Starting phenix.real_space_refine on Mon Jun 23 20:00:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcj_28980/06_2025/8fcj_28980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcj_28980/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fcj_28980/06_2025/8fcj_28980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcj_28980/06_2025/8fcj_28980.map" model { file = "/net/cci-nas-00/data/ceres_data/8fcj_28980/06_2025/8fcj_28980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcj_28980/06_2025/8fcj_28980.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 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): 1.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.14, per 1000 atoms: 0.60 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: 7.04 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 10.40 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: 10.44 Time building geometry restraints manager: 8.27 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: 0.000 Normalize map: mean=0, sd=1: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.040 Extract box with map and model: 0.940 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 67.890 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (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 TRP 0.016 0.001 TRP I 488 HIS 0.005 0.001 HIS I 106 PHE 0.012 0.001 PHE B 125 TYR 0.019 0.001 TYR I 399 ARG 0.013 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.16332 ( 1126) hydrogen bonds : angle 6.61104 ( 3249) covalent geometry : bond 0.00342 (27707) covalent geometry : angle 0.55787 (37934) *********************** 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 : 2.832 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: 1.3548 time to fit residues: 506.5397 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 : 3.009 ------------------------------------------------------------------------------- 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 253 optimal weight: 0.0980 chunk 227 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** G 297 HIS 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.101617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.062388 restraints weight = 46774.653| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.67 r_work: 0.2631 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 27707 Z= 0.254 Angle : 0.613 15.160 37934 Z= 0.325 Chirality : 0.043 0.184 4069 Planarity : 0.005 0.080 4449 Dihedral : 18.683 179.990 4915 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.30 % Favored : 94.36 % Rotamer: Outliers : 3.74 % Allowed : 18.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2943 helix: 1.58 (0.16), residues: 1028 sheet: -0.52 (0.22), residues: 572 loop : -0.22 (0.18), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 79 HIS 0.004 0.001 HIS I 106 PHE 0.016 0.001 PHE H 194 TYR 0.025 0.002 TYR I 399 ARG 0.006 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 1126) hydrogen bonds : angle 4.99628 ( 3249) covalent geometry : bond 0.00585 (27707) covalent geometry : angle 0.61312 (37934) *********************** 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 362 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 263 time to evaluate : 2.934 Fit side-chains revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8775 (ptt90) REVERT: A 166 ASP cc_start: 0.8363 (t0) cc_final: 0.8159 (t0) REVERT: A 178 ASP cc_start: 0.8478 (t0) cc_final: 0.8097 (t0) REVERT: C 284 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8563 (mp10) REVERT: D 134 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.9004 (p0) REVERT: D 137 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8712 (tpp) REVERT: E 246 ASP cc_start: 0.8281 (t0) cc_final: 0.7968 (t0) REVERT: F 243 GLU cc_start: 0.8403 (pp20) cc_final: 0.8154 (pp20) REVERT: H 50 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8546 (mmtm) REVERT: H 117 ASP cc_start: 0.8497 (p0) cc_final: 0.8244 (p0) REVERT: H 140 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9177 (tp) REVERT: H 266 GLN cc_start: 0.7876 (pt0) cc_final: 0.7638 (pt0) REVERT: I 264 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8672 (tp30) REVERT: I 345 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7415 (mtm-85) REVERT: J 59 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8289 (mm) REVERT: J 82 GLN cc_start: 0.8785 (tp40) cc_final: 0.8538 (tp40) REVERT: J 83 GLU cc_start: 0.8144 (pm20) cc_final: 0.7739 (pm20) REVERT: L 79 ASN cc_start: 0.7747 (m110) cc_final: 0.7525 (m110) outliers start: 99 outliers final: 29 residues processed: 329 average time/residue: 1.4971 time to fit residues: 570.6039 Evaluate side-chains 274 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 2.440 ------------------------------------------------------------------------------- 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 27 ASN 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 137 MET 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 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 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 50 LYS 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 163 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 ASN D 30 ASN D 181 GLN E 135 GLN F 30 ASN F 37 ASN F 266 GLN H 30 ASN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN J 53 ASN L 4 ASN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.102275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065972 restraints weight = 44275.379| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.52 r_work: 0.2674 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0942 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= 0.162 Angle : 0.573 14.724 37934 Z= 0.303 Chirality : 0.041 0.176 4069 Planarity : 0.004 0.078 4449 Dihedral : 18.540 179.776 4846 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.37 % Favored : 94.29 % Rotamer: Outliers : 2.95 % Allowed : 19.47 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 2943 helix: 1.62 (0.16), residues: 1026 sheet: -0.63 (0.22), residues: 565 loop : -0.22 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 488 HIS 0.008 0.001 HIS C 171 PHE 0.015 0.001 PHE C 172 TYR 0.013 0.001 TYR J 11 ARG 0.006 0.000 ARG C 34 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 1126) hydrogen bonds : angle 4.75633 ( 3249) covalent geometry : bond 0.00363 (27707) covalent geometry : angle 0.57277 (37934) *********************** 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 339 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 261 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8523 (t0) cc_final: 0.8279 (t0) REVERT: A 178 ASP cc_start: 0.8571 (t0) cc_final: 0.8168 (t0) REVERT: B 99 TYR cc_start: 0.8105 (m-80) cc_final: 0.7794 (m-80) REVERT: B 123 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7102 (ttpp) REVERT: C 261 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: C 284 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8619 (mp10) REVERT: E 246 ASP cc_start: 0.8380 (t0) cc_final: 0.8005 (t0) REVERT: F 243 GLU cc_start: 0.8548 (pp20) cc_final: 0.8239 (pp20) REVERT: H 50 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8631 (mmtm) REVERT: H 117 ASP cc_start: 0.8570 (p0) cc_final: 0.8316 (p0) REVERT: H 140 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9234 (tp) REVERT: H 266 GLN cc_start: 0.8076 (pt0) cc_final: 0.7783 (pt0) REVERT: H 283 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8710 (mt0) REVERT: I 135 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7768 (tptp) REVERT: I 224 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.6891 (mtm-85) REVERT: I 264 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8837 (tp30) REVERT: I 345 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7611 (mtm-85) REVERT: J 82 GLN cc_start: 0.8852 (tp40) cc_final: 0.8635 (tp40) REVERT: J 83 GLU cc_start: 0.8236 (pm20) cc_final: 0.7986 (pm20) REVERT: J 84 GLU cc_start: 0.8991 (pm20) cc_final: 0.8700 (pm20) REVERT: L 53 ASN cc_start: 0.9354 (OUTLIER) cc_final: 0.9139 (m110) outliers start: 78 outliers final: 26 residues processed: 315 average time/residue: 1.3460 time to fit residues: 494.6973 Evaluate side-chains 277 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain C residue 20 VAL 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 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 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 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 140 LEU 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 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 4 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 53 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 238 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 237 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 D 181 GLN E 135 GLN E 181 GLN F 30 ASN ** 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** ** L 82 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 = 0.102475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.066064 restraints weight = 44715.526| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.54 r_work: 0.2676 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27707 Z= 0.162 Angle : 0.563 14.659 37934 Z= 0.296 Chirality : 0.041 0.175 4069 Planarity : 0.004 0.078 4449 Dihedral : 18.517 179.920 4837 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.44 % Favored : 94.22 % Rotamer: Outliers : 3.33 % Allowed : 19.40 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2943 helix: 1.61 (0.16), residues: 1030 sheet: -0.58 (0.22), residues: 579 loop : -0.20 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 488 HIS 0.005 0.001 HIS C 171 PHE 0.012 0.001 PHE B 16 TYR 0.020 0.001 TYR I 442 ARG 0.006 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 1126) hydrogen bonds : angle 4.62250 ( 3249) covalent geometry : bond 0.00367 (27707) covalent geometry : angle 0.56283 (37934) *********************** 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 342 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 254 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.8697 (ptt90) REVERT: A 93 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8662 (tt0) REVERT: A 166 ASP cc_start: 0.8545 (t0) cc_final: 0.8287 (t0) REVERT: A 178 ASP cc_start: 0.8582 (t0) cc_final: 0.8210 (t0) REVERT: C 221 PHE cc_start: 0.9588 (OUTLIER) cc_final: 0.7908 (t80) REVERT: C 261 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: D 137 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8202 (tmm) REVERT: E 246 ASP cc_start: 0.8445 (t0) cc_final: 0.8040 (t0) REVERT: F 243 GLU cc_start: 0.8546 (pp20) cc_final: 0.8200 (pp20) REVERT: F 266 GLN cc_start: 0.7919 (pt0) cc_final: 0.7671 (pt0) REVERT: G 179 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.7112 (mtp85) REVERT: H 117 ASP cc_start: 0.8586 (p0) cc_final: 0.8335 (p0) REVERT: H 266 GLN cc_start: 0.8070 (pt0) cc_final: 0.7753 (pt0) REVERT: H 283 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.8709 (mt0) REVERT: I 224 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.7152 (mtm-85) REVERT: I 345 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7659 (mtm-85) REVERT: J 82 GLN cc_start: 0.8828 (tp40) cc_final: 0.8569 (tp40) REVERT: J 83 GLU cc_start: 0.8217 (pm20) cc_final: 0.7985 (pm20) REVERT: J 84 GLU cc_start: 0.8976 (pm20) cc_final: 0.8647 (pm20) REVERT: J 85 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7393 (tt) REVERT: L 53 ASN cc_start: 0.9349 (OUTLIER) cc_final: 0.9119 (m110) REVERT: L 75 ASN cc_start: 0.8744 (t0) cc_final: 0.8525 (t0) outliers start: 88 outliers final: 32 residues processed: 314 average time/residue: 1.4557 time to fit residues: 528.7809 Evaluate side-chains 280 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 3.037 ------------------------------------------------------------------------------- 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 179 VAL Chi-restraints excluded: chain C residue 20 VAL 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 D residue 305 MET Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 34 ARG 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 F residue 40 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 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 116 LEU Chi-restraints excluded: chain I residue 137 VAL 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 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 53 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 35 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 219 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 135 GLN F 30 ASN H 30 ASN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN L 4 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 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 = 0.3508 r_free = 0.3508 target = 0.101746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.066039 restraints weight = 44464.745| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.49 r_work: 0.2742 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1180 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= 0.185 Angle : 0.574 14.893 37934 Z= 0.301 Chirality : 0.041 0.174 4069 Planarity : 0.004 0.079 4449 Dihedral : 18.491 179.899 4834 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.47 % Favored : 94.19 % Rotamer: Outliers : 3.18 % Allowed : 19.70 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2943 helix: 1.60 (0.16), residues: 1030 sheet: -0.57 (0.22), residues: 574 loop : -0.20 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 488 HIS 0.005 0.001 HIS C 171 PHE 0.013 0.001 PHE K 61 TYR 0.017 0.001 TYR I 399 ARG 0.015 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 1126) hydrogen bonds : angle 4.58057 ( 3249) covalent geometry : bond 0.00422 (27707) covalent geometry : angle 0.57387 (37934) *********************** 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 322 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 238 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.8695 (ptt90) REVERT: A 93 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8701 (tt0) REVERT: A 166 ASP cc_start: 0.8614 (t0) cc_final: 0.8361 (t0) REVERT: A 178 ASP cc_start: 0.8687 (t0) cc_final: 0.8337 (t0) REVERT: B 203 MET cc_start: 0.8644 (mmm) cc_final: 0.8373 (mmm) REVERT: C 221 PHE cc_start: 0.9621 (OUTLIER) cc_final: 0.8026 (t80) REVERT: C 261 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: D 137 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8267 (tmm) REVERT: E 246 ASP cc_start: 0.8446 (t0) cc_final: 0.8056 (t0) REVERT: F 243 GLU cc_start: 0.8583 (pp20) cc_final: 0.8235 (pp20) REVERT: F 266 GLN cc_start: 0.8004 (pt0) cc_final: 0.7756 (pt0) REVERT: G 163 ARG cc_start: 0.8604 (ptm-80) cc_final: 0.8280 (mtm110) REVERT: G 179 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.7293 (mtp85) REVERT: H 50 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8752 (mmtm) REVERT: H 117 ASP cc_start: 0.8611 (p0) cc_final: 0.8376 (p0) REVERT: H 266 GLN cc_start: 0.8143 (pt0) cc_final: 0.7812 (pt0) REVERT: H 283 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8705 (mt0) REVERT: I 155 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9113 (mmtm) REVERT: I 224 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7319 (mtm-85) REVERT: I 345 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.7672 (mtm-85) REVERT: J 63 GLU cc_start: 0.8291 (mp0) cc_final: 0.7935 (mp0) REVERT: J 82 GLN cc_start: 0.8832 (tp40) cc_final: 0.8313 (tp40) REVERT: J 85 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7589 (tt) REVERT: L 53 ASN cc_start: 0.9381 (OUTLIER) cc_final: 0.9176 (m110) REVERT: L 75 ASN cc_start: 0.8835 (t0) cc_final: 0.8580 (t0) outliers start: 84 outliers final: 34 residues processed: 296 average time/residue: 1.4218 time to fit residues: 493.5345 Evaluate side-chains 274 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 2.750 ------------------------------------------------------------------------------- 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 179 VAL 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 137 MET 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 64 LEU Chi-restraints excluded: chain E residue 75 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 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 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 241 CYS 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 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 J residue 85 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 53 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 198 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 294 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 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 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN E 135 GLN F 30 ASN H 287 ASN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN K 53 ASN L 4 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.065613 restraints weight = 44352.740| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.48 r_work: 0.2731 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1267 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= 0.198 Angle : 0.579 15.213 37934 Z= 0.304 Chirality : 0.041 0.185 4069 Planarity : 0.004 0.079 4449 Dihedral : 18.492 179.848 4833 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.40 % Favored : 94.29 % Rotamer: Outliers : 3.52 % Allowed : 19.43 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2943 helix: 1.58 (0.16), residues: 1031 sheet: -0.58 (0.22), residues: 573 loop : -0.21 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 359 HIS 0.005 0.001 HIS C 171 PHE 0.013 0.001 PHE K 61 TYR 0.016 0.001 TYR I 399 ARG 0.009 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 1126) hydrogen bonds : angle 4.55367 ( 3249) covalent geometry : bond 0.00453 (27707) covalent geometry : angle 0.57900 (37934) *********************** 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 334 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 241 time to evaluate : 4.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9413 (OUTLIER) cc_final: 0.8866 (ptt90) REVERT: A 93 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8729 (tt0) REVERT: A 166 ASP cc_start: 0.8604 (t0) cc_final: 0.8342 (t0) REVERT: A 178 ASP cc_start: 0.8701 (t0) cc_final: 0.8346 (t0) REVERT: B 203 MET cc_start: 0.8615 (mmm) cc_final: 0.8298 (mmm) REVERT: C 221 PHE cc_start: 0.9640 (OUTLIER) cc_final: 0.7968 (t80) REVERT: C 261 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: D 137 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8288 (tmm) REVERT: E 246 ASP cc_start: 0.8465 (t0) cc_final: 0.8071 (t0) REVERT: F 136 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7238 (mmm160) REVERT: F 243 GLU cc_start: 0.8565 (pp20) cc_final: 0.8244 (pp20) REVERT: F 266 GLN cc_start: 0.7899 (pt0) cc_final: 0.7643 (pt0) REVERT: G 15 TYR cc_start: 0.9105 (m-80) cc_final: 0.8903 (m-80) REVERT: G 163 ARG cc_start: 0.8599 (ptm-80) cc_final: 0.8227 (mtm110) REVERT: G 179 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.7289 (mtp85) REVERT: H 50 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8764 (mmtm) REVERT: H 117 ASP cc_start: 0.8601 (p0) cc_final: 0.8374 (p0) REVERT: H 179 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.6725 (mtp85) REVERT: H 266 GLN cc_start: 0.8151 (pt0) cc_final: 0.7809 (pt0) REVERT: I 345 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.7555 (mtm-85) REVERT: J 4 ASN cc_start: 0.6975 (OUTLIER) cc_final: 0.6657 (p0) REVERT: J 59 LEU cc_start: 0.8915 (mm) cc_final: 0.7802 (mm) REVERT: J 63 GLU cc_start: 0.8301 (mp0) cc_final: 0.7778 (mp0) REVERT: J 82 GLN cc_start: 0.8832 (tp40) cc_final: 0.8205 (tp40) REVERT: L 75 ASN cc_start: 0.8858 (t0) cc_final: 0.8607 (t0) outliers start: 93 outliers final: 37 residues processed: 307 average time/residue: 1.8207 time to fit residues: 663.0352 Evaluate side-chains 277 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 3.212 ------------------------------------------------------------------------------- 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 137 MET 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 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 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 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 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 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 J residue 4 ASN Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 65 optimal weight: 3.9990 chunk 235 optimal weight: 0.0770 chunk 259 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 53 optimal weight: 0.0370 chunk 127 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- 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** D 30 ASN E 135 GLN F 30 ASN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN K 53 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 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 = 0.3502 r_free = 0.3502 target = 0.101478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.065846 restraints weight = 44432.028| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.47 r_work: 0.2733 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 0.045 27707 Z= 0.194 Angle : 0.583 15.295 37934 Z= 0.305 Chirality : 0.041 0.181 4069 Planarity : 0.004 0.080 4449 Dihedral : 18.497 179.702 4833 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.61 % Favored : 94.09 % Rotamer: Outliers : 3.18 % Allowed : 19.89 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 2943 helix: 1.61 (0.16), residues: 1028 sheet: -0.64 (0.21), residues: 578 loop : -0.20 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 488 HIS 0.005 0.001 HIS C 171 PHE 0.013 0.001 PHE L 61 TYR 0.019 0.001 TYR I 399 ARG 0.009 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 1126) hydrogen bonds : angle 4.54030 ( 3249) covalent geometry : bond 0.00445 (27707) covalent geometry : angle 0.58262 (37934) *********************** 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 320 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 236 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9410 (OUTLIER) cc_final: 0.8871 (ptt90) REVERT: A 93 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8746 (tt0) REVERT: A 166 ASP cc_start: 0.8726 (t0) cc_final: 0.8479 (t0) REVERT: A 178 ASP cc_start: 0.8695 (t0) cc_final: 0.8344 (t0) REVERT: B 203 MET cc_start: 0.8676 (mmm) cc_final: 0.8335 (mmm) REVERT: C 221 PHE cc_start: 0.9647 (OUTLIER) cc_final: 0.7977 (t80) REVERT: C 261 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: D 137 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8314 (tmm) REVERT: E 246 ASP cc_start: 0.8435 (t0) cc_final: 0.8035 (t0) REVERT: F 136 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7250 (mmm160) REVERT: F 243 GLU cc_start: 0.8558 (pp20) cc_final: 0.8235 (pp20) REVERT: F 251 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.5649 (pp20) REVERT: G 163 ARG cc_start: 0.8612 (ptm-80) cc_final: 0.8214 (mtm110) REVERT: G 179 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.7241 (mtp85) REVERT: H 50 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8763 (mmtm) REVERT: H 117 ASP cc_start: 0.8598 (p0) cc_final: 0.8373 (p0) REVERT: H 179 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.6856 (mtp85) REVERT: H 266 GLN cc_start: 0.8149 (pt0) cc_final: 0.7796 (pt0) REVERT: H 283 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8588 (mt0) REVERT: I 345 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8199 (mtm-85) REVERT: I 364 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8102 (pm20) REVERT: J 59 LEU cc_start: 0.8940 (mm) cc_final: 0.7884 (mm) REVERT: J 63 GLU cc_start: 0.8333 (mp0) cc_final: 0.7802 (mp0) REVERT: J 82 GLN cc_start: 0.8808 (tp40) cc_final: 0.8193 (tp40) REVERT: K 71 ARG cc_start: 0.8743 (mtm-85) cc_final: 0.8513 (mtm-85) REVERT: L 75 ASN cc_start: 0.8863 (t0) cc_final: 0.8583 (t0) outliers start: 84 outliers final: 40 residues processed: 293 average time/residue: 1.3807 time to fit residues: 472.0966 Evaluate side-chains 281 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 228 time to evaluate : 3.036 ------------------------------------------------------------------------------- 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 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 295 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 137 MET 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 64 LEU Chi-restraints excluded: chain E residue 75 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 251 GLU 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 241 CYS 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 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 364 GLU Chi-restraints excluded: chain I residue 388 ILE Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 74 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 219 optimal weight: 2.9990 chunk 201 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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** B 171 GLN C 215 ASN D 30 ASN D 287 ASN E 135 GLN F 30 ASN F 266 GLN I 227 HIS ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 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 = 0.3483 r_free = 0.3483 target = 0.100304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.064501 restraints weight = 44689.512| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.48 r_work: 0.2707 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 27707 Z= 0.240 Angle : 0.608 16.073 37934 Z= 0.318 Chirality : 0.042 0.188 4069 Planarity : 0.004 0.081 4449 Dihedral : 18.510 179.800 4833 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.64 % Favored : 94.02 % Rotamer: Outliers : 3.21 % Allowed : 19.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2943 helix: 1.56 (0.16), residues: 1029 sheet: -0.64 (0.22), residues: 573 loop : -0.22 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 488 HIS 0.005 0.001 HIS C 171 PHE 0.016 0.001 PHE K 61 TYR 0.024 0.001 TYR I 399 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 1126) hydrogen bonds : angle 4.58088 ( 3249) covalent geometry : bond 0.00556 (27707) covalent geometry : angle 0.60844 (37934) *********************** 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 320 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 235 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.8880 (ptt90) REVERT: A 93 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8751 (tt0) REVERT: A 111 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8867 (mmmt) REVERT: A 166 ASP cc_start: 0.8734 (t0) cc_final: 0.8477 (t0) REVERT: A 178 ASP cc_start: 0.8731 (t0) cc_final: 0.8373 (t0) REVERT: B 203 MET cc_start: 0.8692 (mmm) cc_final: 0.8333 (mmm) REVERT: C 221 PHE cc_start: 0.9678 (OUTLIER) cc_final: 0.8086 (t80) REVERT: C 261 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: D 137 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8285 (tmm) REVERT: E 246 ASP cc_start: 0.8517 (t0) cc_final: 0.8148 (t0) REVERT: F 136 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7267 (mmm160) REVERT: F 179 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.7816 (mtp85) REVERT: F 243 GLU cc_start: 0.8592 (pp20) cc_final: 0.8223 (pp20) REVERT: G 179 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.6873 (mtp85) REVERT: H 50 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8748 (mmtm) REVERT: H 117 ASP cc_start: 0.8591 (p0) cc_final: 0.8354 (p0) REVERT: H 142 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8631 (mtp) REVERT: H 179 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.6951 (mtp85) REVERT: H 283 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8687 (mt0) REVERT: I 364 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: J 59 LEU cc_start: 0.8932 (mm) cc_final: 0.8714 (mm) REVERT: J 82 GLN cc_start: 0.8799 (tp40) cc_final: 0.8244 (tp40) REVERT: L 75 ASN cc_start: 0.8861 (t0) cc_final: 0.8569 (t0) outliers start: 85 outliers final: 42 residues processed: 293 average time/residue: 1.4664 time to fit residues: 498.2823 Evaluate side-chains 278 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 3.130 ------------------------------------------------------------------------------- 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 226 LEU 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 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 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 F residue 179 ARG Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP 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 170 LEU 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 H residue 285 LEU 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 364 GLU Chi-restraints excluded: chain I residue 388 ILE Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 179 optimal weight: 0.0670 chunk 184 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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** D 30 ASN E 135 GLN F 30 ASN I 227 HIS ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 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 = 0.3394 r_free = 0.3394 target = 0.100051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.063873 restraints weight = 45427.344| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.60 r_work: 0.2609 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1390 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= 0.158 Angle : 0.580 15.018 37934 Z= 0.305 Chirality : 0.041 0.194 4069 Planarity : 0.004 0.082 4449 Dihedral : 18.486 179.977 4833 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.44 % Favored : 94.26 % Rotamer: Outliers : 2.65 % Allowed : 20.38 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2943 helix: 1.62 (0.16), residues: 1027 sheet: -0.65 (0.22), residues: 559 loop : -0.19 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 488 HIS 0.005 0.001 HIS C 171 PHE 0.013 0.001 PHE B 125 TYR 0.021 0.001 TYR I 399 ARG 0.014 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 1126) hydrogen bonds : angle 4.50557 ( 3249) covalent geometry : bond 0.00359 (27707) covalent geometry : angle 0.58000 (37934) *********************** 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 308 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 238 time to evaluate : 3.109 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: 0.9248 (OUTLIER) cc_final: 0.8562 (ptt90) REVERT: A 93 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: A 111 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8802 (mmmt) REVERT: A 166 ASP cc_start: 0.8529 (t0) cc_final: 0.8286 (t0) REVERT: A 178 ASP cc_start: 0.8448 (t0) cc_final: 0.8049 (t0) REVERT: B 203 MET cc_start: 0.8478 (mmm) cc_final: 0.8251 (mmm) REVERT: C 221 PHE cc_start: 0.9629 (OUTLIER) cc_final: 0.7946 (t80) REVERT: C 261 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: D 137 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8206 (tmm) REVERT: E 246 ASP cc_start: 0.8371 (t0) cc_final: 0.7974 (t0) REVERT: F 48 ASN cc_start: 0.9088 (m-40) cc_final: 0.8755 (p0) REVERT: F 136 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7003 (mmm160) REVERT: F 179 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.7837 (mtp85) REVERT: F 243 GLU cc_start: 0.8361 (pp20) cc_final: 0.7981 (pp20) REVERT: G 157 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8644 (tp) REVERT: G 179 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.7007 (mtp85) REVERT: H 50 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8617 (mmtm) REVERT: H 117 ASP cc_start: 0.8477 (p0) cc_final: 0.7485 (t0) REVERT: H 179 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.6667 (mtp85) REVERT: H 283 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8558 (mt0) REVERT: I 345 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.6999 (mtm-85) REVERT: I 364 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: J 82 GLN cc_start: 0.8751 (tp40) cc_final: 0.8216 (tp40) REVERT: K 71 ARG cc_start: 0.8732 (mtm-85) cc_final: 0.8504 (mtm-85) REVERT: L 75 ASN cc_start: 0.8663 (t0) cc_final: 0.8404 (t0) outliers start: 70 outliers final: 31 residues processed: 289 average time/residue: 1.3461 time to fit residues: 456.7515 Evaluate side-chains 281 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 142 MET 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 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 H residue 285 LEU Chi-restraints excluded: chain I residue 84 THR 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 345 ARG Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 388 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 156 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 209 optimal weight: 4.9990 chunk 260 optimal weight: 0.9990 chunk 265 optimal weight: 0.9990 chunk 179 optimal weight: 0.0770 chunk 154 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 93 optimal weight: 0.0040 chunk 114 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 overall best weight: 0.4950 ------------------------------------------------------------------------------- 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 250 GLN K 53 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 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 = 0.3425 r_free = 0.3425 target = 0.101940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.065920 restraints weight = 44998.427| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.59 r_work: 0.2684 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27707 Z= 0.125 Angle : 0.566 13.437 37934 Z= 0.297 Chirality : 0.040 0.215 4069 Planarity : 0.004 0.083 4449 Dihedral : 18.428 179.052 4833 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.27 % Favored : 94.46 % Rotamer: Outliers : 1.85 % Allowed : 21.29 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2943 helix: 1.71 (0.17), residues: 1029 sheet: -0.65 (0.22), residues: 566 loop : -0.16 (0.18), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 488 HIS 0.005 0.001 HIS C 171 PHE 0.014 0.001 PHE B 125 TYR 0.018 0.001 TYR I 399 ARG 0.014 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 1126) hydrogen bonds : angle 4.39987 ( 3249) covalent geometry : bond 0.00280 (27707) covalent geometry : angle 0.56567 (37934) ********************** 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 301 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.9415 (t80) cc_final: 0.9134 (t80) REVERT: A 93 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: A 111 LYS cc_start: 0.9175 (mmmm) cc_final: 0.8794 (mmmt) REVERT: A 166 ASP cc_start: 0.8535 (t0) cc_final: 0.8280 (t0) REVERT: A 178 ASP cc_start: 0.8381 (t0) cc_final: 0.7988 (t0) REVERT: B 203 MET cc_start: 0.8513 (mmm) cc_final: 0.8279 (mmm) REVERT: C 221 PHE cc_start: 0.9590 (OUTLIER) cc_final: 0.7966 (t80) REVERT: E 38 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8387 (ttmt) REVERT: E 246 ASP cc_start: 0.8350 (t0) cc_final: 0.7934 (t0) REVERT: F 48 ASN cc_start: 0.9044 (m-40) cc_final: 0.8754 (p0) REVERT: F 136 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6910 (mmm160) REVERT: F 179 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.7675 (mtp85) REVERT: G 179 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.7053 (mtp85) REVERT: H 50 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8600 (mmtm) REVERT: H 117 ASP cc_start: 0.8453 (p0) cc_final: 0.7658 (t0) REVERT: H 283 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8604 (mt0) REVERT: I 224 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7463 (mtm-85) REVERT: I 334 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.8069 (p90) REVERT: I 345 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7570 (mtm-85) REVERT: I 364 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: J 19 GLN cc_start: 0.8601 (mt0) cc_final: 0.8214 (mt0) REVERT: J 60 SER cc_start: 0.8451 (t) cc_final: 0.8143 (t) REVERT: J 82 GLN cc_start: 0.8731 (tp40) cc_final: 0.8168 (tp40) REVERT: K 59 LEU cc_start: 0.8820 (tp) cc_final: 0.8609 (tm) REVERT: K 71 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8473 (mtm-85) REVERT: L 77 TYR cc_start: 0.8502 (m-80) cc_final: 0.8214 (m-80) outliers start: 49 outliers final: 23 residues processed: 288 average time/residue: 1.3655 time to fit residues: 459.3403 Evaluate side-chains 273 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 221 PHE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 305 MET 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 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 179 ARG 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 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 334 TYR Chi-restraints excluded: chain I residue 345 ARG Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 388 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 293 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 4 optimal weight: 0.0050 chunk 196 optimal weight: 0.1980 chunk 270 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 chunk 188 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 171 HIS D 30 ASN E 30 ASN E 42 GLN E 135 GLN F 30 ASN H 266 GLN J 20 GLN K 53 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 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 = 0.3438 r_free = 0.3438 target = 0.102736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.066853 restraints weight = 45035.194| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.60 r_work: 0.2705 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27707 Z= 0.119 Angle : 0.563 13.128 37934 Z= 0.297 Chirality : 0.040 0.191 4069 Planarity : 0.004 0.084 4449 Dihedral : 18.338 178.890 4826 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.30 % Favored : 94.43 % Rotamer: Outliers : 1.70 % Allowed : 21.81 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2943 helix: 1.74 (0.17), residues: 1031 sheet: -0.47 (0.23), residues: 541 loop : -0.16 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 62 HIS 0.006 0.001 HIS C 171 PHE 0.014 0.001 PHE B 125 TYR 0.019 0.001 TYR I 399 ARG 0.013 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 1126) hydrogen bonds : angle 4.36983 ( 3249) covalent geometry : bond 0.00263 (27707) covalent geometry : angle 0.56348 (37934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19129.58 seconds wall clock time: 331 minutes 18.66 seconds (19878.66 seconds total)