Starting phenix.real_space_refine on Mon Mar 18 11:46:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/03_2024/6nud_0516_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/03_2024/6nud_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_0516/03_2024/6nud_0516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/03_2024/6nud_0516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/03_2024/6nud_0516_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/03_2024/6nud_0516_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.099 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 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. 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-5265/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: 11.44, per 1000 atoms: 0.55 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: 8.19 Conformation dependent library (CDL) restraints added in 3.4 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: 8.48 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: 5.68 Time building geometry restraints manager: 8.79 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: 12728 35.48 - 70.97: 213 70.97 - 106.45: 17 106.45 - 141.94: 0 141.94 - 177.42: 13 Dihedral angle restraints: 12971 sinusoidal: 5914 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 12968 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 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: 4.560 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: 13.310 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 60.210 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4507 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 : 13.139 177.424 8427 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 % Allowed : 5.67 % Favored : 94.04 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP J 733 HIS 0.001 0.000 HIS I 233 PHE 0.004 0.000 PHE J 246 TYR 0.005 0.000 TYR J 473 ARG 0.001 0.000 ARG I 182 *********************** 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 : 2.254 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: A 70 TYR cc_start: 0.2704 (t80) cc_final: 0.2452 (t80) REVERT: J 251 ILE cc_start: 0.7504 (mt) cc_final: 0.7259 (mt) outliers start: 6 outliers final: 0 residues processed: 741 average time/residue: 0.3655 time to fit residues: 393.3268 Evaluate side-chains 320 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.450 ------------------------------------------------------------------------------- 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 266 GLN ** 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 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN P 213 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5405 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21338 Z= 0.234 Angle : 0.672 13.241 29040 Z= 0.338 Chirality : 0.043 0.234 3263 Planarity : 0.004 0.038 3491 Dihedral : 14.971 178.538 3681 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.67 % Favored : 90.20 % Rotamer: Outliers : 3.70 % Allowed : 15.24 % Favored : 81.06 % 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: -4.29 (0.14), residues: 2398 helix: -3.29 (0.14), residues: 579 sheet: -2.40 (0.26), residues: 329 loop : -2.90 (0.13), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 38 HIS 0.005 0.001 HIS J 482 PHE 0.026 0.002 PHE C 102 TYR 0.027 0.002 TYR J 468 ARG 0.010 0.001 ARG I 95 *********************** 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 454 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 377 time to evaluate : 2.200 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: J 336 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6528 (ptt180) REVERT: C 92 LYS cc_start: 0.5823 (OUTLIER) cc_final: 0.5562 (mmtt) REVERT: P 103 LEU cc_start: 0.4812 (tt) cc_final: 0.4229 (tt) outliers start: 77 outliers final: 36 residues processed: 436 average time/residue: 0.3408 time to fit residues: 231.4636 Evaluate side-chains 303 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 265 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain P residue 185 SER Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 239 optimal weight: 0.0980 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN 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 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN J 106 ASN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN ** J 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 389 ASN J 532 GLN J 536 GLN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 584 GLN J 596 ASN J 602 ASN J 626 GLN J 675 GLN E 105 ASN N 85 ASN ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.7377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21338 Z= 0.343 Angle : 0.742 11.469 29040 Z= 0.381 Chirality : 0.046 0.234 3263 Planarity : 0.005 0.051 3491 Dihedral : 15.619 177.089 3681 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.84 % Favored : 89.03 % Rotamer: Outliers : 4.95 % Allowed : 17.50 % Favored : 77.55 % 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: -3.88 (0.14), residues: 2398 helix: -2.47 (0.17), residues: 663 sheet: -1.67 (0.29), residues: 288 loop : -2.96 (0.14), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 343 HIS 0.013 0.002 HIS J 434 PHE 0.029 0.003 PHE P 98 TYR 0.022 0.002 TYR J 74 ARG 0.007 0.001 ARG C 140 *********************** 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 401 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 298 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 8 MET cc_start: 0.7441 (ptt) cc_final: 0.7159 (ptt) REVERT: I 28 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7718 (p) REVERT: I 30 ASP cc_start: 0.6823 (p0) cc_final: 0.6560 (p0) REVERT: J 283 ASP cc_start: 0.4858 (t0) cc_final: 0.4630 (t0) REVERT: J 336 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7017 (ptt-90) REVERT: J 665 LEU cc_start: 0.5252 (OUTLIER) cc_final: 0.5030 (tm) REVERT: C 92 LYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5774 (mmtt) REVERT: E 81 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6679 (pmt100) REVERT: O 119 GLU cc_start: 0.6389 (pm20) cc_final: 0.5803 (pm20) REVERT: P 179 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6796 (mt) outliers start: 103 outliers final: 60 residues processed: 380 average time/residue: 0.3269 time to fit residues: 188.8570 Evaluate side-chains 284 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 218 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 532 GLN Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 665 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 146 THR Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 185 SER Chi-restraints excluded: chain P residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 chunk 222 optimal weight: 0.0050 chunk 235 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- 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 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 461 GLN J 532 GLN C 105 ASN ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.7701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21338 Z= 0.167 Angle : 0.579 10.968 29040 Z= 0.289 Chirality : 0.040 0.163 3263 Planarity : 0.003 0.046 3491 Dihedral : 15.378 179.881 3681 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 3.75 % Allowed : 19.76 % Favored : 76.49 % 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: -3.43 (0.15), residues: 2398 helix: -1.93 (0.18), residues: 663 sheet: -1.38 (0.30), residues: 287 loop : -2.77 (0.14), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 101 HIS 0.005 0.001 HIS J 434 PHE 0.023 0.001 PHE A 103 TYR 0.018 0.001 TYR J 468 ARG 0.006 0.000 ARG I 188 *********************** 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: 78 poor density : 251 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 283 ASP cc_start: 0.4639 (t0) cc_final: 0.4437 (t0) REVERT: J 336 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6689 (ptt180) REVERT: J 623 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.5789 (tmm) REVERT: E 81 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6370 (pmt100) REVERT: E 96 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8118 (mm) REVERT: N 198 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7525 (tp) REVERT: O 119 GLU cc_start: 0.6381 (pm20) cc_final: 0.5832 (pm20) REVERT: P 179 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6749 (mt) outliers start: 78 outliers final: 46 residues processed: 313 average time/residue: 0.3150 time to fit residues: 153.4765 Evaluate side-chains 265 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 213 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 201 optimal weight: 0.0470 chunk 163 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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** ** I 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 GLN J 461 GLN E 105 ASN ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.8102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21338 Z= 0.170 Angle : 0.556 9.896 29040 Z= 0.278 Chirality : 0.040 0.175 3263 Planarity : 0.003 0.045 3491 Dihedral : 15.383 178.769 3681 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 4.18 % Allowed : 19.95 % Favored : 75.87 % 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 (0.16), residues: 2398 helix: -1.66 (0.19), residues: 688 sheet: -1.24 (0.30), residues: 294 loop : -2.59 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 101 HIS 0.005 0.001 HIS J 434 PHE 0.020 0.001 PHE O 102 TYR 0.020 0.001 TYR J 149 ARG 0.006 0.000 ARG I 188 *********************** 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 318 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 231 time to evaluate : 2.274 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: J 283 ASP cc_start: 0.4625 (t0) cc_final: 0.4374 (t0) REVERT: J 336 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6872 (ptt180) REVERT: J 623 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5798 (tmm) REVERT: E 81 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6158 (pmt100) REVERT: N 171 ARG cc_start: 0.5918 (OUTLIER) cc_final: 0.5398 (ptm160) REVERT: O 119 GLU cc_start: 0.6336 (pm20) cc_final: 0.5789 (pm20) REVERT: P 179 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6865 (mt) outliers start: 87 outliers final: 58 residues processed: 298 average time/residue: 0.3195 time to fit residues: 148.6794 Evaluate side-chains 275 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 212 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 663 ASP Chi-restraints excluded: chain J residue 749 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 207 TYR Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 185 SER Chi-restraints excluded: chain P residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 138 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** I 251 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 700 ASN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.8458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21338 Z= 0.170 Angle : 0.555 9.663 29040 Z= 0.276 Chirality : 0.040 0.155 3263 Planarity : 0.003 0.049 3491 Dihedral : 15.421 179.880 3681 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 4.13 % Allowed : 19.71 % Favored : 76.15 % 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: -2.96 (0.16), residues: 2398 helix: -1.40 (0.19), residues: 710 sheet: -1.20 (0.30), residues: 296 loop : -2.55 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 101 HIS 0.004 0.001 HIS J 68 PHE 0.021 0.001 PHE O 102 TYR 0.027 0.001 TYR J 298 ARG 0.005 0.000 ARG I 188 *********************** 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 311 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 225 time to evaluate : 2.390 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: I 4 LYS cc_start: 0.3198 (OUTLIER) cc_final: 0.2575 (tttt) REVERT: I 215 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8426 (pt) REVERT: J 283 ASP cc_start: 0.4635 (t0) cc_final: 0.4356 (t0) REVERT: J 336 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6810 (ptt180) REVERT: J 623 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5734 (tmm) REVERT: E 81 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6271 (pmt100) REVERT: N 171 ARG cc_start: 0.5920 (OUTLIER) cc_final: 0.5366 (ptm160) REVERT: N 198 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7610 (tp) outliers start: 86 outliers final: 60 residues processed: 296 average time/residue: 0.3165 time to fit residues: 145.0482 Evaluate side-chains 277 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 210 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 563 SER Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 663 ASP Chi-restraints excluded: chain J residue 749 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 75 ASP Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 202 THR Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 185 SER Chi-restraints excluded: chain P residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.9980 chunk 26 optimal weight: 0.0020 chunk 134 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- 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** ** I 251 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 471 ASN J 725 GLN C 124 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.9035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21338 Z= 0.229 Angle : 0.604 9.405 29040 Z= 0.302 Chirality : 0.041 0.198 3263 Planarity : 0.004 0.049 3491 Dihedral : 15.598 177.146 3681 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 4.28 % Allowed : 20.00 % Favored : 75.72 % 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: -2.83 (0.16), residues: 2398 helix: -1.27 (0.19), residues: 735 sheet: -1.09 (0.28), residues: 332 loop : -2.52 (0.15), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 343 HIS 0.005 0.001 HIS J 68 PHE 0.023 0.002 PHE O 102 TYR 0.027 0.002 TYR J 298 ARG 0.006 0.000 ARG I 95 *********************** 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 312 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 223 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.6607 (pmm) cc_final: 0.6359 (pmm) REVERT: J 283 ASP cc_start: 0.4946 (t0) cc_final: 0.4734 (t0) REVERT: J 336 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6888 (ptt180) REVERT: J 623 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.5764 (tmm) REVERT: E 81 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6895 (pmt100) REVERT: N 171 ARG cc_start: 0.5810 (OUTLIER) cc_final: 0.5536 (ptm160) REVERT: N 198 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7707 (tp) REVERT: O 119 GLU cc_start: 0.7039 (pp20) cc_final: 0.6508 (pp20) outliers start: 89 outliers final: 58 residues processed: 297 average time/residue: 0.3106 time to fit residues: 143.9290 Evaluate side-chains 268 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 205 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 247 ASP Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 663 ASP Chi-restraints excluded: chain J residue 749 LEU Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 75 ASP Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 202 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 185 SER Chi-restraints excluded: chain P residue 201 THR 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: 5.9990 chunk 140 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 0.0060 chunk 45 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 0.8980 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 251 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** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN ** E 159 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: 0.6316 moved from start: 0.9340 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= 0.204 Angle : 0.591 9.469 29040 Z= 0.295 Chirality : 0.041 0.197 3263 Planarity : 0.003 0.048 3491 Dihedral : 15.626 178.835 3681 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.80 % Allowed : 21.11 % Favored : 75.10 % 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: -2.65 (0.16), residues: 2398 helix: -1.13 (0.19), residues: 722 sheet: -1.10 (0.28), residues: 336 loop : -2.36 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 343 HIS 0.006 0.001 HIS J 482 PHE 0.020 0.001 PHE J 723 TYR 0.021 0.001 TYR N 181 ARG 0.006 0.000 ARG I 95 *********************** 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 298 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 219 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 283 ASP cc_start: 0.4910 (t0) cc_final: 0.4676 (t0) REVERT: J 336 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6860 (ptt180) REVERT: J 623 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5709 (tmm) REVERT: E 81 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6791 (pmt100) REVERT: N 171 ARG cc_start: 0.5828 (OUTLIER) cc_final: 0.5337 (ptm160) REVERT: N 198 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7763 (tp) REVERT: P 120 VAL cc_start: 0.7708 (p) cc_final: 0.7360 (m) outliers start: 79 outliers final: 60 residues processed: 283 average time/residue: 0.3207 time to fit residues: 140.7121 Evaluate side-chains 268 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 203 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 247 ASP Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 332 ASN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 563 SER Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 657 ILE Chi-restraints excluded: chain J residue 663 ASP Chi-restraints excluded: chain J residue 749 LEU Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 202 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 185 SER Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 206 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 0.0970 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 218 optimal weight: 0.1980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 251 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 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN E 105 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 GLN ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.9373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21338 Z= 0.147 Angle : 0.581 9.523 29040 Z= 0.286 Chirality : 0.040 0.250 3263 Planarity : 0.003 0.047 3491 Dihedral : 15.542 179.732 3681 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.17 % Allowed : 22.26 % Favored : 74.57 % 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: -2.53 (0.16), residues: 2398 helix: -1.01 (0.19), residues: 723 sheet: -0.95 (0.29), residues: 329 loop : -2.32 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 101 HIS 0.007 0.001 HIS J 482 PHE 0.022 0.001 PHE J 723 TYR 0.023 0.001 TYR A 106 ARG 0.006 0.000 ARG I 95 *********************** 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 291 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 225 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 283 ASP cc_start: 0.4804 (t0) cc_final: 0.4509 (t0) REVERT: J 336 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6716 (ptt180) REVERT: J 602 ASN cc_start: 0.5048 (t0) cc_final: 0.4539 (t0) REVERT: J 623 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5667 (tmm) REVERT: M 36 ARG cc_start: 0.5061 (mmt180) cc_final: 0.4767 (mmt180) REVERT: E 81 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6704 (pmt100) REVERT: N 171 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.5205 (ptm160) REVERT: N 198 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7722 (tp) REVERT: O 119 GLU cc_start: 0.6820 (pp20) cc_final: 0.6473 (pt0) outliers start: 66 outliers final: 54 residues processed: 274 average time/residue: 0.3264 time to fit residues: 139.0707 Evaluate side-chains 266 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 207 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 247 ASP Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 647 SER Chi-restraints excluded: chain J residue 657 ILE Chi-restraints excluded: chain J residue 749 LEU Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 202 THR Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 206 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.0970 chunk 231 optimal weight: 8.9990 chunk 141 optimal weight: 0.0470 chunk 109 optimal weight: 3.9990 chunk 161 optimal weight: 0.5980 chunk 243 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 118 optimal weight: 0.0570 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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 251 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 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.9372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21338 Z= 0.136 Angle : 0.576 10.228 29040 Z= 0.282 Chirality : 0.040 0.196 3263 Planarity : 0.003 0.051 3491 Dihedral : 15.459 179.855 3681 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.55 % Allowed : 22.74 % Favored : 74.71 % 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: -2.38 (0.17), residues: 2398 helix: -0.83 (0.19), residues: 716 sheet: -0.89 (0.29), residues: 325 loop : -2.25 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 101 HIS 0.006 0.001 HIS J 482 PHE 0.022 0.001 PHE J 723 TYR 0.022 0.001 TYR P 207 ARG 0.007 0.000 ARG C 136 ********************** 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 277 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 224 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 283 ASP cc_start: 0.4780 (t0) cc_final: 0.4533 (t0) REVERT: J 336 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6797 (ptt180) REVERT: J 602 ASN cc_start: 0.5071 (t0) cc_final: 0.4551 (t0) REVERT: J 623 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5731 (tmm) REVERT: M 36 ARG cc_start: 0.5040 (mmt180) cc_final: 0.4802 (mmt180) REVERT: E 81 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6767 (pmt100) REVERT: N 171 ARG cc_start: 0.5808 (OUTLIER) cc_final: 0.5277 (ptm160) REVERT: O 119 GLU cc_start: 0.6823 (pp20) cc_final: 0.6474 (pt0) REVERT: P 132 GLU cc_start: 0.4589 (tm-30) cc_final: 0.3072 (pt0) outliers start: 53 outliers final: 46 residues processed: 267 average time/residue: 0.3191 time to fit residues: 132.1342 Evaluate side-chains 263 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 213 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 647 SER Chi-restraints excluded: chain J residue 657 ILE Chi-restraints excluded: chain J residue 749 LEU Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 206 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 193 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 432 HIS ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN E 105 ASN ** E 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.154381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.124258 restraints weight = 42639.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.127415 restraints weight = 24109.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.129464 restraints weight = 16921.114| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.9489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 21338 Z= 0.155 Angle : 0.577 10.285 29040 Z= 0.283 Chirality : 0.040 0.182 3263 Planarity : 0.003 0.049 3491 Dihedral : 15.476 179.090 3681 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.93 % Allowed : 22.50 % Favored : 74.57 % 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: -2.32 (0.17), residues: 2398 helix: -0.73 (0.20), residues: 723 sheet: -0.90 (0.29), residues: 325 loop : -2.24 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 101 HIS 0.006 0.001 HIS J 482 PHE 0.021 0.001 PHE J 723 TYR 0.023 0.001 TYR A 106 ARG 0.009 0.000 ARG I 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4402.81 seconds wall clock time: 80 minutes 13.75 seconds (4813.75 seconds total)