Starting phenix.real_space_refine (version: dev) on Thu Feb 23 18:49:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/02_2023/6nud_0516_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/02_2023/6nud_0516.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/02_2023/6nud_0516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/02_2023/6nud_0516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/02_2023/6nud_0516_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/02_2023/6nud_0516_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= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 370": "NH1" <-> "NH2" Residue "J ARG 383": "NH1" <-> "NH2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "J ARG 397": "NH1" <-> "NH2" Residue "J ARG 421": "NH1" <-> "NH2" Residue "J ARG 515": "NH1" <-> "NH2" Residue "J ARG 531": "NH1" <-> "NH2" Residue "J ARG 655": "NH1" <-> "NH2" Residue "J ARG 678": "NH1" <-> "NH2" Residue "J ARG 720": "NH1" <-> "NH2" Residue "M ARG 65": "NH1" <-> "NH2" Residue "M ARG 74": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 171": "NH1" <-> "NH2" Residue "E ARG 188": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 115": "NH1" <-> "NH2" Residue "N ARG 128": "NH1" <-> "NH2" Residue "N ARG 143": "NH1" <-> "NH2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "N ARG 188": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "O ARG 171": "NH1" <-> "NH2" Residue "O ARG 188": "NH1" <-> "NH2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 115": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ARG 143": "NH1" <-> "NH2" Residue "P ARG 171": "NH1" <-> "NH2" Residue "P ARG 188": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 20831 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "B" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "H" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 832 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 14, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 19} Chain: "I" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2352 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 283} Chain: "J" Number of atoms: 5997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5997 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 8, 'TRANS': 732} Chain breaks: 1 Chain: "M" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "U" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 602 Classifications: {'RNA': 28} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 5} Link IDs: {'rna2p': 6, 'rna3p': 21} Chain: "C" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "E" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "N" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "O" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "P" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.02, per 1000 atoms: 0.58 Number of scatterers: 20831 At special positions: 0 Unit cell: (93.28, 119.78, 212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 69 15.00 O 4188 8.00 N 3532 7.00 C 13003 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: 8.56 Conformation dependent library (CDL) restraints added in 2.8 seconds 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 17 sheets defined 28.4% alpha, 6.3% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'A' and resid 16 through 19 No H-bonds generated for 'chain 'A' and resid 16 through 19' Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.653A pdb=" N SER A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 46 " --> pdb=" O CYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.823A pdb=" N ARG A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 removed outlier: 3.942A pdb=" N ASP A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.615A pdb=" N LEU A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 93' Processing helix chain 'A' and resid 97 through 116 removed outlier: 3.832A pdb=" N ARG A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU A 108 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 19 No H-bonds generated for 'chain 'B' and resid 16 through 19' Processing helix chain 'B' and resid 39 through 46 removed outlier: 3.874A pdb=" N SER B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 46 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.823A pdb=" N ARG B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 67' Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 76 through 85 removed outlier: 3.897A pdb=" N ASP B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 93 removed outlier: 3.527A pdb=" N LEU B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 93' Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.771A pdb=" N ARG B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU B 108 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 110 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 111 " --> pdb=" O MET B 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 43 removed outlier: 3.775A pdb=" N ALA I 35 " --> pdb=" O ARG I 31 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL I 37 " --> pdb=" O PHE I 33 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 53 removed outlier: 3.875A pdb=" N LEU I 50 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU I 52 " --> pdb=" O ALA I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 101 removed outlier: 3.922A pdb=" N ARG I 95 " --> pdb=" O LYS I 91 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU I 99 " --> pdb=" O ARG I 95 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER I 100 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 117 No H-bonds generated for 'chain 'I' and resid 114 through 117' Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'I' and resid 226 through 229 No H-bonds generated for 'chain 'I' and resid 226 through 229' Processing helix chain 'J' and resid 6 through 11 removed outlier: 3.950A pdb=" N TYR J 10 " --> pdb=" O ILE J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 24 removed outlier: 3.589A pdb=" N VAL J 20 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE J 21 " --> pdb=" O GLY J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 42 removed outlier: 4.187A pdb=" N GLY J 35 " --> pdb=" O HIS J 31 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE J 42 " --> pdb=" O TRP J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 53 removed outlier: 3.874A pdb=" N GLN J 51 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 80 removed outlier: 3.570A pdb=" N ILE J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 75 through 80' Processing helix chain 'J' and resid 111 through 113 No H-bonds generated for 'chain 'J' and resid 111 through 113' Processing helix chain 'J' and resid 174 through 177 No H-bonds generated for 'chain 'J' and resid 174 through 177' Processing helix chain 'J' and resid 181 through 183 No H-bonds generated for 'chain 'J' and resid 181 through 183' Processing helix chain 'J' and resid 198 through 218 removed outlier: 3.857A pdb=" N ARG J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA J 207 " --> pdb=" O ARG J 203 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE J 208 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU J 210 " --> pdb=" O ALA J 206 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 237 removed outlier: 3.829A pdb=" N GLU J 237 " --> pdb=" O SER J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 289 removed outlier: 4.150A pdb=" N LYS J 268 " --> pdb=" O LYS J 265 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA J 269 " --> pdb=" O GLN J 266 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU J 272 " --> pdb=" O ALA J 269 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU J 274 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP J 275 " --> pdb=" O LEU J 272 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE J 276 " --> pdb=" O TYR J 273 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET J 277 " --> pdb=" O LEU J 274 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER J 278 " --> pdb=" O ASP J 275 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER J 284 " --> pdb=" O ILE J 281 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU J 285 " --> pdb=" O ALA J 282 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU J 286 " --> pdb=" O ASP J 283 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP J 287 " --> pdb=" O SER J 284 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS J 288 " --> pdb=" O LEU J 285 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU J 289 " --> pdb=" O LEU J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 295 No H-bonds generated for 'chain 'J' and resid 293 through 295' Processing helix chain 'J' and resid 313 through 325 removed outlier: 3.634A pdb=" N THR J 317 " --> pdb=" O LYS J 313 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU J 318 " --> pdb=" O THR J 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL J 319 " --> pdb=" O VAL J 315 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS J 323 " --> pdb=" O VAL J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 328 through 331 No H-bonds generated for 'chain 'J' and resid 328 through 331' Processing helix chain 'J' and resid 348 through 350 No H-bonds generated for 'chain 'J' and resid 348 through 350' Processing helix chain 'J' and resid 358 through 368 removed outlier: 4.375A pdb=" N ILE J 364 " --> pdb=" O SER J 360 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR J 365 " --> pdb=" O TYR J 361 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA J 368 " --> pdb=" O ILE J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 375 No H-bonds generated for 'chain 'J' and resid 372 through 375' Processing helix chain 'J' and resid 385 through 387 No H-bonds generated for 'chain 'J' and resid 385 through 387' Processing helix chain 'J' and resid 421 through 427 removed outlier: 4.324A pdb=" N GLN J 425 " --> pdb=" O ARG J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 540 through 551 removed outlier: 3.818A pdb=" N MET J 550 " --> pdb=" O PHE J 546 " (cutoff:3.500A) Processing helix chain 'J' and resid 556 through 560 removed outlier: 3.681A pdb=" N GLN J 560 " --> pdb=" O VAL J 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 556 through 560' Processing helix chain 'J' and resid 583 through 600 removed outlier: 4.281A pdb=" N ILE J 587 " --> pdb=" O TRP J 583 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ALA J 588 " --> pdb=" O GLN J 584 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL J 591 " --> pdb=" O ILE J 587 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG J 594 " --> pdb=" O THR J 590 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 595 " --> pdb=" O VAL J 591 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN J 596 " --> pdb=" O GLU J 592 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE J 597 " --> pdb=" O LEU J 593 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS J 599 " --> pdb=" O GLN J 595 " (cutoff:3.500A) Processing helix chain 'J' and resid 620 through 626 removed outlier: 4.304A pdb=" N HIS J 625 " --> pdb=" O SER J 621 " (cutoff:3.500A) Processing helix chain 'J' and resid 629 through 636 removed outlier: 3.756A pdb=" N LYS J 635 " --> pdb=" O GLU J 631 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY J 636 " --> pdb=" O GLU J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 654 through 658 Processing helix chain 'J' and resid 663 through 666 No H-bonds generated for 'chain 'J' and resid 663 through 666' Processing helix chain 'J' and resid 673 through 675 No H-bonds generated for 'chain 'J' and resid 673 through 675' Processing helix chain 'J' and resid 680 through 689 removed outlier: 4.078A pdb=" N LYS J 685 " --> pdb=" O PHE J 682 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE J 687 " --> pdb=" O TYR J 684 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU J 688 " --> pdb=" O LYS J 685 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU J 689 " --> pdb=" O LEU J 686 " (cutoff:3.500A) Processing helix chain 'J' and resid 697 through 707 removed outlier: 3.502A pdb=" N VAL J 701 " --> pdb=" O GLU J 697 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA J 702 " --> pdb=" O LYS J 698 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU J 704 " --> pdb=" O ASN J 700 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR J 706 " --> pdb=" O ALA J 702 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR J 707 " --> pdb=" O ARG J 703 " (cutoff:3.500A) Processing helix chain 'J' and resid 709 through 713 removed outlier: 3.579A pdb=" N GLU J 712 " --> pdb=" O THR J 709 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU J 713 " --> pdb=" O ARG J 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 709 through 713' Processing helix chain 'J' and resid 720 through 722 No H-bonds generated for 'chain 'J' and resid 720 through 722' Processing helix chain 'J' and resid 724 through 732 removed outlier: 3.668A pdb=" N LEU J 729 " --> pdb=" O GLN J 725 " (cutoff:3.500A) Processing helix chain 'J' and resid 741 through 754 removed outlier: 3.533A pdb=" N TYR J 751 " --> pdb=" O ALA J 747 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL J 752 " --> pdb=" O LEU J 748 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR J 753 " --> pdb=" O LEU J 749 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 40 through 49 removed outlier: 3.509A pdb=" N SER M 44 " --> pdb=" O SER M 40 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR M 46 " --> pdb=" O CYS M 42 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP M 47 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG M 48 " --> pdb=" O SER M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 72 removed outlier: 3.799A pdb=" N TYR M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG M 65 " --> pdb=" O VAL M 61 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL M 66 " --> pdb=" O SER M 62 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN M 67 " --> pdb=" O TYR M 63 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL M 69 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN M 71 " --> pdb=" O GLN M 67 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA M 72 " --> pdb=" O PHE M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 85 removed outlier: 3.963A pdb=" N ASP M 80 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU M 81 " --> pdb=" O ALA M 77 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS M 84 " --> pdb=" O ASP M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 93 removed outlier: 3.510A pdb=" N LEU M 91 " --> pdb=" O ILE M 87 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU M 93 " --> pdb=" O GLU M 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 87 through 93' Processing helix chain 'M' and resid 97 through 112 removed outlier: 3.769A pdb=" N ARG M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE M 103 " --> pdb=" O THR M 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG M 105 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU M 108 " --> pdb=" O CYS M 104 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA M 109 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU M 110 " --> pdb=" O TYR M 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL M 111 " --> pdb=" O MET M 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.572A pdb=" N LYS C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 removed outlier: 3.964A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 108 " --> pdb=" O ASN C 105 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 109 " --> pdb=" O ALA C 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 109' Processing helix chain 'C' and resid 163 through 178 removed outlier: 3.591A pdb=" N PHE C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 62 removed outlier: 3.629A pdb=" N LYS E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS E 62 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 83 No H-bonds generated for 'chain 'E' and resid 80 through 83' Processing helix chain 'E' and resid 105 through 112 removed outlier: 3.607A pdb=" N GLU E 108 " --> pdb=" O ASN E 105 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU E 109 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASP E 110 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER E 111 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 179 removed outlier: 3.742A pdb=" N LYS E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU E 179 " --> pdb=" O LYS E 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 62 removed outlier: 3.538A pdb=" N ARG N 57 " --> pdb=" O LYS N 53 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR N 58 " --> pdb=" O GLY N 54 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS N 62 " --> pdb=" O THR N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 105 through 112 removed outlier: 3.739A pdb=" N GLU N 108 " --> pdb=" O ASN N 105 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU N 109 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP N 110 " --> pdb=" O ASP N 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER N 111 " --> pdb=" O GLU N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 163 through 179 removed outlier: 3.922A pdb=" N LYS N 168 " --> pdb=" O GLU N 164 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL N 169 " --> pdb=" O GLU N 165 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU N 178 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU N 179 " --> pdb=" O LYS N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'O' and resid 50 through 60 removed outlier: 3.608A pdb=" N GLY O 54 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 83 No H-bonds generated for 'chain 'O' and resid 80 through 83' Processing helix chain 'O' and resid 104 through 112 removed outlier: 4.149A pdb=" N ASP O 107 " --> pdb=" O SER O 104 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU O 109 " --> pdb=" O ALA O 106 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ASP O 110 " --> pdb=" O ASP O 107 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER O 111 " --> pdb=" O GLU O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 179 removed outlier: 4.532A pdb=" N LYS O 168 " --> pdb=" O GLU O 164 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL O 169 " --> pdb=" O GLU O 165 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU O 178 " --> pdb=" O LEU O 174 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU O 179 " --> pdb=" O LYS O 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 60 removed outlier: 3.724A pdb=" N MET P 56 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR P 58 " --> pdb=" O GLY P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 83 No H-bonds generated for 'chain 'P' and resid 80 through 83' Processing helix chain 'P' and resid 105 through 112 removed outlier: 3.895A pdb=" N LEU P 109 " --> pdb=" O ALA P 106 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASP P 110 " --> pdb=" O ASP P 107 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER P 111 " --> pdb=" O GLU P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 179 removed outlier: 3.708A pdb=" N LYS P 168 " --> pdb=" O GLU P 164 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL P 169 " --> pdb=" O GLU P 165 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU P 178 " --> pdb=" O LEU P 174 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU P 179 " --> pdb=" O LYS P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 186 through 188 No H-bonds generated for 'chain 'P' and resid 186 through 188' Processing sheet with id= A, first strand: chain 'I' and resid 64 through 66 removed outlier: 4.258A pdb=" N PHE I 64 " --> pdb=" O TYR I 157 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 129 through 132 removed outlier: 3.607A pdb=" N ASP I 129 " --> pdb=" O THR I 147 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL I 145 " --> pdb=" O VAL I 131 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 303 through 307 removed outlier: 4.465A pdb=" N ALA J 304 " --> pdb=" O PHE J 246 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE J 246 " --> pdb=" O ALA J 304 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA J 340 " --> pdb=" O ASP J 247 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR J 338 " --> pdb=" O SER J 249 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'J' and resid 434 through 436 removed outlier: 4.315A pdb=" N HIS J 434 " --> pdb=" O VAL J 454 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 611 through 614 removed outlier: 3.512A pdb=" N PHE J 614 " --> pdb=" O LEU J 511 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU J 511 " --> pdb=" O PHE J 614 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA J 512 " --> pdb=" O GLY J 581 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY J 581 " --> pdb=" O ALA J 512 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL J 514 " --> pdb=" O ALA J 579 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE J 580 " --> pdb=" O SER J 568 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER J 568 " --> pdb=" O ILE J 580 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 148 through 154 Processing sheet with id= G, first strand: chain 'C' and resid 11 through 14 Processing sheet with id= H, first strand: chain 'C' and resid 119 through 122 Processing sheet with id= I, first strand: chain 'E' and resid 148 through 154 Processing sheet with id= J, first strand: chain 'E' and resid 119 through 122 Processing sheet with id= K, first strand: chain 'N' and resid 5 through 7 Processing sheet with id= L, first strand: chain 'N' and resid 11 through 14 Processing sheet with id= M, first strand: chain 'N' and resid 119 through 122 Processing sheet with id= N, first strand: chain 'O' and resid 148 through 154 Processing sheet with id= O, first strand: chain 'O' and resid 118 through 122 Processing sheet with id= P, first strand: chain 'P' and resid 148 through 154 Processing sheet with id= Q, first strand: chain 'P' and resid 119 through 122 removed outlier: 3.531A pdb=" N LYS P 121 " --> pdb=" O ILE P 138 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5978 1.33 - 1.45: 3663 1.45 - 1.57: 11494 1.57 - 1.69: 137 1.69 - 1.81: 66 Bond restraints: 21338 Sorted by residual: bond pdb=" C4 ATP J 801 " pdb=" C5 ATP J 801 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C5 ATP J 801 " pdb=" C6 ATP J 801 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C8 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.29e+01 bond pdb=" C5 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.74e+01 bond pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.51e+01 ... (remaining 21333 not shown) Histogram of bond angle deviations from ideal: 100.87 - 107.91: 822 107.91 - 114.95: 12724 114.95 - 121.99: 11005 121.99 - 129.03: 4386 129.03 - 136.07: 103 Bond angle restraints: 29040 Sorted by residual: angle pdb=" PB ATP J 801 " pdb=" O3B ATP J 801 " pdb=" PG ATP J 801 " ideal model delta sigma weight residual 139.87 120.91 18.96 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PA ATP J 801 " pdb=" O3A ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 136.83 120.59 16.24 1.00e+00 1.00e+00 2.64e+02 angle pdb=" C5 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N3 ATP J 801 " ideal model delta sigma weight residual 126.80 118.63 8.17 1.00e+00 1.00e+00 6.67e+01 angle pdb=" N3 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 127.04 135.06 -8.02 1.15e+00 7.59e-01 4.88e+01 angle pdb=" N VAL O 63 " pdb=" CA VAL O 63 " pdb=" C VAL O 63 " ideal model delta sigma weight residual 113.71 108.94 4.77 9.50e-01 1.11e+00 2.52e+01 ... (remaining 29035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 12590 35.48 - 70.97: 139 70.97 - 106.45: 6 106.45 - 141.94: 0 141.94 - 177.42: 13 Dihedral angle restraints: 12748 sinusoidal: 5691 harmonic: 7057 Sorted by residual: dihedral pdb=" O4' U U 21 " pdb=" C1' U U 21 " pdb=" N1 U U 21 " pdb=" C2 U U 21 " ideal model delta sinusoidal sigma weight residual 200.00 50.16 149.84 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" O4' C H 17 " pdb=" C1' C H 17 " pdb=" N1 C H 17 " pdb=" C2 C H 17 " ideal model delta sinusoidal sigma weight residual 200.00 54.59 145.41 1 1.50e+01 4.44e-03 7.78e+01 dihedral pdb=" O4' U U 14 " pdb=" C1' U U 14 " pdb=" N1 U U 14 " pdb=" C2 U U 14 " ideal model delta sinusoidal sigma weight residual 200.00 54.64 145.36 1 1.50e+01 4.44e-03 7.78e+01 ... (remaining 12745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2099 0.028 - 0.056: 881 0.056 - 0.084: 153 0.084 - 0.112: 106 0.112 - 0.140: 24 Chirality restraints: 3263 Sorted by residual: chirality pdb=" CB ILE J 755 " pdb=" CA ILE J 755 " pdb=" CG1 ILE J 755 " pdb=" CG2 ILE J 755 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE N 32 " pdb=" N ILE N 32 " pdb=" C ILE N 32 " pdb=" CB ILE N 32 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" C1' C H 40 " pdb=" O4' C H 40 " pdb=" C2' C H 40 " pdb=" N1 C H 40 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 3260 not shown) Planarity restraints: 3491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 196 " -0.015 5.00e-02 4.00e+02 2.30e-02 8.44e-01 pdb=" N PRO I 197 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO I 197 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO I 197 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 71 " -0.014 5.00e-02 4.00e+02 2.09e-02 6.99e-01 pdb=" N PRO E 72 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO E 72 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO E 72 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE O 44 " 0.014 5.00e-02 4.00e+02 2.09e-02 6.96e-01 pdb=" N PRO O 45 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO O 45 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO O 45 " 0.012 5.00e-02 4.00e+02 ... (remaining 3488 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6121 2.81 - 3.33: 17529 3.33 - 3.86: 31540 3.86 - 4.38: 36063 4.38 - 4.90: 62037 Nonbonded interactions: 153290 Sorted by model distance: nonbonded pdb=" O HIS I 233 " pdb=" OG SER I 264 " model vdw 2.290 2.440 nonbonded pdb=" OE2 GLU N 123 " pdb=" OH TYR N 190 " model vdw 2.313 2.440 nonbonded pdb=" O2' G U 20 " pdb=" O2 U U 21 " model vdw 2.315 2.440 nonbonded pdb=" O2' A U 23 " pdb=" OD1 ASN N 134 " model vdw 2.318 2.440 nonbonded pdb=" OG1 THR I 130 " pdb=" O VAL I 145 " model vdw 2.322 2.440 ... (remaining 153285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 5 Type Number sf(0) Gaussians P 69 5.49 5 S 39 5.16 5 C 13003 2.51 5 N 3532 2.21 5 O 4188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.250 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: 0.020 Extract box with map and model: 14.060 Check model and map are aligned: 0.320 Process input model: 56.020 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.200 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4591 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 : 0.002 0.083 21338 Z= 0.109 Angle : 0.430 18.961 29040 Z= 0.290 Chirality : 0.035 0.140 3263 Planarity : 0.002 0.023 3491 Dihedral : 11.757 177.424 8204 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 1.54 % Allowed : 14.97 % Favored : 83.49 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -5.22 (0.12), residues: 2398 helix: -4.63 (0.08), residues: 528 sheet: -2.72 (0.24), residues: 339 loop : -3.39 (0.12), residues: 1531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 737 time to evaluate : 2.337 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 outliers start: 6 outliers final: 0 residues processed: 741 average time/residue: 0.3932 time to fit residues: 425.7078 Evaluate side-chains 320 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.383 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 142 optimal weight: 0.0870 chunk 221 optimal weight: 9.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN I 12 ASN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 ASN I 284 HIS J 129 ASN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN J 412 HIS J 414 GLN J 489 GLN J 502 ASN J 534 ASN ** J 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 ASN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN J 700 ASN J 725 GLN M 27 ASN C 85 ASN C 105 ASN C 144 ASN E 11 GLN E 206 ASN E 213 ASN N 11 GLN N 85 ASN ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 213 ASN O 105 ASN O 213 ASN P 105 ASN P 206 ASN P 213 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 21338 Z= 0.249 Angle : 0.694 13.309 29040 Z= 0.349 Chirality : 0.043 0.235 3263 Planarity : 0.004 0.040 3491 Dihedral : 12.321 178.192 3458 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.38 % Favored : 90.49 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.29 (0.14), residues: 2398 helix: -3.27 (0.15), residues: 576 sheet: -2.46 (0.27), residues: 309 loop : -2.89 (0.13), residues: 1513 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 384 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 36 residues processed: 443 average time/residue: 0.3268 time to fit residues: 223.2318 Evaluate side-chains 299 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 263 time to evaluate : 2.402 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.1877 time to fit residues: 16.1260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 221 optimal weight: 5.9990 chunk 239 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 178 optimal weight: 0.0670 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN J 106 ASN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN ** J 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 303 HIS J 389 ASN J 532 GLN ** J 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN J 675 GLN C 105 ASN E 105 ASN ** N 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 21338 Z= 0.197 Angle : 0.585 8.841 29040 Z= 0.293 Chirality : 0.040 0.174 3263 Planarity : 0.004 0.049 3491 Dihedral : 12.448 178.989 3458 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.67 % Favored : 90.24 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.76 (0.14), residues: 2398 helix: -2.43 (0.17), residues: 629 sheet: -1.67 (0.29), residues: 273 loop : -2.83 (0.14), residues: 1496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 283 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 27 residues processed: 318 average time/residue: 0.3268 time to fit residues: 162.9702 Evaluate side-chains 257 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 230 time to evaluate : 2.489 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1909 time to fit residues: 13.0193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 0.0980 chunk 222 optimal weight: 0.0050 chunk 235 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN I 12 ASN I 14 HIS ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 536 GLN J 584 GLN J 596 ASN J 602 ASN J 626 GLN ** N 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.8193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.111 21338 Z= 0.288 Angle : 0.691 10.802 29040 Z= 0.354 Chirality : 0.044 0.172 3263 Planarity : 0.004 0.057 3491 Dihedral : 13.256 177.715 3458 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.48 (0.15), residues: 2398 helix: -1.97 (0.18), residues: 689 sheet: -1.53 (0.29), residues: 297 loop : -2.78 (0.14), residues: 1412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 267 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 25 residues processed: 315 average time/residue: 0.3307 time to fit residues: 161.7090 Evaluate side-chains 228 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 2.500 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2464 time to fit residues: 13.7570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 532 GLN N 85 ASN ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 GLN P 105 ASN ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.8525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 21338 Z= 0.199 Angle : 0.602 10.899 29040 Z= 0.302 Chirality : 0.041 0.225 3263 Planarity : 0.003 0.047 3491 Dihedral : 13.165 178.851 3458 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.14 (0.15), residues: 2398 helix: -1.60 (0.18), residues: 714 sheet: -1.34 (0.29), residues: 300 loop : -2.62 (0.15), residues: 1384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 239 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 29 residues processed: 279 average time/residue: 0.3243 time to fit residues: 143.3245 Evaluate side-chains 245 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 2.565 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2360 time to fit residues: 15.4670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 1.9990 chunk 212 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 GLN ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 471 ASN J 532 GLN J 700 ASN ** N 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.9030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 21338 Z= 0.220 Angle : 0.612 9.736 29040 Z= 0.306 Chirality : 0.041 0.183 3263 Planarity : 0.003 0.046 3491 Dihedral : 13.283 177.190 3458 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.84 (0.16), residues: 2398 helix: -1.26 (0.19), residues: 717 sheet: -1.33 (0.29), residues: 310 loop : -2.45 (0.15), residues: 1371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 261 average time/residue: 0.3333 time to fit residues: 135.9893 Evaluate side-chains 216 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 2.236 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1989 time to fit residues: 8.0121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 134 optimal weight: 0.0030 chunk 172 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 235 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 532 GLN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.9097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 21338 Z= 0.145 Angle : 0.563 10.112 29040 Z= 0.278 Chirality : 0.039 0.186 3263 Planarity : 0.003 0.046 3491 Dihedral : 13.162 179.757 3458 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.54 (0.16), residues: 2398 helix: -1.02 (0.20), residues: 687 sheet: -1.21 (0.29), residues: 310 loop : -2.22 (0.15), residues: 1401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 240 average time/residue: 0.3356 time to fit residues: 127.0560 Evaluate side-chains 213 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 2.353 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1991 time to fit residues: 5.9825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 GLN ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 HIS ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.9636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 21338 Z= 0.241 Angle : 0.622 9.060 29040 Z= 0.312 Chirality : 0.042 0.217 3263 Planarity : 0.003 0.044 3491 Dihedral : 13.379 177.252 3458 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.54 (0.16), residues: 2398 helix: -1.01 (0.19), residues: 719 sheet: -1.18 (0.29), residues: 303 loop : -2.25 (0.16), residues: 1376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 239 average time/residue: 0.3266 time to fit residues: 123.4814 Evaluate side-chains 219 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 2.433 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1923 time to fit residues: 7.2896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 7.9990 chunk 225 optimal weight: 0.9980 chunk 205 optimal weight: 0.0170 chunk 219 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 HIS E 134 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.9647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 21338 Z= 0.151 Angle : 0.581 9.718 29040 Z= 0.286 Chirality : 0.040 0.198 3263 Planarity : 0.003 0.046 3491 Dihedral : 13.276 178.974 3458 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.36 (0.17), residues: 2398 helix: -0.83 (0.19), residues: 723 sheet: -1.07 (0.30), residues: 301 loop : -2.16 (0.16), residues: 1374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 220 average time/residue: 0.3307 time to fit residues: 114.3231 Evaluate side-chains 210 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 206 time to evaluate : 2.303 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1884 time to fit residues: 4.5458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 243 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 149 optimal weight: 0.0010 chunk 118 optimal weight: 0.0670 overall best weight: 1.7728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 1.0087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 21338 Z= 0.256 Angle : 0.654 9.888 29040 Z= 0.325 Chirality : 0.043 0.207 3263 Planarity : 0.004 0.046 3491 Dihedral : 13.503 177.879 3458 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.44 (0.16), residues: 2398 helix: -0.94 (0.19), residues: 744 sheet: -1.24 (0.29), residues: 295 loop : -2.16 (0.16), residues: 1359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 211 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 216 average time/residue: 0.3476 time to fit residues: 117.6695 Evaluate side-chains 212 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1996 time to fit residues: 6.5714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.147225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.116790 restraints weight = 43001.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.119895 restraints weight = 23860.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.121872 restraints weight = 16644.704| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 1.0441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 21338 Z= 0.261 Angle : 0.655 9.592 29040 Z= 0.327 Chirality : 0.043 0.186 3263 Planarity : 0.004 0.044 3491 Dihedral : 13.670 177.817 3458 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.41 (0.16), residues: 2398 helix: -0.85 (0.19), residues: 734 sheet: -1.29 (0.29), residues: 295 loop : -2.17 (0.16), residues: 1369 =============================================================================== Job complete usr+sys time: 4203.75 seconds wall clock time: 77 minutes 27.60 seconds (4647.60 seconds total)