Starting phenix.real_space_refine on Mon Aug 25 11:14:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcj_28980/08_2025/8fcj_28980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcj_28980/08_2025/8fcj_28980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fcj_28980/08_2025/8fcj_28980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcj_28980/08_2025/8fcj_28980.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fcj_28980/08_2025/8fcj_28980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcj_28980/08_2025/8fcj_28980.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 1.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 746 atoms to isotropic. 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 113 5.49 5 S 94 5.16 5 C 16810 2.51 5 N 4558 2.21 5 O 5245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26820 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1745 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "B" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1727 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2345 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 10, 'TRANS': 277} Chain breaks: 1 Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2351 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Chain: "H" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2420 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 1 Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4147 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 10, 'rna3p_pur': 18, 'rna3p_pyr': 20} Link IDs: {'rna2p': 25, 'rna3p': 37} Chain: "N" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 772 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "O" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 6.93, per 1000 atoms: 0.26 Number of scatterers: 26820 At special positions: 0 Unit cell: (102.238, 119.102, 198.152, 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 94 16.00 P 113 15.00 O 5245 8.00 N 4558 7.00 C 16810 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 - 3.00 Amino acid : True - 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: 2.02 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5590 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 52 sheets defined 39.5% alpha, 22.9% beta 32 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.539A pdb=" N TRP A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 40 through 45 removed outlier: 4.329A pdb=" N GLU B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.827A pdb=" N MET B 204 " --> pdb=" O ARG B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.641A pdb=" N THR B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.729A pdb=" N ILE C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 196 through 206 Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.618A pdb=" N ASP C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 318 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 56 through 71 removed outlier: 3.534A pdb=" N ILE D 60 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.536A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.763A pdb=" N GLY D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 277 through 284 removed outlier: 4.120A pdb=" N ASP D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.588A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.504A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.902A pdb=" N GLY E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 277 through 284 removed outlier: 4.132A pdb=" N ASP E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 301 through 318 Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.616A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 189 through 191 No H-bonds generated for 'chain 'F' and resid 189 through 191' Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.618A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.825A pdb=" N GLY F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.975A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 56 through 71 removed outlier: 3.717A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 105 Processing helix chain 'G' and resid 189 through 191 No H-bonds generated for 'chain 'G' and resid 189 through 191' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 206 removed outlier: 3.652A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 277 through 284 removed outlier: 4.028A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 318 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 56 through 71 removed outlier: 3.532A pdb=" N ILE H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 Processing helix chain 'H' and resid 109 through 112 Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 206 removed outlier: 3.586A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.700A pdb=" N GLY H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 270 No H-bonds generated for 'chain 'H' and resid 268 through 270' Processing helix chain 'H' and resid 277 through 285 removed outlier: 3.977A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 removed outlier: 3.620A pdb=" N LYS H 295 " --> pdb=" O PRO H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 317 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.723A pdb=" N ILE I 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.550A pdb=" N ALA I 70 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 113 Processing helix chain 'I' and resid 116 through 118 No H-bonds generated for 'chain 'I' and resid 116 through 118' Processing helix chain 'I' and resid 148 through 157 removed outlier: 5.367A pdb=" N ALA I 153 " --> pdb=" O HIS I 149 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU I 154 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 238 through 250 Processing helix chain 'I' and resid 251 through 252 No H-bonds generated for 'chain 'I' and resid 251 through 252' Processing helix chain 'I' and resid 253 through 256 Processing helix chain 'I' and resid 261 through 270 removed outlier: 3.834A pdb=" N TYR I 270 " --> pdb=" O GLY I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 Processing helix chain 'I' and resid 361 through 367 removed outlier: 3.506A pdb=" N LYS I 365 " --> pdb=" O ASN I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 382 removed outlier: 4.033A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU I 379 " --> pdb=" O LEU I 375 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE I 380 " --> pdb=" O PHE I 376 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER I 381 " --> pdb=" O ASN I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 392 Processing helix chain 'I' and resid 396 through 421 removed outlier: 3.997A pdb=" N LEU I 400 " --> pdb=" O ASP I 396 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE I 417 " --> pdb=" O ASN I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 removed outlier: 3.850A pdb=" N LYS I 432 " --> pdb=" O PRO I 428 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS I 443 " --> pdb=" O GLU I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 460 Processing helix chain 'I' and resid 463 through 469 Processing helix chain 'I' and resid 469 through 480 Processing helix chain 'I' and resid 481 through 495 Processing helix chain 'J' and resid 6 through 33 Processing helix chain 'J' and resid 41 through 54 Processing helix chain 'J' and resid 58 through 72 removed outlier: 5.907A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 80 Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 93 through 107 Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.511A pdb=" N LYS J 111 " --> pdb=" O TYR J 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 42 through 54 Processing helix chain 'K' and resid 56 through 73 removed outlier: 3.922A pdb=" N SER K 60 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE K 61 " --> pdb=" O ASP K 57 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY K 73 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 81 Processing helix chain 'K' and resid 82 through 91 Processing helix chain 'K' and resid 93 through 107 Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.778A pdb=" N CYS L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.794A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 Processing helix chain 'L' and resid 81 through 92 Processing helix chain 'L' and resid 93 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.891A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 13.531A pdb=" N LEU A 57 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ARG A 165 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG A 186 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 150 removed outlier: 6.690A pdb=" N PHE A 13 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER A 97 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.064A pdb=" N ARG B 19 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 100 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.332A pdb=" N LEU B 109 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N GLU B 10 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N LYS B 107 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N VAL B 12 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N ASP B 105 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 160 through 165 Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.661A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.661A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR C 180 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR C 15 " --> pdb=" O TRP C 230 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP C 230 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR C 17 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE C 228 " --> pdb=" O TYR C 17 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR C 19 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU C 226 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU C 21 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 276 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.648A pdb=" N GLY C 25 " --> pdb=" O THR C 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB3, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB4, first strand: chain 'C' and resid 155 through 160 removed outlier: 3.750A pdb=" N SER C 169 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB6, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.659A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.659A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TYR D 180 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.513A pdb=" N GLY D 25 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.944A pdb=" N THR D 39 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AC2, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AC3, first strand: chain 'D' and resid 242 through 244 Processing sheet with id=AC4, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.473A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.473A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=AC7, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC8, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC9, first strand: chain 'E' and resid 106 through 107 removed outlier: 3.574A pdb=" N PHE E 106 " --> pdb=" O ARG E 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 242 through 244 Processing sheet with id=AD2, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.748A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.748A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD5, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.510A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD7, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.541A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.541A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR G 15 " --> pdb=" O TRP G 230 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRP G 230 " --> pdb=" O TYR G 15 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR G 17 " --> pdb=" O PHE G 228 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE G 228 " --> pdb=" O TYR G 17 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR G 19 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU G 226 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU G 21 " --> pdb=" O ASP G 224 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AE1, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AE2, first strand: chain 'G' and resid 77 through 80 removed outlier: 3.664A pdb=" N ILE G 85 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 106 through 107 removed outlier: 3.654A pdb=" N PHE G 106 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AE5, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.547A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.547A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR H 15 " --> pdb=" O TRP H 230 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP H 230 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE8, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AE9, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AF1, first strand: chain 'H' and resid 105 through 107 Processing sheet with id=AF2, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.527A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AF4, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.467A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AF6, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.243A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 329 through 333 1107 hydrogen bonds defined for protein. 3093 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6656 1.33 - 1.45: 6117 1.45 - 1.57: 14562 1.57 - 1.69: 223 1.69 - 1.81: 149 Bond restraints: 27707 Sorted by residual: bond pdb=" N VAL A 11 " pdb=" CA VAL A 11 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.00e-03 1.23e+04 1.57e+01 bond pdb=" N ASP A 196 " pdb=" CA ASP A 196 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.10e-02 8.26e+03 9.32e+00 bond pdb=" N ILE A 6 " pdb=" CA ILE A 6 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 7.93e+00 bond pdb=" C1' DA O 12 " pdb=" N9 DA O 12 " ideal model delta sigma weight residual 1.460 1.404 0.056 2.00e-02 2.50e+03 7.84e+00 bond pdb=" N THR A 14 " pdb=" CA THR A 14 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.87e+00 ... (remaining 27702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 37638 2.61 - 5.22: 270 5.22 - 7.83: 21 7.83 - 10.44: 4 10.44 - 13.05: 1 Bond angle restraints: 37934 Sorted by residual: angle pdb=" N ASP E 224 " pdb=" CA ASP E 224 " pdb=" C ASP E 224 " ideal model delta sigma weight residual 114.56 107.52 7.04 1.27e+00 6.20e-01 3.07e+01 angle pdb=" CB ARG B 59 " pdb=" CG ARG B 59 " pdb=" CD ARG B 59 " ideal model delta sigma weight residual 111.30 119.96 -8.66 2.30e+00 1.89e-01 1.42e+01 angle pdb=" N LYS K 109 " pdb=" CA LYS K 109 " pdb=" C LYS K 109 " ideal model delta sigma weight residual 109.81 117.66 -7.85 2.21e+00 2.05e-01 1.26e+01 angle pdb=" C3' G M 48 " pdb=" O3' G M 48 " pdb=" P U M 49 " ideal model delta sigma weight residual 120.20 125.50 -5.30 1.50e+00 4.44e-01 1.25e+01 angle pdb=" CA GLU F 243 " pdb=" CB GLU F 243 " pdb=" CG GLU F 243 " ideal model delta sigma weight residual 114.10 121.01 -6.91 2.00e+00 2.50e-01 1.20e+01 ... (remaining 37929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 15576 35.98 - 71.97: 843 71.97 - 107.95: 42 107.95 - 143.94: 3 143.94 - 179.92: 7 Dihedral angle restraints: 16471 sinusoidal: 7746 harmonic: 8725 Sorted by residual: dihedral pdb=" O4' U M 60 " pdb=" C1' U M 60 " pdb=" N1 U M 60 " pdb=" C2 U M 60 " ideal model delta sinusoidal sigma weight residual 200.00 40.45 159.55 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U M 20 " pdb=" C1' U M 20 " pdb=" N1 U M 20 " pdb=" C2 U M 20 " ideal model delta sinusoidal sigma weight residual 200.00 72.13 127.87 1 1.50e+01 4.44e-03 6.89e+01 dihedral pdb=" O4' C M 50 " pdb=" C1' C M 50 " pdb=" N1 C M 50 " pdb=" C2 C M 50 " ideal model delta sinusoidal sigma weight residual -128.00 51.92 -179.92 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2897 0.036 - 0.071: 833 0.071 - 0.107: 254 0.107 - 0.143: 69 0.143 - 0.179: 16 Chirality restraints: 4069 Sorted by residual: chirality pdb=" C1' U M 20 " pdb=" O4' U M 20 " pdb=" C2' U M 20 " pdb=" N1 U M 20 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA PRO F 247 " pdb=" N PRO F 247 " pdb=" C PRO F 247 " pdb=" CB PRO F 247 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA LEU A 7 " pdb=" N LEU A 7 " pdb=" C LEU A 7 " pdb=" CB LEU A 7 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 4066 not shown) Planarity restraints: 4449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C PHE J 61 " 0.065 2.00e-02 2.50e+03 pdb=" O PHE J 61 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " -0.052 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO F 247 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 209 " -0.043 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO B 210 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.036 5.00e-02 4.00e+02 ... (remaining 4446 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 745 2.68 - 3.23: 25084 3.23 - 3.79: 44111 3.79 - 4.34: 61876 4.34 - 4.90: 99915 Nonbonded interactions: 231731 Sorted by model distance: nonbonded pdb=" O LEU B 184 " pdb=" ND2 ASN B 185 " model vdw 2.120 3.120 nonbonded pdb=" N GLU G 257 " pdb=" OE1 GLU G 257 " model vdw 2.188 3.120 nonbonded pdb=" ND2 ASN H 30 " pdb=" OE1 GLN H 42 " model vdw 2.198 3.120 nonbonded pdb=" O ASP F 152 " pdb=" OH TYR L 56 " model vdw 2.211 3.040 nonbonded pdb=" N GLN B 68 " pdb=" OE1 GLN B 68 " model vdw 2.212 3.120 ... (remaining 231726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = (chain 'G' and (resid 12 through 109 or resid 133 through 319)) selection = (chain 'H' and (resid 12 through 109 or resid 133 through 319)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.910 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:8.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 : 0.003 0.056 27707 Z= 0.165 Angle : 0.558 13.050 37934 Z= 0.304 Chirality : 0.040 0.179 4069 Planarity : 0.004 0.079 4449 Dihedral : 19.325 179.920 10881 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.50 % Favored : 94.22 % Rotamer: Outliers : 2.91 % Allowed : 20.68 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.16), residues: 2943 helix: 1.67 (0.17), residues: 1016 sheet: -0.48 (0.21), residues: 618 loop : -0.10 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 19 TYR 0.019 0.001 TYR I 399 PHE 0.012 0.001 PHE B 125 TRP 0.016 0.001 TRP I 488 HIS 0.005 0.001 HIS I 106 Details of bonding type rmsd covalent geometry : bond 0.00342 (27707) covalent geometry : angle 0.55787 (37934) hydrogen bonds : bond 0.16332 ( 1126) hydrogen bonds : angle 6.61104 ( 3249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 253 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 117 ASP cc_start: 0.8332 (p0) cc_final: 0.8104 (p0) REVERT: I 264 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8480 (tp30) REVERT: J 59 LEU cc_start: 0.8599 (mm) cc_final: 0.8071 (mm) REVERT: L 75 ASN cc_start: 0.8577 (t0) cc_final: 0.8259 (t0) outliers start: 77 outliers final: 58 residues processed: 317 average time/residue: 0.5974 time to fit residues: 222.9389 Evaluate side-chains 297 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 238 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 286 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 264 GLU Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 5 SER Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 112 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 ASN C 171 HIS D 30 ASN D 181 GLN E 135 GLN F 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN H 42 GLN H 266 GLN I 117 ASN I 227 HIS ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN K 53 ASN L 4 ASN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.063757 restraints weight = 46818.410| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.68 r_work: 0.2657 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 27707 Z= 0.202 Angle : 0.586 14.226 37934 Z= 0.312 Chirality : 0.041 0.181 4069 Planarity : 0.005 0.079 4449 Dihedral : 18.657 179.721 4915 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.99 % Favored : 94.67 % Rotamer: Outliers : 3.52 % Allowed : 18.34 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.16), residues: 2943 helix: 1.66 (0.16), residues: 1026 sheet: -0.58 (0.22), residues: 558 loop : -0.19 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.020 0.001 TYR I 399 PHE 0.013 0.001 PHE I 449 TRP 0.008 0.001 TRP I 359 HIS 0.004 0.001 HIS G 84 Details of bonding type rmsd covalent geometry : bond 0.00459 (27707) covalent geometry : angle 0.58595 (37934) hydrogen bonds : bond 0.04390 ( 1126) hydrogen bonds : angle 5.02760 ( 3249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 265 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8639 (ptt90) REVERT: A 81 ASP cc_start: 0.8663 (t0) cc_final: 0.8457 (t0) REVERT: A 178 ASP cc_start: 0.8398 (t0) cc_final: 0.8051 (t0) REVERT: D 134 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8979 (p0) REVERT: E 246 ASP cc_start: 0.8208 (t0) cc_final: 0.7902 (t0) REVERT: F 243 GLU cc_start: 0.8360 (pp20) cc_final: 0.8122 (pp20) REVERT: G 163 ARG cc_start: 0.8654 (ptm-80) cc_final: 0.8451 (ptm-80) REVERT: H 117 ASP cc_start: 0.8496 (p0) cc_final: 0.8236 (p0) REVERT: H 140 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9172 (tp) REVERT: H 266 GLN cc_start: 0.7853 (pt0) cc_final: 0.7625 (pt0) REVERT: H 283 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8755 (mt0) REVERT: I 264 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8664 (tp30) REVERT: I 345 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7522 (mtm-85) REVERT: J 59 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8249 (mm) REVERT: J 83 GLU cc_start: 0.8150 (pm20) cc_final: 0.7745 (pm20) REVERT: L 82 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7845 (mt0) outliers start: 93 outliers final: 31 residues processed: 327 average time/residue: 0.6358 time to fit residues: 240.7969 Evaluate side-chains 284 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 264 GLU Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 345 ARG Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 82 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 194 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 chunk 45 optimal weight: 0.0050 chunk 221 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 ASN B 166 ASN C 301 ASN D 30 ASN D 181 GLN E 135 GLN F 37 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN L 4 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.103990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.065307 restraints weight = 46459.723| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.65 r_work: 0.2692 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27707 Z= 0.138 Angle : 0.556 13.833 37934 Z= 0.294 Chirality : 0.040 0.177 4069 Planarity : 0.004 0.079 4449 Dihedral : 18.505 179.640 4846 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.30 % Favored : 94.39 % Rotamer: Outliers : 2.99 % Allowed : 19.28 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.16), residues: 2943 helix: 1.65 (0.16), residues: 1029 sheet: -0.60 (0.22), residues: 559 loop : -0.19 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 34 TYR 0.013 0.001 TYR J 11 PHE 0.014 0.001 PHE C 172 TRP 0.008 0.001 TRP I 359 HIS 0.008 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00306 (27707) covalent geometry : angle 0.55551 (37934) hydrogen bonds : bond 0.03754 ( 1126) hydrogen bonds : angle 4.73111 ( 3249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 266 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8703 (t0) cc_final: 0.8496 (t0) REVERT: A 178 ASP cc_start: 0.8387 (t0) cc_final: 0.7960 (t0) REVERT: B 99 TYR cc_start: 0.8023 (m-80) cc_final: 0.7716 (m-80) REVERT: E 246 ASP cc_start: 0.8266 (t0) cc_final: 0.7887 (t0) REVERT: F 243 GLU cc_start: 0.8324 (pp20) cc_final: 0.8003 (pp20) REVERT: G 163 ARG cc_start: 0.8611 (ptm-80) cc_final: 0.8324 (ptm-80) REVERT: H 50 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8547 (mmtm) REVERT: H 117 ASP cc_start: 0.8486 (p0) cc_final: 0.8232 (p0) REVERT: H 266 GLN cc_start: 0.7997 (pt0) cc_final: 0.7738 (pt0) REVERT: H 283 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8694 (mt0) REVERT: I 224 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.6868 (mtm-85) REVERT: I 264 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8699 (tp30) REVERT: I 345 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7433 (mtm-85) REVERT: J 83 GLU cc_start: 0.8132 (pm20) cc_final: 0.7883 (pm20) REVERT: J 84 GLU cc_start: 0.8962 (pm20) cc_final: 0.8663 (pm20) REVERT: L 53 ASN cc_start: 0.9296 (OUTLIER) cc_final: 0.9072 (m110) REVERT: L 79 ASN cc_start: 0.7651 (m110) cc_final: 0.7403 (m110) REVERT: L 82 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7806 (mt0) outliers start: 79 outliers final: 26 residues processed: 319 average time/residue: 0.5824 time to fit residues: 215.7548 Evaluate side-chains 277 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 264 GLU Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 345 ARG Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 82 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 206 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 67 optimal weight: 0.0070 chunk 138 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 ASN B 185 ASN D 30 ASN E 42 GLN E 135 GLN E 181 GLN F 30 ASN F 266 GLN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN L 4 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 ASN L 79 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.101737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.062462 restraints weight = 46892.997| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.67 r_work: 0.2700 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27707 Z= 0.235 Angle : 0.598 15.500 37934 Z= 0.313 Chirality : 0.042 0.178 4069 Planarity : 0.004 0.078 4449 Dihedral : 18.495 179.763 4834 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.16 % Favored : 94.50 % Rotamer: Outliers : 3.48 % Allowed : 19.21 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.16), residues: 2943 helix: 1.57 (0.16), residues: 1030 sheet: -0.55 (0.22), residues: 568 loop : -0.21 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 71 TYR 0.023 0.001 TYR I 442 PHE 0.016 0.001 PHE H 194 TRP 0.009 0.001 TRP I 359 HIS 0.004 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00542 (27707) covalent geometry : angle 0.59757 (37934) hydrogen bonds : bond 0.04035 ( 1126) hydrogen bonds : angle 4.67932 ( 3249) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 252 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9392 (OUTLIER) cc_final: 0.8750 (ptt90) REVERT: A 93 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: A 178 ASP cc_start: 0.8609 (t0) cc_final: 0.8279 (t0) REVERT: B 23 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8183 (pt) REVERT: D 137 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8207 (tmm) REVERT: E 137 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8004 (tmm) REVERT: E 246 ASP cc_start: 0.8314 (t0) cc_final: 0.7955 (t0) REVERT: F 243 GLU cc_start: 0.8459 (pp20) cc_final: 0.8141 (pp20) REVERT: F 251 GLU cc_start: 0.6874 (pp20) cc_final: 0.6537 (pm20) REVERT: G 179 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.7252 (mtp85) REVERT: H 50 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8696 (mmtm) REVERT: H 117 ASP cc_start: 0.8499 (p0) cc_final: 0.8271 (p0) REVERT: H 283 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8736 (mt0) REVERT: I 224 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7141 (mtm-85) REVERT: I 345 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.7565 (mtm-85) REVERT: I 483 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8495 (mm-40) REVERT: J 83 GLU cc_start: 0.8173 (pm20) cc_final: 0.7949 (pm20) REVERT: J 84 GLU cc_start: 0.8927 (pm20) cc_final: 0.8600 (pm20) REVERT: J 85 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7455 (tt) REVERT: L 79 ASN cc_start: 0.7889 (m-40) cc_final: 0.7623 (m110) REVERT: L 80 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: L 82 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7952 (mt0) outliers start: 92 outliers final: 32 residues processed: 314 average time/residue: 0.6247 time to fit residues: 226.4864 Evaluate side-chains 272 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 345 ARG Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 483 GLN Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 82 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 128 optimal weight: 0.1980 chunk 260 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN E 42 GLN E 135 GLN F 30 ASN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN J 53 ASN K 53 ASN L 4 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.102313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065940 restraints weight = 44259.867| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.53 r_work: 0.2746 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27707 Z= 0.161 Angle : 0.570 14.636 37934 Z= 0.299 Chirality : 0.041 0.176 4069 Planarity : 0.004 0.079 4449 Dihedral : 18.459 179.905 4831 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.37 % Favored : 94.33 % Rotamer: Outliers : 3.18 % Allowed : 19.62 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.16), residues: 2943 helix: 1.59 (0.16), residues: 1031 sheet: -0.61 (0.22), residues: 571 loop : -0.21 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 153 TYR 0.018 0.001 TYR I 399 PHE 0.013 0.001 PHE K 61 TRP 0.009 0.001 TRP I 488 HIS 0.004 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00365 (27707) covalent geometry : angle 0.57000 (37934) hydrogen bonds : bond 0.03647 ( 1126) hydrogen bonds : angle 4.56742 ( 3249) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 240 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 ASP cc_start: 0.8687 (t0) cc_final: 0.8347 (t0) REVERT: B 203 MET cc_start: 0.8585 (mmm) cc_final: 0.8266 (mmm) REVERT: C 221 PHE cc_start: 0.9595 (OUTLIER) cc_final: 0.7931 (t80) REVERT: C 284 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: E 246 ASP cc_start: 0.8462 (t0) cc_final: 0.8065 (t0) REVERT: F 136 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7207 (mmm160) REVERT: F 243 GLU cc_start: 0.8565 (pp20) cc_final: 0.8227 (pp20) REVERT: G 179 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.7253 (mtp85) REVERT: H 50 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8764 (mmtm) REVERT: H 117 ASP cc_start: 0.8613 (p0) cc_final: 0.8378 (p0) REVERT: H 266 GLN cc_start: 0.8057 (pt0) cc_final: 0.7754 (pt0) REVERT: H 283 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8705 (mt0) REVERT: I 155 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9111 (mmtm) REVERT: I 224 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7404 (mtm-85) REVERT: I 345 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.7613 (mtm-85) REVERT: I 483 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8538 (mm-40) REVERT: J 63 GLU cc_start: 0.8243 (mp0) cc_final: 0.7843 (mp0) REVERT: J 82 GLN cc_start: 0.8761 (tp40) cc_final: 0.8492 (tp40) REVERT: K 95 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8667 (mt0) REVERT: L 79 ASN cc_start: 0.8005 (m-40) cc_final: 0.7695 (m110) REVERT: L 82 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7992 (mt0) outliers start: 84 outliers final: 35 residues processed: 299 average time/residue: 0.5742 time to fit residues: 200.6168 Evaluate side-chains 277 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 345 ARG Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 388 ILE Chi-restraints excluded: chain I residue 483 GLN Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 82 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 44 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 72 optimal weight: 0.0980 chunk 163 optimal weight: 3.9990 chunk 299 optimal weight: 20.0000 chunk 246 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN D 287 ASN E 135 GLN F 30 ASN G 297 HIS H 287 ASN I 227 HIS ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN L 4 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.099931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.064172 restraints weight = 44591.081| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.47 r_work: 0.2699 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 27707 Z= 0.266 Angle : 0.616 16.085 37934 Z= 0.322 Chirality : 0.043 0.186 4069 Planarity : 0.004 0.080 4449 Dihedral : 18.484 179.776 4831 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.37 % Favored : 94.29 % Rotamer: Outliers : 3.78 % Allowed : 19.32 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.16), residues: 2943 helix: 1.52 (0.16), residues: 1031 sheet: -0.64 (0.22), residues: 574 loop : -0.25 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 19 TYR 0.021 0.002 TYR I 399 PHE 0.016 0.001 PHE K 61 TRP 0.010 0.001 TRP I 488 HIS 0.004 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00615 (27707) covalent geometry : angle 0.61609 (37934) hydrogen bonds : bond 0.04065 ( 1126) hydrogen bonds : angle 4.63947 ( 3249) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 233 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9404 (OUTLIER) cc_final: 0.8884 (ptt90) REVERT: A 93 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8756 (tt0) REVERT: A 178 ASP cc_start: 0.8748 (t0) cc_final: 0.8389 (t0) REVERT: B 203 MET cc_start: 0.8637 (mmm) cc_final: 0.8291 (mmm) REVERT: C 221 PHE cc_start: 0.9652 (OUTLIER) cc_final: 0.8111 (t80) REVERT: D 137 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8280 (tmm) REVERT: E 246 ASP cc_start: 0.8529 (t0) cc_final: 0.8154 (t0) REVERT: F 136 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7419 (mmm160) REVERT: G 15 TYR cc_start: 0.9133 (m-80) cc_final: 0.8896 (m-80) REVERT: G 179 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.6936 (mtp85) REVERT: H 50 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8763 (mmtm) REVERT: H 117 ASP cc_start: 0.8595 (p0) cc_final: 0.8372 (p0) REVERT: H 142 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8574 (mtp) REVERT: H 179 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.6957 (mtp85) REVERT: H 283 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8706 (mt0) REVERT: I 345 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8224 (mtm-85) REVERT: I 483 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8594 (mm-40) REVERT: J 59 LEU cc_start: 0.8932 (mm) cc_final: 0.7870 (mm) REVERT: J 63 GLU cc_start: 0.8301 (mp0) cc_final: 0.7782 (mp0) REVERT: K 95 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8749 (mt0) REVERT: L 79 ASN cc_start: 0.8100 (m-40) cc_final: 0.7802 (m110) REVERT: L 82 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.8067 (mt0) outliers start: 100 outliers final: 38 residues processed: 302 average time/residue: 0.6109 time to fit residues: 214.0756 Evaluate side-chains 279 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 227 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 345 ARG Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 388 ILE Chi-restraints excluded: chain I residue 483 GLN Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 82 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 186 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 233 optimal weight: 0.4980 chunk 265 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN E 135 GLN F 30 ASN I 227 HIS ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.066252 restraints weight = 44105.030| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.47 r_work: 0.2672 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27707 Z= 0.158 Angle : 0.572 14.846 37934 Z= 0.301 Chirality : 0.041 0.183 4069 Planarity : 0.004 0.081 4449 Dihedral : 18.472 179.767 4830 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.44 % Favored : 94.26 % Rotamer: Outliers : 2.65 % Allowed : 20.34 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.16), residues: 2943 helix: 1.61 (0.16), residues: 1028 sheet: -0.64 (0.22), residues: 563 loop : -0.21 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.020 0.001 TYR I 399 PHE 0.013 0.001 PHE K 61 TRP 0.014 0.001 TRP I 488 HIS 0.005 0.001 HIS I 106 Details of bonding type rmsd covalent geometry : bond 0.00359 (27707) covalent geometry : angle 0.57183 (37934) hydrogen bonds : bond 0.03606 ( 1126) hydrogen bonds : angle 4.52013 ( 3249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 241 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.8695 (ptt90) REVERT: A 93 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8693 (tt0) REVERT: A 178 ASP cc_start: 0.8604 (t0) cc_final: 0.8239 (t0) REVERT: B 203 MET cc_start: 0.8549 (mmm) cc_final: 0.8211 (mmm) REVERT: C 221 PHE cc_start: 0.9623 (OUTLIER) cc_final: 0.8018 (t80) REVERT: E 246 ASP cc_start: 0.8475 (t0) cc_final: 0.8054 (t0) REVERT: F 136 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7159 (mmm160) REVERT: F 179 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.7982 (mtp85) REVERT: F 243 GLU cc_start: 0.8508 (pp20) cc_final: 0.8184 (pp20) REVERT: G 15 TYR cc_start: 0.9038 (m-80) cc_final: 0.8795 (m-80) REVERT: G 179 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7114 (mtp85) REVERT: H 50 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8672 (mmtm) REVERT: H 117 ASP cc_start: 0.8583 (p0) cc_final: 0.8351 (p0) REVERT: H 142 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8465 (mtp) REVERT: H 179 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.6795 (mtp180) REVERT: H 283 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8609 (mt0) REVERT: I 345 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8132 (mtm-85) REVERT: I 483 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8521 (mm-40) REVERT: J 59 LEU cc_start: 0.8887 (mm) cc_final: 0.7892 (mm) REVERT: J 63 GLU cc_start: 0.8320 (mp0) cc_final: 0.7816 (mp0) REVERT: K 67 ASP cc_start: 0.9020 (t70) cc_final: 0.8686 (t0) REVERT: K 71 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8326 (mtm-85) REVERT: K 95 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8644 (mt0) REVERT: L 79 ASN cc_start: 0.8021 (m-40) cc_final: 0.7689 (m110) REVERT: L 82 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7940 (mt0) outliers start: 70 outliers final: 31 residues processed: 292 average time/residue: 0.5916 time to fit residues: 201.1798 Evaluate side-chains 276 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 334 TYR Chi-restraints excluded: chain I residue 345 ARG Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 388 ILE Chi-restraints excluded: chain I residue 483 GLN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 82 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 265 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 251 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN E 135 GLN F 30 ASN F 266 GLN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065876 restraints weight = 44522.199| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.49 r_work: 0.2739 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27707 Z= 0.179 Angle : 0.578 14.949 37934 Z= 0.303 Chirality : 0.041 0.179 4069 Planarity : 0.004 0.082 4449 Dihedral : 18.454 179.591 4830 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.44 % Favored : 94.26 % Rotamer: Outliers : 2.80 % Allowed : 20.30 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.16), residues: 2943 helix: 1.60 (0.16), residues: 1029 sheet: -0.66 (0.22), residues: 575 loop : -0.22 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 49 TYR 0.022 0.001 TYR I 399 PHE 0.013 0.001 PHE K 61 TRP 0.010 0.001 TRP I 488 HIS 0.005 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00410 (27707) covalent geometry : angle 0.57809 (37934) hydrogen bonds : bond 0.03652 ( 1126) hydrogen bonds : angle 4.49462 ( 3249) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 236 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8697 (ptt90) REVERT: A 93 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8759 (tt0) REVERT: A 178 ASP cc_start: 0.8682 (t0) cc_final: 0.8340 (t0) REVERT: B 203 MET cc_start: 0.8607 (mmm) cc_final: 0.8259 (mmm) REVERT: C 221 PHE cc_start: 0.9635 (OUTLIER) cc_final: 0.8060 (t80) REVERT: C 284 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8098 (mp10) REVERT: E 246 ASP cc_start: 0.8505 (t0) cc_final: 0.8093 (t0) REVERT: F 48 ASN cc_start: 0.9183 (m-40) cc_final: 0.8818 (p0) REVERT: F 179 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8041 (mtp85) REVERT: F 243 GLU cc_start: 0.8546 (pp20) cc_final: 0.8216 (pp20) REVERT: G 15 TYR cc_start: 0.9092 (m-80) cc_final: 0.8803 (m-80) REVERT: G 179 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.6945 (mtp85) REVERT: H 50 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8741 (mmtm) REVERT: H 142 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8557 (mtp) REVERT: H 179 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.6845 (mtp85) REVERT: H 283 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8612 (mt0) REVERT: I 345 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8071 (mtm-85) REVERT: I 483 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8559 (mm-40) REVERT: J 59 LEU cc_start: 0.8920 (mm) cc_final: 0.7905 (mm) REVERT: J 63 GLU cc_start: 0.8385 (mp0) cc_final: 0.7852 (mp0) REVERT: K 67 ASP cc_start: 0.9080 (t70) cc_final: 0.8835 (t0) REVERT: K 95 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8701 (mt0) REVERT: L 79 ASN cc_start: 0.8146 (m-40) cc_final: 0.7826 (m110) REVERT: L 82 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7993 (mt0) outliers start: 74 outliers final: 37 residues processed: 288 average time/residue: 0.6341 time to fit residues: 211.4057 Evaluate side-chains 279 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 334 TYR Chi-restraints excluded: chain I residue 345 ARG Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 388 ILE Chi-restraints excluded: chain I residue 483 GLN Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 82 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 274 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN D 30 ASN E 135 GLN F 30 ASN ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.099947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.063870 restraints weight = 45327.756| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.59 r_work: 0.2612 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27707 Z= 0.170 Angle : 0.579 14.694 37934 Z= 0.304 Chirality : 0.041 0.180 4069 Planarity : 0.004 0.082 4449 Dihedral : 18.440 179.726 4830 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.40 % Favored : 94.29 % Rotamer: Outliers : 2.53 % Allowed : 20.83 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.16), residues: 2943 helix: 1.62 (0.16), residues: 1028 sheet: -0.76 (0.21), residues: 593 loop : -0.19 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 19 TYR 0.021 0.001 TYR I 399 PHE 0.013 0.001 PHE B 125 TRP 0.014 0.001 TRP I 488 HIS 0.005 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00389 (27707) covalent geometry : angle 0.57936 (37934) hydrogen bonds : bond 0.03579 ( 1126) hydrogen bonds : angle 4.47681 ( 3249) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 229 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8612 (ptt90) REVERT: A 111 LYS cc_start: 0.9198 (mmmm) cc_final: 0.8805 (mmmt) REVERT: A 178 ASP cc_start: 0.8426 (t0) cc_final: 0.8047 (t0) REVERT: B 203 MET cc_start: 0.8427 (mmm) cc_final: 0.8058 (mmm) REVERT: C 221 PHE cc_start: 0.9603 (OUTLIER) cc_final: 0.7982 (t80) REVERT: C 284 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: C 305 MET cc_start: 0.9103 (ttt) cc_final: 0.8892 (ttt) REVERT: E 246 ASP cc_start: 0.8401 (t0) cc_final: 0.7975 (t0) REVERT: F 48 ASN cc_start: 0.9077 (m-40) cc_final: 0.8722 (p0) REVERT: F 136 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7074 (mmm160) REVERT: F 179 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.7913 (mtp85) REVERT: F 243 GLU cc_start: 0.8342 (pp20) cc_final: 0.7989 (pp20) REVERT: G 15 TYR cc_start: 0.8870 (m-80) cc_final: 0.8561 (m-80) REVERT: G 157 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8649 (tp) REVERT: G 179 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.6763 (mtp85) REVERT: H 50 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8568 (mmtm) REVERT: H 117 ASP cc_start: 0.8458 (p0) cc_final: 0.7495 (t0) REVERT: H 179 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.6724 (mtp180) REVERT: H 283 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8595 (mt0) REVERT: I 345 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7962 (mtm-85) REVERT: I 483 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8446 (mm-40) REVERT: K 95 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8509 (mt0) REVERT: L 79 ASN cc_start: 0.7925 (m-40) cc_final: 0.7592 (m110) REVERT: L 82 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7818 (mt0) outliers start: 67 outliers final: 36 residues processed: 275 average time/residue: 0.6487 time to fit residues: 206.6196 Evaluate side-chains 282 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 232 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 295 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 334 TYR Chi-restraints excluded: chain I residue 345 ARG Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 388 ILE Chi-restraints excluded: chain I residue 483 GLN Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 82 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 214 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 260 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 269 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN D 30 ASN E 135 GLN F 30 ASN I 250 GLN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.064568 restraints weight = 45143.139| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.59 r_work: 0.2653 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27707 Z= 0.153 Angle : 0.574 14.295 37934 Z= 0.301 Chirality : 0.041 0.185 4069 Planarity : 0.004 0.083 4449 Dihedral : 18.405 179.881 4830 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.47 % Favored : 94.26 % Rotamer: Outliers : 2.27 % Allowed : 20.91 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.16), residues: 2943 helix: 1.62 (0.16), residues: 1028 sheet: -0.69 (0.22), residues: 574 loop : -0.18 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 19 TYR 0.020 0.001 TYR I 399 PHE 0.014 0.001 PHE B 125 TRP 0.014 0.001 TRP I 488 HIS 0.005 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00347 (27707) covalent geometry : angle 0.57389 (37934) hydrogen bonds : bond 0.03519 ( 1126) hydrogen bonds : angle 4.44985 ( 3249) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8653 (ptt90) REVERT: A 111 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8813 (mmmt) REVERT: A 178 ASP cc_start: 0.8444 (t0) cc_final: 0.8046 (t0) REVERT: C 221 PHE cc_start: 0.9598 (OUTLIER) cc_final: 0.7951 (t80) REVERT: C 284 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: C 305 MET cc_start: 0.9114 (ttt) cc_final: 0.8895 (ttt) REVERT: E 246 ASP cc_start: 0.8406 (t0) cc_final: 0.7990 (t0) REVERT: F 48 ASN cc_start: 0.9048 (m-40) cc_final: 0.8758 (p0) REVERT: F 136 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7116 (mmm160) REVERT: F 179 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.7918 (mtp85) REVERT: F 243 GLU cc_start: 0.8319 (pp20) cc_final: 0.7998 (pp20) REVERT: G 15 TYR cc_start: 0.8880 (m-80) cc_final: 0.8609 (m-80) REVERT: G 157 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8670 (tp) REVERT: G 179 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.6861 (mtp85) REVERT: H 50 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8631 (mmtm) REVERT: H 117 ASP cc_start: 0.8437 (p0) cc_final: 0.7685 (t0) REVERT: H 140 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9133 (tp) REVERT: H 179 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.6743 (mtp180) REVERT: H 283 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8621 (mt0) REVERT: I 224 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7475 (mtm-85) REVERT: I 345 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7210 (mtm-85) REVERT: I 483 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8448 (mm-40) REVERT: J 20 GLN cc_start: 0.8955 (mm110) cc_final: 0.8513 (mm-40) REVERT: J 63 GLU cc_start: 0.8320 (mp0) cc_final: 0.7739 (mp0) REVERT: K 71 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8156 (mtm-85) REVERT: K 95 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8488 (mt0) REVERT: L 79 ASN cc_start: 0.7950 (m-40) cc_final: 0.7618 (m110) REVERT: L 82 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7795 (mt0) outliers start: 60 outliers final: 33 residues processed: 279 average time/residue: 0.6215 time to fit residues: 201.4046 Evaluate side-chains 283 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 334 TYR Chi-restraints excluded: chain I residue 345 ARG Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 388 ILE Chi-restraints excluded: chain I residue 483 GLN Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 82 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 19 optimal weight: 2.9990 chunk 121 optimal weight: 0.3980 chunk 292 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN E 135 GLN F 30 ASN ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.100256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.064191 restraints weight = 45081.691| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.59 r_work: 0.2618 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27707 Z= 0.170 Angle : 0.587 14.557 37934 Z= 0.306 Chirality : 0.041 0.176 4069 Planarity : 0.004 0.084 4449 Dihedral : 18.366 179.697 4826 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.40 % Favored : 94.33 % Rotamer: Outliers : 2.23 % Allowed : 21.32 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.16), residues: 2943 helix: 1.60 (0.16), residues: 1030 sheet: -0.74 (0.21), residues: 593 loop : -0.17 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 71 TYR 0.021 0.001 TYR I 399 PHE 0.014 0.001 PHE B 125 TRP 0.009 0.001 TRP I 359 HIS 0.005 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00390 (27707) covalent geometry : angle 0.58660 (37934) hydrogen bonds : bond 0.03591 ( 1126) hydrogen bonds : angle 4.45509 ( 3249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7644.23 seconds wall clock time: 131 minutes 24.61 seconds (7884.61 seconds total)