 Z= 0.380 Chirality : 0.044 0.314 2412 Planarity : 0.007 0.165 2464 Dihedral : 19.207 83.580 2582 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.62 % 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: -0.50 (0.20), residues: 1640 helix: 0.12 (0.19), residues: 766 sheet: 0.13 (0.33), residues: 220 loop : -0.92 (0.24), residues: 654 ********************** 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 524 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 515 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: symmetry clash outliers start: 9 outliers final: 5 residues processed: 517 average time/residue: 0.3327 time to fit residues: 236.4691 Evaluate side-chains 508 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 503 time to evaluate : 1.618 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1582 time to fit residues: 3.7013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 55 optimal weight: 0.0470 chunk 137 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 117 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN E 118 HIS E 195 ASN F 206 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 118 HIS B 130 GLN B 177 ASN B 201 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.141605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112478 restraints weight = 25644.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116206 restraints weight = 11807.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118555 restraints weight = 7137.776| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.149 15676 Z= 0.247 Angle : 0.760 16.754 21688 Z= 0.375 Chirality : 0.044 0.328 2412 Planarity : 0.007 0.145 2464 Dihedral : 19.153 82.771 2582 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.69 % 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: -0.45 (0.20), residues: 1640 helix: 0.19 (0.19), residues: 756 sheet: 0.18 (0.33), residues: 220 loop : -0.92 (0.23), residues: 664 =============================================================================== Job complete usr+sys time: 4257.83 seconds wall clock time: 77 minutes 14.08 seconds (4634.08 seconds total)