Starting phenix.real_space_refine on Fri Dec 27 04:05:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dex_27402/12_2024/8dex_27402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dex_27402/12_2024/8dex_27402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dex_27402/12_2024/8dex_27402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dex_27402/12_2024/8dex_27402.map" model { file = "/net/cci-nas-00/data/ceres_data/8dex_27402/12_2024/8dex_27402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dex_27402/12_2024/8dex_27402.cif" } resolution = 2.7 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= -0.000 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 S 133 5.16 5 C 14591 2.51 5 N 4199 2.21 5 O 4507 1.98 5 H 22829 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 46307 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3537 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "B" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4193 Classifications: {'peptide': 270} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 2 Chain: "C" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "D" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "F" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "G" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "H" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "I" Number of atoms: 6531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6531 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 26, 'TRANS': 390} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1864 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain breaks: 1 Chain: "K" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1863 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1547 Classifications: {'RNA': 48} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 17, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 27} Time building chain proxies: 17.40, per 1000 atoms: 0.38 Number of scatterers: 46307 At special positions: 0 Unit cell: (114.68, 121.26, 202.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 133 16.00 P 48 15.00 O 4507 8.00 N 4199 7.00 C 14591 6.00 H 22829 1.00 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: 10.60 Conformation dependent library (CDL) restraints added in 2.9 seconds 5614 Ramachandran restraints generated. 2807 Oldfield, 0 Emsley, 2807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5354 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 34 sheets defined 38.2% alpha, 25.1% beta 0 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 18.85 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.745A pdb=" N LYS A 28 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 removed outlier: 3.525A pdb=" N ILE A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.891A pdb=" N MET A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'B' and resid 43 through 60 removed outlier: 3.724A pdb=" N LEU B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.540A pdb=" N LYS B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 247 through 254 removed outlier: 3.720A pdb=" N LEU B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'C' and resid 43 through 60 Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.607A pdb=" N ALA C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 removed outlier: 3.635A pdb=" N ASN C 112 " --> pdb=" O TRP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.506A pdb=" N LYS C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 217 through 221 removed outlier: 4.279A pdb=" N HIS C 220 " --> pdb=" O MET C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'D' and resid 43 through 60 removed outlier: 3.612A pdb=" N LEU D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 98 through 113 removed outlier: 3.637A pdb=" N THR D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'D' and resid 218 through 221 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 269 through 271 No H-bonds generated for 'chain 'D' and resid 269 through 271' Processing helix chain 'E' and resid 43 through 60 removed outlier: 3.535A pdb=" N LEU E 47 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 86 removed outlier: 3.540A pdb=" N THR E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 removed outlier: 3.731A pdb=" N MET E 109 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 120 Processing helix chain 'E' and resid 193 through 201 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 217 through 221 removed outlier: 4.214A pdb=" N HIS E 220 " --> pdb=" O MET E 217 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP E 221 " --> pdb=" O PHE E 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 217 through 221' Processing helix chain 'E' and resid 247 through 253 Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'F' and resid 43 through 60 removed outlier: 3.529A pdb=" N LEU F 47 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 113 through 120 Processing helix chain 'F' and resid 193 through 201 Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 4.262A pdb=" N HIS F 220 " --> pdb=" O MET F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'G' and resid 43 through 60 removed outlier: 3.521A pdb=" N LEU G 47 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 86 removed outlier: 3.528A pdb=" N ARG G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA G 82 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 113 removed outlier: 3.518A pdb=" N ASN G 112 " --> pdb=" O TRP G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'G' and resid 193 through 201 Processing helix chain 'G' and resid 203 through 216 Processing helix chain 'G' and resid 217 through 221 removed outlier: 3.937A pdb=" N HIS G 220 " --> pdb=" O MET G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 253 Processing helix chain 'G' and resid 269 through 271 No H-bonds generated for 'chain 'G' and resid 269 through 271' Processing helix chain 'H' and resid 24 through 28 removed outlier: 3.881A pdb=" N GLY H 28 " --> pdb=" O PRO H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 74 through 87 removed outlier: 3.731A pdb=" N THR H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 113 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'H' and resid 193 through 201 Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 247 through 253 Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'I' and resid 2 through 16 removed outlier: 3.933A pdb=" N ASP I 16 " --> pdb=" O ARG I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 226 Processing helix chain 'I' and resid 231 through 236 Processing helix chain 'I' and resid 239 through 255 Processing helix chain 'I' and resid 278 through 288 removed outlier: 4.438A pdb=" N ALA I 284 " --> pdb=" O GLU I 280 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY I 285 " --> pdb=" O ASP I 281 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET I 286 " --> pdb=" O ILE I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 336 Processing helix chain 'I' and resid 338 through 342 Processing helix chain 'I' and resid 374 through 389 Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 420 through 427 Processing helix chain 'I' and resid 430 through 434 Processing helix chain 'I' and resid 440 through 452 Processing helix chain 'I' and resid 455 through 459 Processing helix chain 'I' and resid 468 through 482 Processing helix chain 'I' and resid 497 through 517 Processing helix chain 'I' and resid 523 through 528 removed outlier: 3.832A pdb=" N ARG I 527 " --> pdb=" O THR I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 535 Processing helix chain 'I' and resid 535 through 557 removed outlier: 3.818A pdb=" N VAL I 539 " --> pdb=" O ASN I 535 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N HIS I 541 " --> pdb=" O GLY I 537 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N MET I 542 " --> pdb=" O GLN I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 564 through 577 removed outlier: 4.015A pdb=" N ASN I 577 " --> pdb=" O GLU I 573 " (cutoff:3.500A) Processing helix chain 'I' and resid 586 through 604 Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 47 removed outlier: 5.771A pdb=" N ALA J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N SER J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 68 removed outlier: 3.706A pdb=" N VAL J 51 " --> pdb=" O ASN J 47 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N HIS J 53 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N MET J 54 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.766A pdb=" N ASN J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 118 Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 35 through 47 removed outlier: 6.240A pdb=" N ALA K 42 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 69 removed outlier: 3.550A pdb=" N VAL K 51 " --> pdb=" O ASN K 47 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS K 53 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN K 61 " --> pdb=" O LYS K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 90 Processing helix chain 'K' and resid 98 through 118 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.695A pdb=" N ARG A 31 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU A 115 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG A 116 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR A 19 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 78 removed outlier: 4.576A pdb=" N VAL A 69 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASP A 119 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL A 64 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 121 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE A 62 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A 123 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 removed outlier: 5.681A pdb=" N PHE A 99 " --> pdb=" O GLN B 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 196 removed outlier: 5.570A pdb=" N ALA A 208 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR A 190 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE A 206 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU A 192 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU A 204 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP A 194 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR A 202 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 42 removed outlier: 5.436A pdb=" N GLY B 40 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU B 185 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N TYR B 183 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 136 through 138 removed outlier: 6.860A pdb=" N ASP B 15 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N SER B 231 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLU B 17 " --> pdb=" O MET B 229 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N MET B 229 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU B 234 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AA8, first strand: chain 'B' and resid 255 through 259 Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB1, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.517A pdb=" N GLY C 19 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR C 183 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU C 17 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 185 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASP C 15 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL C 187 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU C 13 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N HIS C 189 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 11 " --> pdb=" O HIS C 189 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE C 191 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU C 9 " --> pdb=" O PHE C 191 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU C 9 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL C 236 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL C 11 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU C 234 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU C 13 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AB3, first strand: chain 'C' and resid 255 through 259 Processing sheet with id=AB4, first strand: chain 'D' and resid 39 through 42 removed outlier: 5.261A pdb=" N GLY D 40 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU D 185 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR D 183 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 154 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.674A pdb=" N GLU D 9 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL D 236 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL D 11 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU D 234 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU D 13 " --> pdb=" O ARG D 232 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB7, first strand: chain 'D' and resid 255 through 259 Processing sheet with id=AB8, first strand: chain 'E' and resid 41 through 42 Processing sheet with id=AB9, first strand: chain 'E' and resid 136 through 138 removed outlier: 6.838A pdb=" N ASP E 15 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N SER E 231 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLU E 17 " --> pdb=" O MET E 229 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N MET E 229 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU E 234 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 121 through 124 removed outlier: 3.957A pdb=" N GLY E 130 " --> pdb=" O MET E 123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 255 through 259 Processing sheet with id=AC3, first strand: chain 'F' and resid 41 through 42 Processing sheet with id=AC4, first strand: chain 'F' and resid 136 through 138 removed outlier: 6.778A pdb=" N ASP F 15 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER F 231 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLU F 17 " --> pdb=" O MET F 229 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET F 229 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU F 234 " --> pdb=" O MET F 289 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 122 through 124 removed outlier: 5.891A pdb=" N MET F 123 " --> pdb=" O CYS F 129 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 255 through 259 Processing sheet with id=AC7, first strand: chain 'G' and resid 41 through 42 removed outlier: 3.555A pdb=" N THR G 174 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE G 180 " --> pdb=" O GLN G 150 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 136 through 138 removed outlier: 6.685A pdb=" N GLU G 9 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL G 236 " --> pdb=" O GLU G 9 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL G 11 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU G 234 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU G 13 " --> pdb=" O ARG G 232 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER G 230 " --> pdb=" O ASP G 15 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 121 through 124 removed outlier: 4.970A pdb=" N GLY G 130 " --> pdb=" O MET G 123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 255 through 259 Processing sheet with id=AD2, first strand: chain 'H' and resid 41 through 42 Processing sheet with id=AD3, first strand: chain 'H' and resid 136 through 138 removed outlier: 6.649A pdb=" N GLU H 9 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL H 236 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL H 11 " --> pdb=" O LEU H 234 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU H 234 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU H 13 " --> pdb=" O ARG H 232 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU H 234 " --> pdb=" O MET H 289 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 121 through 122 Processing sheet with id=AD5, first strand: chain 'H' and resid 255 through 259 Processing sheet with id=AD6, first strand: chain 'I' and resid 181 through 182 Processing sheet with id=AD7, first strand: chain 'I' and resid 261 through 264 removed outlier: 3.589A pdb=" N PHE I 368 " --> pdb=" O GLY I 356 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER I 358 " --> pdb=" O VAL I 366 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL I 366 " --> pdb=" O SER I 358 " (cutoff:3.500A) 989 hydrogen bonds defined for protein. 2811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 16.50 Time building geometry restraints manager: 12.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.26: 26676 1.26 - 1.70: 19976 1.70 - 2.13: 234 2.13 - 2.56: 0 2.56 - 2.99: 1 Bond restraints: 46887 Sorted by residual: bond pdb=" C LYS I 561 " pdb=" N SER I 563 " ideal model delta sigma weight residual 1.331 2.990 -1.659 1.62e-02 3.81e+03 1.05e+04 bond pdb=" C ILE I 2 " pdb=" O ILE I 2 " ideal model delta sigma weight residual 1.236 1.104 0.133 1.19e-02 7.06e+03 1.24e+02 bond pdb=" C LEU I 3 " pdb=" O LEU I 3 " ideal model delta sigma weight residual 1.236 1.141 0.096 1.26e-02 6.30e+03 5.78e+01 bond pdb=" C ALA I 5 " pdb=" O ALA I 5 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.22e-02 6.72e+03 4.50e+01 bond pdb=" CA ILE I 2 " pdb=" C ILE I 2 " ideal model delta sigma weight residual 1.523 1.444 0.079 1.27e-02 6.20e+03 3.82e+01 ... (remaining 46882 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.01: 84702 15.01 - 30.02: 1 30.02 - 45.03: 1 45.03 - 60.04: 0 60.04 - 75.05: 1 Bond angle restraints: 84705 Sorted by residual: angle pdb=" O LYS I 561 " pdb=" C LYS I 561 " pdb=" N SER I 563 " ideal model delta sigma weight residual 122.59 47.54 75.05 1.33e+00 5.65e-01 3.18e+03 angle pdb=" C LYS I 561 " pdb=" N SER I 563 " pdb=" CA SER I 563 " ideal model delta sigma weight residual 122.31 85.03 37.28 2.00e+00 2.50e-01 3.47e+02 angle pdb=" CA PRO K 70 " pdb=" N PRO K 70 " pdb=" CD PRO K 70 " ideal model delta sigma weight residual 112.00 94.02 17.98 1.40e+00 5.10e-01 1.65e+02 angle pdb=" C2' U L 19 " pdb=" C1' U L 19 " pdb=" N1 U L 19 " ideal model delta sigma weight residual 112.00 124.24 -12.24 1.50e+00 4.44e-01 6.66e+01 angle pdb=" N PRO K 70 " pdb=" CD PRO K 70 " pdb=" CG PRO K 70 " ideal model delta sigma weight residual 103.20 90.98 12.22 1.50e+00 4.44e-01 6.63e+01 ... (remaining 84700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 21141 34.87 - 69.74: 897 69.74 - 104.60: 72 104.60 - 139.47: 6 139.47 - 174.34: 29 Dihedral angle restraints: 22145 sinusoidal: 12556 harmonic: 9589 Sorted by residual: dihedral pdb=" C5' G L 31 " pdb=" C4' G L 31 " pdb=" C3' G L 31 " pdb=" O3' G L 31 " ideal model delta sinusoidal sigma weight residual 147.00 73.98 73.02 1 8.00e+00 1.56e-02 1.06e+02 dihedral pdb=" C5' C L 43 " pdb=" C4' C L 43 " pdb=" C3' C L 43 " pdb=" O3' C L 43 " ideal model delta sinusoidal sigma weight residual 147.00 74.38 72.62 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C4' C L 18 " pdb=" C3' C L 18 " pdb=" C2' C L 18 " pdb=" C1' C L 18 " ideal model delta sinusoidal sigma weight residual -35.00 37.43 -72.43 1 8.00e+00 1.56e-02 1.05e+02 ... (remaining 22142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3309 0.099 - 0.197: 277 0.197 - 0.296: 33 0.296 - 0.394: 25 0.394 - 0.493: 2 Chirality restraints: 3646 Sorted by residual: chirality pdb=" CG LEU I 3 " pdb=" CB LEU I 3 " pdb=" CD1 LEU I 3 " pdb=" CD2 LEU I 3 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CA ILE I 2 " pdb=" N ILE I 2 " pdb=" C ILE I 2 " pdb=" CB ILE I 2 " both_signs ideal model delta sigma weight residual False 2.43 1.95 0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" P G L 22 " pdb=" OP1 G L 22 " pdb=" OP2 G L 22 " pdb=" O5' G L 22 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 3643 not shown) Planarity restraints: 6841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 561 " -0.158 2.00e-02 2.50e+03 2.62e-01 6.87e+02 pdb=" C LYS I 561 " 0.408 2.00e-02 2.50e+03 pdb=" O LYS I 561 " -0.287 2.00e-02 2.50e+03 pdb=" N SER I 563 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS I 561 " -0.035 2.00e-02 2.50e+03 1.59e-01 2.54e+02 pdb=" N SER I 563 " 0.260 2.00e-02 2.50e+03 pdb=" CA SER I 563 " -0.051 2.00e-02 2.50e+03 pdb=" H SER I 563 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN I 4 " -0.048 2.00e-02 2.50e+03 5.82e-02 5.09e+01 pdb=" CD GLN I 4 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN I 4 " 0.059 2.00e-02 2.50e+03 pdb=" NE2 GLN I 4 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN I 4 " 0.087 2.00e-02 2.50e+03 pdb="HE22 GLN I 4 " -0.082 2.00e-02 2.50e+03 ... (remaining 6838 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 744 2.05 - 2.69: 70262 2.69 - 3.32: 136601 3.32 - 3.96: 181513 3.96 - 4.60: 283161 Nonbonded interactions: 672281 Sorted by model distance: nonbonded pdb=" OE1 GLU A 135 " pdb=" H GLU A 135 " model vdw 1.408 2.450 nonbonded pdb=" OE1 GLU G 126 " pdb=" H GLU G 126 " model vdw 1.433 2.450 nonbonded pdb="HH12 ARG B 259 " pdb=" O GLY B 265 " model vdw 1.464 2.450 nonbonded pdb="HH12 ARG C 259 " pdb=" O GLY C 265 " model vdw 1.531 2.450 nonbonded pdb=" OE1 GLU B 261 " pdb=" H GLU B 261 " model vdw 1.535 2.450 ... (remaining 672276 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 'B' selection = (chain 'C' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'D' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'E' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'F' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'G' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'H' and (resid 1 through 84 or resid 101 through 290)) } ncs_group { reference = (chain 'J' and (resid 1 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 112 through 119)) selection = chain 'K' } 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=0.00 max=1.00 mean=0.98 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.590 Extract box with map and model: 1.400 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 94.490 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 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 : 0.012 1.659 24058 Z= 0.920 Angle : 0.952 75.047 32762 Z= 0.540 Chirality : 0.060 0.493 3646 Planarity : 0.006 0.262 4126 Dihedral : 18.599 174.341 9373 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.79 % Rotamer: Outliers : 0.96 % Allowed : 12.58 % Favored : 86.46 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.16), residues: 2807 helix: 1.63 (0.17), residues: 935 sheet: 0.66 (0.22), residues: 568 loop : -0.50 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.006 0.001 HIS K 62 PHE 0.012 0.001 PHE K 105 TYR 0.011 0.001 TYR D 68 ARG 0.012 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5614 Ramachandran restraints generated. 2807 Oldfield, 0 Emsley, 2807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5614 Ramachandran restraints generated. 2807 Oldfield, 0 Emsley, 2807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Evaluate side-chains 472 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 449 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6358 (tppp) cc_final: 0.6154 (mptp) REVERT: A 61 ARG cc_start: 0.6908 (mpp80) cc_final: 0.6625 (mtp180) REVERT: A 105 SER cc_start: 0.6300 (t) cc_final: 0.5904 (p) REVERT: A 199 ARG cc_start: 0.5675 (mpt-90) cc_final: 0.5449 (mtt-85) REVERT: A 207 LYS cc_start: 0.6661 (ptmm) cc_final: 0.5932 (tppt) REVERT: A 211 GLU cc_start: 0.6257 (pm20) cc_final: 0.5589 (tp30) REVERT: B 17 GLU cc_start: 0.7176 (tt0) cc_final: 0.6941 (tt0) REVERT: B 156 ARG cc_start: 0.6437 (ttp-170) cc_final: 0.5600 (ttp-170) REVERT: B 240 GLN cc_start: 0.7861 (tp40) cc_final: 0.6721 (tt0) REVERT: B 241 ASN cc_start: 0.7231 (t0) cc_final: 0.6534 (t0) REVERT: B 250 LYS cc_start: 0.6779 (mtpp) cc_final: 0.6309 (mmpt) REVERT: C 126 GLU cc_start: 0.6681 (tp30) cc_final: 0.6063 (mp0) REVERT: C 133 ARG cc_start: 0.6290 (mtp180) cc_final: 0.6035 (ttt180) REVERT: C 203 SER cc_start: 0.6777 (t) cc_final: 0.6564 (p) REVERT: C 233 LYS cc_start: 0.7547 (mttt) cc_final: 0.7283 (mttt) REVERT: C 240 GLN cc_start: 0.7378 (tp40) cc_final: 0.6295 (tm-30) REVERT: C 256 LYS cc_start: 0.7277 (mtpp) cc_final: 0.6202 (mtmt) REVERT: D 17 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7310 (mt-10) REVERT: D 36 GLU cc_start: 0.6917 (mt-10) cc_final: 0.5851 (mt-10) REVERT: D 63 GLU cc_start: 0.7072 (tp30) cc_final: 0.6062 (tt0) REVERT: D 71 GLU cc_start: 0.6498 (tm-30) cc_final: 0.6278 (tp30) REVERT: D 74 ILE cc_start: 0.6518 (mt) cc_final: 0.6202 (mp) REVERT: D 98 LYS cc_start: 0.6309 (mmmm) cc_final: 0.6031 (tppt) REVERT: D 112 ASN cc_start: 0.7224 (m-40) cc_final: 0.6878 (m110) REVERT: D 138 MET cc_start: 0.8417 (mtp) cc_final: 0.8167 (mtm) REVERT: D 177 ARG cc_start: 0.7477 (ttm110) cc_final: 0.6264 (tpp-160) REVERT: D 240 GLN cc_start: 0.7769 (tt0) cc_final: 0.7555 (tt0) REVERT: D 256 LYS cc_start: 0.7570 (mmtm) cc_final: 0.6709 (mptt) REVERT: D 279 GLN cc_start: 0.7167 (tp40) cc_final: 0.6925 (mm-40) REVERT: D 285 GLU cc_start: 0.8010 (tt0) cc_final: 0.7237 (tt0) REVERT: E 63 GLU cc_start: 0.6879 (tt0) cc_final: 0.6461 (tt0) REVERT: E 64 ARG cc_start: 0.6264 (mtp85) cc_final: 0.5665 (mmm160) REVERT: E 151 GLU cc_start: 0.7557 (tt0) cc_final: 0.7278 (tt0) REVERT: E 212 ASP cc_start: 0.7100 (t70) cc_final: 0.6894 (t0) REVERT: E 221 ASP cc_start: 0.7255 (p0) cc_final: 0.6683 (p0) REVERT: E 250 LYS cc_start: 0.6632 (mtpp) cc_final: 0.6044 (tttm) REVERT: E 285 GLU cc_start: 0.7717 (tt0) cc_final: 0.7443 (tt0) REVERT: F 60 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7438 (mt-10) REVERT: F 71 GLU cc_start: 0.5484 (pm20) cc_final: 0.5022 (tt0) REVERT: F 77 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6895 (mt-10) REVERT: F 90 PRO cc_start: 0.7724 (Cg_endo) cc_final: 0.7500 (Cg_exo) REVERT: F 123 MET cc_start: 0.7467 (mtm) cc_final: 0.7258 (mtm) REVERT: F 175 MET cc_start: 0.6414 (tpp) cc_final: 0.6051 (tpp) REVERT: F 250 LYS cc_start: 0.6070 (mtpt) cc_final: 0.5574 (ttpp) REVERT: F 287 LYS cc_start: 0.6088 (mtpt) cc_final: 0.4832 (tmtt) REVERT: G 64 ARG cc_start: 0.6613 (mtm110) cc_final: 0.6010 (mtp85) REVERT: G 97 LYS cc_start: 0.7617 (mppt) cc_final: 0.7173 (mmmt) REVERT: G 203 SER cc_start: 0.6888 (t) cc_final: 0.6436 (m) REVERT: G 245 ASN cc_start: 0.7718 (m-40) cc_final: 0.7516 (m110) REVERT: G 266 PRO cc_start: 0.7374 (Cg_exo) cc_final: 0.7099 (Cg_endo) REVERT: G 279 GLN cc_start: 0.7028 (mm-40) cc_final: 0.5993 (mp-120) REVERT: G 285 GLU cc_start: 0.7419 (pt0) cc_final: 0.6665 (pt0) REVERT: G 289 MET cc_start: 0.3305 (mpp) cc_final: 0.2492 (ppp) REVERT: H 8 TYR cc_start: 0.6550 (m-80) cc_final: 0.6114 (m-80) REVERT: H 84 THR cc_start: 0.6714 (m) cc_final: 0.6486 (p) REVERT: H 94 LYS cc_start: 0.6137 (mttt) cc_final: 0.5797 (mtmm) REVERT: H 97 LYS cc_start: 0.7107 (mppt) cc_final: 0.6774 (mmtm) REVERT: H 203 SER cc_start: 0.5546 (t) cc_final: 0.5190 (m) REVERT: H 256 LYS cc_start: 0.6849 (mtmm) cc_final: 0.6113 (mmtt) REVERT: H 276 THR cc_start: 0.4948 (m) cc_final: 0.4641 (p) REVERT: H 289 MET cc_start: 0.7208 (mmm) cc_final: 0.6319 (mtt) REVERT: I 190 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7249 (mtm110) REVERT: I 191 GLN cc_start: 0.6890 (mm-40) cc_final: 0.6677 (mt0) REVERT: I 202 LYS cc_start: 0.6364 (mtpp) cc_final: 0.6016 (ttmm) REVERT: I 209 ARG cc_start: 0.6897 (ttm-80) cc_final: 0.6688 (ttm-80) REVERT: I 241 GLU cc_start: 0.5323 (mm-30) cc_final: 0.4893 (tt0) REVERT: I 337 LYS cc_start: 0.5920 (mmpt) cc_final: 0.5504 (mtpm) REVERT: I 351 ARG cc_start: 0.5736 (ptm160) cc_final: 0.4400 (ptm-80) REVERT: I 383 ARG cc_start: 0.5776 (mtp85) cc_final: 0.4854 (ttt180) REVERT: I 450 ARG cc_start: 0.6011 (ttm170) cc_final: 0.4894 (ttt180) REVERT: I 484 LYS cc_start: 0.6988 (mmtt) cc_final: 0.6736 (mptt) REVERT: I 568 GLU cc_start: 0.6172 (mm-30) cc_final: 0.5696 (mm-30) REVERT: I 570 MET cc_start: 0.6082 (mmt) cc_final: 0.5838 (mtp) REVERT: K 4 ASP cc_start: 0.6475 (t0) cc_final: 0.6066 (t0) REVERT: K 26 GLU cc_start: 0.4930 (tp30) cc_final: 0.4244 (mt-10) REVERT: K 80 GLU cc_start: 0.5244 (tp30) cc_final: 0.4682 (mt-10) REVERT: K 99 SER cc_start: 0.6150 (p) cc_final: 0.5831 (p) REVERT: K 113 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.5469 (ttp-170) outliers start: 23 outliers final: 12 residues processed: 462 average time/residue: 2.3535 time to fit residues: 1250.8187 Evaluate side-chains 337 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 324 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 349 SER Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 113 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 249 HIS E 39 HIS H 20 ASN I 395 ASN J 58 ASN K 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24058 Z= 0.334 Angle : 0.727 10.318 32762 Z= 0.404 Chirality : 0.051 0.482 3646 Planarity : 0.006 0.074 4126 Dihedral : 17.759 178.894 3898 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 2.59 % Allowed : 13.50 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 2809 helix: 1.50 (0.17), residues: 953 sheet: 0.56 (0.23), residues: 529 loop : -0.69 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 57 HIS 0.006 0.001 HIS A 141 PHE 0.018 0.002 PHE I 593 TYR 0.015 0.002 TYR B 83 ARG 0.007 0.001 ARG I 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Evaluate side-chains 380 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 318 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6337 (tppp) cc_final: 0.6091 (mptp) REVERT: A 61 ARG cc_start: 0.7012 (mpp80) cc_final: 0.6647 (mtp180) REVERT: A 105 SER cc_start: 0.6537 (t) cc_final: 0.6100 (p) REVERT: A 207 LYS cc_start: 0.6794 (ptmm) cc_final: 0.6057 (tppt) REVERT: A 211 GLU cc_start: 0.6450 (pm20) cc_final: 0.5610 (tp30) REVERT: B 63 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5594 (tm-30) REVERT: B 156 ARG cc_start: 0.6582 (ttp-170) cc_final: 0.5833 (ttp-170) REVERT: B 240 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7181 (mt0) REVERT: B 241 ASN cc_start: 0.7219 (t0) cc_final: 0.6690 (t0) REVERT: C 80 GLU cc_start: 0.5797 (mm-30) cc_final: 0.5014 (mt-10) REVERT: C 126 GLU cc_start: 0.6691 (tp30) cc_final: 0.6085 (mp0) REVERT: C 177 ARG cc_start: 0.7254 (ptm160) cc_final: 0.6970 (ptp-110) REVERT: C 240 GLN cc_start: 0.7290 (tp40) cc_final: 0.6175 (tm-30) REVERT: C 256 LYS cc_start: 0.7434 (mtpp) cc_final: 0.6364 (mtmt) REVERT: C 287 LYS cc_start: 0.6377 (mtpp) cc_final: 0.5171 (tptm) REVERT: D 17 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6182 (mp0) REVERT: D 36 GLU cc_start: 0.6944 (mt-10) cc_final: 0.5858 (mt-10) REVERT: D 63 GLU cc_start: 0.7263 (tp30) cc_final: 0.6250 (tt0) REVERT: D 71 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6501 (tp30) REVERT: D 109 MET cc_start: 0.6447 (mmm) cc_final: 0.6223 (mmm) REVERT: D 112 ASN cc_start: 0.7239 (m110) cc_final: 0.6841 (m110) REVERT: D 138 MET cc_start: 0.8313 (mtp) cc_final: 0.8038 (mtm) REVERT: D 177 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6200 (tpp-160) REVERT: D 256 LYS cc_start: 0.7649 (mmtm) cc_final: 0.6804 (mptt) REVERT: D 279 GLN cc_start: 0.7165 (tp40) cc_final: 0.6906 (mm110) REVERT: D 285 GLU cc_start: 0.8191 (tt0) cc_final: 0.7376 (tt0) REVERT: E 60 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6798 (mp0) REVERT: E 63 GLU cc_start: 0.7079 (tt0) cc_final: 0.6636 (tm-30) REVERT: E 109 MET cc_start: 0.5708 (OUTLIER) cc_final: 0.5507 (mtp) REVERT: E 221 ASP cc_start: 0.7313 (p0) cc_final: 0.6787 (p0) REVERT: E 250 LYS cc_start: 0.6767 (mtpp) cc_final: 0.6233 (tttm) REVERT: E 282 GLU cc_start: 0.7100 (tp30) cc_final: 0.6559 (tm-30) REVERT: E 286 VAL cc_start: 0.8297 (p) cc_final: 0.8019 (t) REVERT: F 11 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7666 (t) REVERT: F 60 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7421 (mt-10) REVERT: F 71 GLU cc_start: 0.5496 (pm20) cc_final: 0.5049 (tt0) REVERT: F 87 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6880 (t0) REVERT: F 175 MET cc_start: 0.6636 (tpp) cc_final: 0.6284 (tpp) REVERT: F 250 LYS cc_start: 0.6233 (mtpt) cc_final: 0.5724 (ttpp) REVERT: F 287 LYS cc_start: 0.6405 (mtpt) cc_final: 0.5086 (tmtt) REVERT: G 64 ARG cc_start: 0.6248 (mtm110) cc_final: 0.5856 (mtp85) REVERT: G 97 LYS cc_start: 0.7490 (mppt) cc_final: 0.7108 (mmmt) REVERT: G 126 GLU cc_start: 0.6481 (mm-30) cc_final: 0.6256 (mm-30) REVERT: G 145 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: G 153 SER cc_start: 0.6733 (OUTLIER) cc_final: 0.6131 (m) REVERT: G 245 ASN cc_start: 0.7691 (m-40) cc_final: 0.7452 (m110) REVERT: G 266 PRO cc_start: 0.7268 (Cg_exo) cc_final: 0.6961 (Cg_endo) REVERT: G 279 GLN cc_start: 0.7016 (mm-40) cc_final: 0.5977 (mp-120) REVERT: G 285 GLU cc_start: 0.7587 (pt0) cc_final: 0.6949 (pt0) REVERT: G 289 MET cc_start: 0.3331 (mpp) cc_final: 0.2463 (ppp) REVERT: H 8 TYR cc_start: 0.6714 (m-80) cc_final: 0.5927 (m-80) REVERT: H 94 LYS cc_start: 0.6206 (mttt) cc_final: 0.5936 (mtmm) REVERT: H 109 MET cc_start: 0.5417 (OUTLIER) cc_final: 0.5150 (mmm) REVERT: H 203 SER cc_start: 0.5780 (t) cc_final: 0.5330 (m) REVERT: H 256 LYS cc_start: 0.6832 (mtmm) cc_final: 0.6084 (mmtt) REVERT: H 276 THR cc_start: 0.5065 (m) cc_final: 0.4773 (p) REVERT: H 289 MET cc_start: 0.7238 (mmm) cc_final: 0.6383 (mtt) REVERT: I 190 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7448 (mtm110) REVERT: I 191 GLN cc_start: 0.6862 (mm-40) cc_final: 0.6656 (mt0) REVERT: I 197 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7378 (tm) REVERT: I 202 LYS cc_start: 0.6429 (mtpp) cc_final: 0.6080 (ttmm) REVERT: I 209 ARG cc_start: 0.6819 (ttm-80) cc_final: 0.6594 (ttm-80) REVERT: I 241 GLU cc_start: 0.5361 (mm-30) cc_final: 0.4934 (tt0) REVERT: I 337 LYS cc_start: 0.5896 (mmpt) cc_final: 0.5646 (mttt) REVERT: I 351 ARG cc_start: 0.5762 (ptm160) cc_final: 0.4303 (ptm-80) REVERT: I 383 ARG cc_start: 0.5767 (mtp85) cc_final: 0.4988 (ttt180) REVERT: I 390 ILE cc_start: 0.5811 (OUTLIER) cc_final: 0.5602 (mm) REVERT: I 408 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.5877 (ttm170) REVERT: I 450 ARG cc_start: 0.6069 (ttm170) cc_final: 0.4883 (ttt180) REVERT: I 484 LYS cc_start: 0.7097 (mmtt) cc_final: 0.6807 (mptt) REVERT: I 568 GLU cc_start: 0.6230 (mm-30) cc_final: 0.5675 (mm-30) REVERT: I 570 MET cc_start: 0.6162 (mmt) cc_final: 0.5902 (mtp) REVERT: J 39 ARG cc_start: 0.6302 (mtm-85) cc_final: 0.5183 (mtp180) REVERT: K 4 ASP cc_start: 0.6488 (t0) cc_final: 0.6066 (t0) REVERT: K 26 GLU cc_start: 0.5244 (tp30) cc_final: 0.4570 (mt-10) REVERT: K 80 GLU cc_start: 0.5381 (tp30) cc_final: 0.4841 (mt-10) REVERT: K 99 SER cc_start: 0.6301 (p) cc_final: 0.6001 (p) REVERT: K 113 ARG cc_start: 0.5652 (OUTLIER) cc_final: 0.5448 (ttp-170) outliers start: 62 outliers final: 23 residues processed: 354 average time/residue: 2.5808 time to fit residues: 1048.3769 Evaluate side-chains 332 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 296 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 287 LYS Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 131 GLN Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 408 ARG Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 113 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 230 optimal weight: 0.6980 chunk 256 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN C 131 GLN E 220 HIS F 39 HIS ** G 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 395 ASN J 53 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24058 Z= 0.309 Angle : 0.664 10.947 32762 Z= 0.363 Chirality : 0.050 0.360 3646 Planarity : 0.005 0.055 4126 Dihedral : 16.329 178.996 3895 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 2.72 % Allowed : 13.04 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.16), residues: 2809 helix: 1.67 (0.17), residues: 941 sheet: 0.56 (0.23), residues: 519 loop : -0.83 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 57 HIS 0.009 0.001 HIS J 111 PHE 0.015 0.002 PHE I 593 TYR 0.014 0.002 TYR C 68 ARG 0.006 0.001 ARG I 495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Evaluate side-chains 369 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6349 (tppp) cc_final: 0.6108 (mptp) REVERT: A 61 ARG cc_start: 0.7109 (mpp80) cc_final: 0.6864 (mtp180) REVERT: A 105 SER cc_start: 0.6719 (t) cc_final: 0.6315 (p) REVERT: A 163 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7389 (mtp180) REVERT: A 199 ARG cc_start: 0.6094 (mpt-90) cc_final: 0.5325 (mtt-85) REVERT: A 207 LYS cc_start: 0.6799 (ptmm) cc_final: 0.6060 (tppt) REVERT: A 211 GLU cc_start: 0.6436 (pm20) cc_final: 0.5592 (tp30) REVERT: B 63 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5786 (tm-30) REVERT: B 156 ARG cc_start: 0.6565 (ttp-170) cc_final: 0.5637 (ttp-170) REVERT: B 240 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7264 (mt0) REVERT: C 80 GLU cc_start: 0.5867 (mm-30) cc_final: 0.5053 (mt-10) REVERT: C 126 GLU cc_start: 0.6688 (tp30) cc_final: 0.6112 (mp0) REVERT: C 177 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.7039 (ptp-110) REVERT: C 233 LYS cc_start: 0.7706 (mttt) cc_final: 0.7321 (mtpp) REVERT: C 240 GLN cc_start: 0.7263 (tp40) cc_final: 0.6122 (tm-30) REVERT: C 256 LYS cc_start: 0.7496 (mtpp) cc_final: 0.6407 (mtmt) REVERT: C 287 LYS cc_start: 0.6376 (mtpp) cc_final: 0.5278 (tptm) REVERT: D 17 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6157 (mp0) REVERT: D 36 GLU cc_start: 0.6959 (mt-10) cc_final: 0.5886 (mt-10) REVERT: D 63 GLU cc_start: 0.7356 (tp30) cc_final: 0.6288 (tt0) REVERT: D 71 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6423 (tp30) REVERT: D 112 ASN cc_start: 0.7246 (m110) cc_final: 0.6851 (m110) REVERT: D 138 MET cc_start: 0.8282 (mtp) cc_final: 0.8045 (mtm) REVERT: D 157 MET cc_start: 0.7223 (ptm) cc_final: 0.6777 (ptm) REVERT: D 177 ARG cc_start: 0.7580 (ttm110) cc_final: 0.6271 (tpp-160) REVERT: D 256 LYS cc_start: 0.7652 (mmtm) cc_final: 0.6903 (mppt) REVERT: D 279 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6988 (mm-40) REVERT: D 285 GLU cc_start: 0.8130 (tt0) cc_final: 0.7366 (tt0) REVERT: D 286 VAL cc_start: 0.8306 (p) cc_final: 0.8084 (t) REVERT: E 60 GLU cc_start: 0.7606 (mm-30) cc_final: 0.6973 (mp0) REVERT: E 63 GLU cc_start: 0.7126 (tt0) cc_final: 0.6741 (tt0) REVERT: E 97 LYS cc_start: 0.8126 (tppp) cc_final: 0.7377 (mptt) REVERT: E 156 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.5699 (ttm-80) REVERT: E 191 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: E 221 ASP cc_start: 0.7627 (p0) cc_final: 0.7108 (p0) REVERT: E 250 LYS cc_start: 0.6678 (mtpp) cc_final: 0.6115 (tttm) REVERT: E 279 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6868 (mp10) REVERT: E 282 GLU cc_start: 0.7103 (tp30) cc_final: 0.6589 (tm-30) REVERT: E 286 VAL cc_start: 0.8300 (p) cc_final: 0.8045 (t) REVERT: F 60 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7400 (mt-10) REVERT: F 71 GLU cc_start: 0.5634 (pm20) cc_final: 0.5409 (tt0) REVERT: F 133 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.4288 (tmm-80) REVERT: F 175 MET cc_start: 0.6436 (tpp) cc_final: 0.6151 (tpp) REVERT: F 240 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.7096 (mt0) REVERT: F 250 LYS cc_start: 0.6181 (mtpt) cc_final: 0.5964 (ttmm) REVERT: F 287 LYS cc_start: 0.6509 (mtpt) cc_final: 0.5232 (tmtt) REVERT: G 64 ARG cc_start: 0.6157 (mtm110) cc_final: 0.5860 (mtp85) REVERT: G 97 LYS cc_start: 0.7192 (mppt) cc_final: 0.6852 (mmmt) REVERT: G 126 GLU cc_start: 0.6440 (mm-30) cc_final: 0.6168 (mm-30) REVERT: G 145 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: G 153 SER cc_start: 0.6771 (OUTLIER) cc_final: 0.6200 (m) REVERT: G 191 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6639 (m-80) REVERT: G 245 ASN cc_start: 0.7745 (m-40) cc_final: 0.7493 (m110) REVERT: G 266 PRO cc_start: 0.7280 (Cg_exo) cc_final: 0.6968 (Cg_endo) REVERT: G 285 GLU cc_start: 0.7480 (pt0) cc_final: 0.6850 (pt0) REVERT: H 15 ASP cc_start: 0.5729 (m-30) cc_final: 0.4896 (p0) REVERT: H 94 LYS cc_start: 0.6300 (mttt) cc_final: 0.5996 (mtmm) REVERT: H 109 MET cc_start: 0.5392 (OUTLIER) cc_final: 0.5108 (mmm) REVERT: H 203 SER cc_start: 0.5926 (t) cc_final: 0.5428 (m) REVERT: H 256 LYS cc_start: 0.6884 (mtmm) cc_final: 0.6138 (mmtt) REVERT: H 276 THR cc_start: 0.5023 (m) cc_final: 0.4726 (p) REVERT: H 289 MET cc_start: 0.7191 (mmm) cc_final: 0.6357 (mtt) REVERT: I 190 ARG cc_start: 0.7882 (ttm110) cc_final: 0.7430 (mtm110) REVERT: I 191 GLN cc_start: 0.6852 (mm-40) cc_final: 0.6636 (mt0) REVERT: I 197 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7368 (tm) REVERT: I 202 LYS cc_start: 0.6408 (mtpp) cc_final: 0.6060 (ttmm) REVERT: I 209 ARG cc_start: 0.6839 (ttm-80) cc_final: 0.5853 (ttt-90) REVERT: I 241 GLU cc_start: 0.5385 (mm-30) cc_final: 0.5043 (tt0) REVERT: I 337 LYS cc_start: 0.6188 (mmpt) cc_final: 0.5708 (mttt) REVERT: I 351 ARG cc_start: 0.5803 (ptm160) cc_final: 0.5139 (mmm160) REVERT: I 383 ARG cc_start: 0.5719 (mtp85) cc_final: 0.4921 (ttt180) REVERT: I 408 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5894 (ttm170) REVERT: I 450 ARG cc_start: 0.6124 (ttm170) cc_final: 0.4932 (ttt180) REVERT: I 484 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6721 (mptt) REVERT: I 568 GLU cc_start: 0.6369 (mm-30) cc_final: 0.5877 (mm-30) REVERT: I 570 MET cc_start: 0.6238 (mmt) cc_final: 0.5979 (mtp) REVERT: J 39 ARG cc_start: 0.6224 (mtm-85) cc_final: 0.5260 (mtp180) REVERT: K 4 ASP cc_start: 0.6507 (t0) cc_final: 0.6060 (t0) REVERT: K 26 GLU cc_start: 0.5417 (tp30) cc_final: 0.4650 (mt-10) REVERT: K 80 GLU cc_start: 0.5398 (tp30) cc_final: 0.4859 (mt-10) REVERT: K 83 MET cc_start: 0.4520 (mtp) cc_final: 0.4215 (mtt) REVERT: K 99 SER cc_start: 0.6265 (p) cc_final: 0.5955 (p) REVERT: K 113 ARG cc_start: 0.5621 (OUTLIER) cc_final: 0.5364 (ttp-170) outliers start: 65 outliers final: 22 residues processed: 340 average time/residue: 2.5788 time to fit residues: 1000.4098 Evaluate side-chains 329 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 290 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 287 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 191 PHE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 131 GLN Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 408 ARG Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 113 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN G 240 GLN ** G 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24058 Z= 0.308 Angle : 0.653 9.612 32762 Z= 0.353 Chirality : 0.048 0.330 3646 Planarity : 0.005 0.055 4126 Dihedral : 15.654 174.313 3893 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 3.01 % Allowed : 13.12 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.16), residues: 2809 helix: 1.65 (0.17), residues: 941 sheet: 0.50 (0.23), residues: 524 loop : -0.90 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 57 HIS 0.007 0.001 HIS J 111 PHE 0.017 0.002 PHE A 126 TYR 0.015 0.002 TYR C 68 ARG 0.005 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 293 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6277 (tppp) cc_final: 0.6031 (mptp) REVERT: A 61 ARG cc_start: 0.7095 (mpp80) cc_final: 0.6852 (mtp180) REVERT: A 105 SER cc_start: 0.6792 (t) cc_final: 0.6386 (p) REVERT: A 114 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6683 (pp) REVERT: A 199 ARG cc_start: 0.6116 (mpt-90) cc_final: 0.5350 (mtt-85) REVERT: A 207 LYS cc_start: 0.6816 (ptmm) cc_final: 0.6100 (tppt) REVERT: A 211 GLU cc_start: 0.6456 (pm20) cc_final: 0.5669 (tp30) REVERT: B 63 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5774 (tm-30) REVERT: B 123 MET cc_start: 0.7222 (mpp) cc_final: 0.6914 (mtm) REVERT: B 156 ARG cc_start: 0.6669 (ttp-170) cc_final: 0.6449 (ttm170) REVERT: B 240 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7019 (mt0) REVERT: B 243 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.4745 (pp) REVERT: C 80 GLU cc_start: 0.5822 (mm-30) cc_final: 0.5071 (mt-10) REVERT: C 126 GLU cc_start: 0.6687 (tp30) cc_final: 0.6133 (mp0) REVERT: C 240 GLN cc_start: 0.7302 (tp40) cc_final: 0.6161 (tm-30) REVERT: C 256 LYS cc_start: 0.7511 (mtpp) cc_final: 0.6427 (mtmt) REVERT: C 287 LYS cc_start: 0.6304 (mtpp) cc_final: 0.5229 (tptm) REVERT: D 17 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6167 (mp0) REVERT: D 36 GLU cc_start: 0.6892 (mt-10) cc_final: 0.5846 (mt-10) REVERT: D 63 GLU cc_start: 0.7327 (tp30) cc_final: 0.6216 (tt0) REVERT: D 71 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6342 (tp30) REVERT: D 112 ASN cc_start: 0.7254 (m110) cc_final: 0.6824 (m110) REVERT: D 138 MET cc_start: 0.8255 (mtp) cc_final: 0.7963 (mtm) REVERT: D 157 MET cc_start: 0.7203 (ptm) cc_final: 0.6791 (ptm) REVERT: D 177 ARG cc_start: 0.7616 (ttm110) cc_final: 0.6291 (tpp-160) REVERT: D 256 LYS cc_start: 0.7712 (mmtm) cc_final: 0.6977 (mppt) REVERT: D 285 GLU cc_start: 0.8021 (tt0) cc_final: 0.7325 (tt0) REVERT: D 286 VAL cc_start: 0.8315 (p) cc_final: 0.8110 (t) REVERT: E 60 GLU cc_start: 0.7694 (mm-30) cc_final: 0.6972 (mt-10) REVERT: E 63 GLU cc_start: 0.7100 (tt0) cc_final: 0.6730 (tt0) REVERT: E 156 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.5733 (ttm-80) REVERT: E 175 MET cc_start: 0.7581 (mmt) cc_final: 0.7301 (mmt) REVERT: E 191 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: E 221 ASP cc_start: 0.7720 (p0) cc_final: 0.7201 (p0) REVERT: E 250 LYS cc_start: 0.6690 (mtpp) cc_final: 0.6140 (tttm) REVERT: E 279 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6847 (mp10) REVERT: E 282 GLU cc_start: 0.7089 (tp30) cc_final: 0.6559 (tm-30) REVERT: E 286 VAL cc_start: 0.8331 (p) cc_final: 0.8070 (t) REVERT: F 71 GLU cc_start: 0.5643 (pm20) cc_final: 0.5430 (tt0) REVERT: F 133 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.4226 (tmm-80) REVERT: F 175 MET cc_start: 0.6431 (tpp) cc_final: 0.6146 (tpp) REVERT: F 240 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.7026 (mt0) REVERT: F 287 LYS cc_start: 0.6482 (mtpt) cc_final: 0.5203 (tmtt) REVERT: G 64 ARG cc_start: 0.6154 (mtm110) cc_final: 0.5760 (mtp85) REVERT: G 97 LYS cc_start: 0.7152 (mppt) cc_final: 0.6795 (mmmt) REVERT: G 126 GLU cc_start: 0.6423 (mm-30) cc_final: 0.6172 (mm-30) REVERT: G 153 SER cc_start: 0.6780 (OUTLIER) cc_final: 0.6243 (m) REVERT: G 191 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: G 245 ASN cc_start: 0.7723 (m-40) cc_final: 0.7477 (m110) REVERT: G 266 PRO cc_start: 0.7286 (Cg_exo) cc_final: 0.6986 (Cg_endo) REVERT: H 15 ASP cc_start: 0.5668 (m-30) cc_final: 0.4944 (p0) REVERT: H 94 LYS cc_start: 0.6299 (mttt) cc_final: 0.6033 (mtmm) REVERT: H 109 MET cc_start: 0.5288 (OUTLIER) cc_final: 0.4977 (mmm) REVERT: H 150 GLN cc_start: 0.4569 (OUTLIER) cc_final: 0.3844 (pp30) REVERT: H 203 SER cc_start: 0.6020 (t) cc_final: 0.5513 (m) REVERT: H 256 LYS cc_start: 0.6941 (mtmm) cc_final: 0.6308 (mmtt) REVERT: H 259 ARG cc_start: 0.4938 (mtp180) cc_final: 0.4668 (ttt180) REVERT: H 289 MET cc_start: 0.7215 (mmm) cc_final: 0.6415 (mtt) REVERT: I 190 ARG cc_start: 0.7829 (ttm110) cc_final: 0.7435 (mtm110) REVERT: I 191 GLN cc_start: 0.6880 (mm-40) cc_final: 0.6604 (mt0) REVERT: I 197 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7276 (tm) REVERT: I 202 LYS cc_start: 0.6393 (mtpp) cc_final: 0.6051 (ttmm) REVERT: I 241 GLU cc_start: 0.5350 (mm-30) cc_final: 0.5058 (tt0) REVERT: I 276 SER cc_start: 0.8208 (t) cc_final: 0.7913 (p) REVERT: I 337 LYS cc_start: 0.6218 (mmpt) cc_final: 0.5749 (mttt) REVERT: I 351 ARG cc_start: 0.5750 (ptm160) cc_final: 0.5101 (mmm160) REVERT: I 383 ARG cc_start: 0.5683 (mtp85) cc_final: 0.4895 (ttt180) REVERT: I 408 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.5867 (ttm170) REVERT: I 450 ARG cc_start: 0.6159 (ttm170) cc_final: 0.4966 (ttt180) REVERT: I 484 LYS cc_start: 0.7063 (mmtt) cc_final: 0.6750 (mptt) REVERT: I 568 GLU cc_start: 0.6441 (mm-30) cc_final: 0.5955 (mm-30) REVERT: I 570 MET cc_start: 0.5995 (mmt) cc_final: 0.5696 (mtp) REVERT: J 39 ARG cc_start: 0.6306 (mtm-85) cc_final: 0.5329 (mtp180) REVERT: K 4 ASP cc_start: 0.6497 (t0) cc_final: 0.6011 (t0) REVERT: K 9 ASP cc_start: 0.6140 (m-30) cc_final: 0.5785 (m-30) REVERT: K 26 GLU cc_start: 0.5566 (tp30) cc_final: 0.4800 (mt-10) REVERT: K 80 GLU cc_start: 0.5446 (tp30) cc_final: 0.4854 (mt-10) REVERT: K 83 MET cc_start: 0.4422 (mtp) cc_final: 0.4053 (mtt) REVERT: K 99 SER cc_start: 0.6178 (p) cc_final: 0.5869 (p) REVERT: K 113 ARG cc_start: 0.5649 (OUTLIER) cc_final: 0.5323 (ttp-170) outliers start: 72 outliers final: 27 residues processed: 331 average time/residue: 2.5084 time to fit residues: 951.3147 Evaluate side-chains 324 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 287 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 191 PHE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 131 GLN Chi-restraints excluded: chain H residue 150 GLN Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 408 ARG Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 579 SER Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 113 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 395 ASN J 47 ASN J 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24058 Z= 0.340 Angle : 0.650 10.891 32762 Z= 0.350 Chirality : 0.049 0.340 3646 Planarity : 0.006 0.059 4126 Dihedral : 15.430 176.673 3893 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 3.18 % Allowed : 13.25 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2809 helix: 1.61 (0.17), residues: 941 sheet: 0.43 (0.22), residues: 524 loop : -1.00 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 57 HIS 0.008 0.001 HIS J 111 PHE 0.016 0.002 PHE I 593 TYR 0.016 0.002 TYR I 246 ARG 0.006 0.001 ARG F 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Evaluate side-chains 369 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 293 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6398 (tppp) cc_final: 0.6144 (mptp) REVERT: A 61 ARG cc_start: 0.7045 (mpp80) cc_final: 0.6781 (mtp180) REVERT: A 105 SER cc_start: 0.6893 (t) cc_final: 0.6475 (p) REVERT: A 199 ARG cc_start: 0.6134 (mpt-90) cc_final: 0.5368 (mtt-85) REVERT: A 207 LYS cc_start: 0.6871 (ptmm) cc_final: 0.6104 (tppt) REVERT: A 211 GLU cc_start: 0.6551 (pm20) cc_final: 0.5781 (tp30) REVERT: B 9 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: B 63 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5782 (tm-30) REVERT: B 123 MET cc_start: 0.7248 (mpp) cc_final: 0.6985 (mtm) REVERT: B 156 ARG cc_start: 0.6835 (ttp-170) cc_final: 0.6005 (ttp-170) REVERT: B 175 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.7025 (tpp) REVERT: B 240 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6995 (mt0) REVERT: C 80 GLU cc_start: 0.5889 (mm-30) cc_final: 0.5071 (mt-10) REVERT: C 126 GLU cc_start: 0.6633 (tp30) cc_final: 0.6099 (mp0) REVERT: C 240 GLN cc_start: 0.7280 (tp40) cc_final: 0.6153 (tm-30) REVERT: C 287 LYS cc_start: 0.6356 (mtpp) cc_final: 0.5276 (tptm) REVERT: D 17 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6230 (mp0) REVERT: D 36 GLU cc_start: 0.6913 (mt-10) cc_final: 0.5854 (mt-10) REVERT: D 63 GLU cc_start: 0.7505 (tp30) cc_final: 0.6480 (tt0) REVERT: D 71 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6303 (tp30) REVERT: D 112 ASN cc_start: 0.7267 (m110) cc_final: 0.7030 (m110) REVERT: D 157 MET cc_start: 0.7232 (ptm) cc_final: 0.6838 (ptm) REVERT: D 177 ARG cc_start: 0.7679 (ttm110) cc_final: 0.6385 (tpp-160) REVERT: D 256 LYS cc_start: 0.7705 (mmtm) cc_final: 0.6976 (mppt) REVERT: D 285 GLU cc_start: 0.8008 (tt0) cc_final: 0.7485 (tt0) REVERT: D 286 VAL cc_start: 0.8307 (p) cc_final: 0.8085 (t) REVERT: E 60 GLU cc_start: 0.7683 (mm-30) cc_final: 0.6969 (mt-10) REVERT: E 63 GLU cc_start: 0.7095 (tt0) cc_final: 0.6722 (tt0) REVERT: E 156 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.5679 (ttm-80) REVERT: E 191 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: E 221 ASP cc_start: 0.7809 (p0) cc_final: 0.7341 (p0) REVERT: E 250 LYS cc_start: 0.6664 (mtpp) cc_final: 0.6108 (tttm) REVERT: E 282 GLU cc_start: 0.7026 (tp30) cc_final: 0.6509 (tm-30) REVERT: E 286 VAL cc_start: 0.8311 (p) cc_final: 0.8026 (t) REVERT: F 133 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.4251 (tmm-80) REVERT: F 175 MET cc_start: 0.6290 (tpp) cc_final: 0.5989 (tpp) REVERT: F 191 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7030 (m-80) REVERT: F 240 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.7063 (mt0) REVERT: F 287 LYS cc_start: 0.6577 (mtpt) cc_final: 0.5954 (mttt) REVERT: G 64 ARG cc_start: 0.6263 (mtm110) cc_final: 0.5806 (mtp85) REVERT: G 97 LYS cc_start: 0.7145 (mppt) cc_final: 0.6801 (mmmt) REVERT: G 126 GLU cc_start: 0.6400 (mm-30) cc_final: 0.6158 (mm-30) REVERT: G 153 SER cc_start: 0.6729 (OUTLIER) cc_final: 0.6222 (m) REVERT: G 191 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6615 (m-80) REVERT: G 245 ASN cc_start: 0.7757 (m-40) cc_final: 0.7498 (m110) REVERT: G 266 PRO cc_start: 0.7237 (Cg_exo) cc_final: 0.6913 (Cg_endo) REVERT: H 15 ASP cc_start: 0.5568 (m-30) cc_final: 0.4923 (p0) REVERT: H 94 LYS cc_start: 0.6338 (mttt) cc_final: 0.6071 (mtmm) REVERT: H 98 LYS cc_start: 0.6290 (tttm) cc_final: 0.6067 (ttmm) REVERT: H 133 ARG cc_start: 0.6168 (ttp80) cc_final: 0.5853 (ttt180) REVERT: H 203 SER cc_start: 0.6030 (t) cc_final: 0.5524 (m) REVERT: H 256 LYS cc_start: 0.6932 (mtmm) cc_final: 0.6191 (mmtt) REVERT: H 276 THR cc_start: 0.5160 (m) cc_final: 0.4723 (p) REVERT: H 289 MET cc_start: 0.7102 (mmm) cc_final: 0.6349 (mtt) REVERT: I 190 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7422 (mtm110) REVERT: I 191 GLN cc_start: 0.6938 (mm-40) cc_final: 0.6639 (mt0) REVERT: I 197 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7231 (tm) REVERT: I 202 LYS cc_start: 0.6395 (mtpp) cc_final: 0.5709 (mtmm) REVERT: I 241 GLU cc_start: 0.5275 (mm-30) cc_final: 0.4997 (tt0) REVERT: I 276 SER cc_start: 0.8202 (t) cc_final: 0.7901 (p) REVERT: I 337 LYS cc_start: 0.6260 (mmpt) cc_final: 0.5838 (mttt) REVERT: I 351 ARG cc_start: 0.5792 (ptm160) cc_final: 0.5176 (mmm160) REVERT: I 383 ARG cc_start: 0.5676 (mtp85) cc_final: 0.4879 (ttt180) REVERT: I 408 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.5979 (ttm170) REVERT: I 450 ARG cc_start: 0.6172 (ttm170) cc_final: 0.4974 (ttt180) REVERT: I 484 LYS cc_start: 0.6979 (mmtt) cc_final: 0.6753 (mptt) REVERT: I 539 VAL cc_start: 0.6507 (OUTLIER) cc_final: 0.6228 (p) REVERT: I 568 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5900 (mm-30) REVERT: I 570 MET cc_start: 0.6134 (mmt) cc_final: 0.5812 (mtp) REVERT: J 26 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6071 (pt0) REVERT: J 39 ARG cc_start: 0.6263 (mtm-85) cc_final: 0.5293 (mtp180) REVERT: K 4 ASP cc_start: 0.6616 (t0) cc_final: 0.6016 (t0) REVERT: K 26 GLU cc_start: 0.5550 (tp30) cc_final: 0.4765 (mt-10) REVERT: K 80 GLU cc_start: 0.5470 (tp30) cc_final: 0.4863 (mt-10) REVERT: K 83 MET cc_start: 0.4465 (mtp) cc_final: 0.4111 (mtt) REVERT: K 99 SER cc_start: 0.6223 (p) cc_final: 0.5924 (p) REVERT: K 113 ARG cc_start: 0.5646 (OUTLIER) cc_final: 0.5441 (ttp-170) outliers start: 76 outliers final: 35 residues processed: 332 average time/residue: 2.5012 time to fit residues: 952.4577 Evaluate side-chains 333 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 287 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 191 PHE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 131 GLN Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 266 ASP Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 408 ARG Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 579 SER Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 113 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 0.9990 chunk 247 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** G 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24058 Z= 0.228 Angle : 0.584 6.447 32762 Z= 0.313 Chirality : 0.046 0.293 3646 Planarity : 0.005 0.055 4126 Dihedral : 15.242 173.127 3893 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 2.72 % Allowed : 14.00 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.16), residues: 2809 helix: 1.82 (0.17), residues: 947 sheet: 0.36 (0.22), residues: 529 loop : -0.95 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 57 HIS 0.004 0.001 HIS E 249 PHE 0.013 0.001 PHE B 10 TYR 0.013 0.002 TYR C 68 ARG 0.004 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Evaluate side-chains 355 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 290 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6273 (tppp) cc_final: 0.5993 (mptp) REVERT: A 61 ARG cc_start: 0.7051 (mpp80) cc_final: 0.6795 (mtp180) REVERT: A 105 SER cc_start: 0.6812 (t) cc_final: 0.6394 (p) REVERT: A 114 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6704 (pp) REVERT: A 140 LYS cc_start: 0.6814 (mmtm) cc_final: 0.6136 (tmmt) REVERT: A 199 ARG cc_start: 0.6107 (mpt-90) cc_final: 0.5354 (mtt-85) REVERT: A 207 LYS cc_start: 0.6871 (ptmm) cc_final: 0.6124 (tppt) REVERT: A 211 GLU cc_start: 0.6508 (pm20) cc_final: 0.5735 (tp30) REVERT: B 63 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5723 (tm-30) REVERT: B 123 MET cc_start: 0.7186 (mpp) cc_final: 0.6841 (mtm) REVERT: B 156 ARG cc_start: 0.6942 (ttp-170) cc_final: 0.5981 (ttp-170) REVERT: B 175 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.7021 (tpp) REVERT: B 240 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7161 (mt0) REVERT: C 80 GLU cc_start: 0.5817 (mm-30) cc_final: 0.5019 (mt-10) REVERT: C 126 GLU cc_start: 0.6649 (tp30) cc_final: 0.6100 (mp0) REVERT: C 240 GLN cc_start: 0.7307 (tp40) cc_final: 0.6165 (tm-30) REVERT: C 256 LYS cc_start: 0.7539 (mtpp) cc_final: 0.6443 (mtmt) REVERT: C 287 LYS cc_start: 0.6355 (mtpp) cc_final: 0.5265 (tptm) REVERT: D 17 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6255 (mp0) REVERT: D 36 GLU cc_start: 0.6963 (mt-10) cc_final: 0.5875 (mt-10) REVERT: D 63 GLU cc_start: 0.7295 (tp30) cc_final: 0.6179 (tt0) REVERT: D 71 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6340 (tp30) REVERT: D 89 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6563 (mptt) REVERT: D 109 MET cc_start: 0.6510 (mmm) cc_final: 0.6259 (mmm) REVERT: D 112 ASN cc_start: 0.7242 (m110) cc_final: 0.6827 (m110) REVERT: D 138 MET cc_start: 0.8255 (mtp) cc_final: 0.7960 (mtm) REVERT: D 157 MET cc_start: 0.7186 (ptm) cc_final: 0.6785 (ptm) REVERT: D 177 ARG cc_start: 0.7666 (ttm110) cc_final: 0.6342 (tpp-160) REVERT: D 256 LYS cc_start: 0.7700 (mmtm) cc_final: 0.6990 (mppt) REVERT: D 285 GLU cc_start: 0.8038 (tt0) cc_final: 0.7477 (tt0) REVERT: E 60 GLU cc_start: 0.7661 (mm-30) cc_final: 0.6974 (mt-10) REVERT: E 63 GLU cc_start: 0.7065 (tt0) cc_final: 0.6708 (tt0) REVERT: E 156 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.5591 (ttm-80) REVERT: E 191 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: E 221 ASP cc_start: 0.7687 (p0) cc_final: 0.7211 (p0) REVERT: E 250 LYS cc_start: 0.6589 (mtpp) cc_final: 0.6072 (tttm) REVERT: E 282 GLU cc_start: 0.6975 (tp30) cc_final: 0.6481 (tm-30) REVERT: E 286 VAL cc_start: 0.8289 (p) cc_final: 0.8012 (t) REVERT: F 133 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.4204 (tmm-80) REVERT: F 191 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7037 (m-80) REVERT: F 240 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.7019 (mt0) REVERT: F 287 LYS cc_start: 0.6580 (mtpt) cc_final: 0.5289 (tmtt) REVERT: G 64 ARG cc_start: 0.6151 (mtm110) cc_final: 0.5688 (mtp85) REVERT: G 97 LYS cc_start: 0.7104 (mppt) cc_final: 0.6797 (mmmt) REVERT: G 153 SER cc_start: 0.6850 (OUTLIER) cc_final: 0.6352 (m) REVERT: G 191 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: G 245 ASN cc_start: 0.7821 (m-40) cc_final: 0.7568 (m110) REVERT: G 266 PRO cc_start: 0.7230 (Cg_exo) cc_final: 0.6903 (Cg_endo) REVERT: H 15 ASP cc_start: 0.5514 (m-30) cc_final: 0.4973 (p0) REVERT: H 26 ASP cc_start: 0.5503 (m-30) cc_final: 0.5212 (m-30) REVERT: H 94 LYS cc_start: 0.6348 (mttt) cc_final: 0.6088 (mtmm) REVERT: H 98 LYS cc_start: 0.6211 (tttm) cc_final: 0.5990 (ttmm) REVERT: H 133 ARG cc_start: 0.6103 (ttp80) cc_final: 0.5846 (ttt180) REVERT: H 203 SER cc_start: 0.6019 (t) cc_final: 0.5509 (m) REVERT: H 256 LYS cc_start: 0.6933 (mtmm) cc_final: 0.6296 (mmtt) REVERT: H 259 ARG cc_start: 0.4862 (mtp180) cc_final: 0.4594 (ttt180) REVERT: H 289 MET cc_start: 0.7102 (mmm) cc_final: 0.6373 (mtt) REVERT: I 190 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7531 (ttm-80) REVERT: I 191 GLN cc_start: 0.6943 (mm-40) cc_final: 0.6586 (mt0) REVERT: I 202 LYS cc_start: 0.6409 (mtpp) cc_final: 0.6056 (ttmm) REVERT: I 241 GLU cc_start: 0.5226 (mm-30) cc_final: 0.4964 (tt0) REVERT: I 276 SER cc_start: 0.8178 (t) cc_final: 0.7878 (p) REVERT: I 337 LYS cc_start: 0.6264 (mmpt) cc_final: 0.5793 (mttt) REVERT: I 351 ARG cc_start: 0.5816 (ptm160) cc_final: 0.5243 (mmm160) REVERT: I 370 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: I 383 ARG cc_start: 0.5678 (mtp85) cc_final: 0.4886 (ttt180) REVERT: I 408 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.5990 (ttm170) REVERT: I 450 ARG cc_start: 0.5973 (ttm170) cc_final: 0.4884 (ttt180) REVERT: I 484 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6884 (mptt) REVERT: I 539 VAL cc_start: 0.6472 (OUTLIER) cc_final: 0.6178 (p) REVERT: I 555 ARG cc_start: 0.5743 (ttm110) cc_final: 0.5374 (ttm-80) REVERT: I 568 GLU cc_start: 0.6341 (mm-30) cc_final: 0.5906 (mm-30) REVERT: I 570 MET cc_start: 0.6091 (mmt) cc_final: 0.5778 (mtp) REVERT: J 39 ARG cc_start: 0.6284 (mtm-85) cc_final: 0.5331 (mtp180) REVERT: J 113 ARG cc_start: 0.5952 (ttt90) cc_final: 0.5528 (ttt-90) REVERT: K 4 ASP cc_start: 0.6586 (t0) cc_final: 0.6000 (t0) REVERT: K 26 GLU cc_start: 0.5561 (tp30) cc_final: 0.4762 (mt-10) REVERT: K 80 GLU cc_start: 0.5397 (tp30) cc_final: 0.4832 (mt-10) REVERT: K 83 MET cc_start: 0.4461 (mtp) cc_final: 0.4089 (mtt) REVERT: K 99 SER cc_start: 0.6128 (p) cc_final: 0.5819 (p) outliers start: 65 outliers final: 29 residues processed: 325 average time/residue: 2.6396 time to fit residues: 989.5011 Evaluate side-chains 327 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 287 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 191 PHE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 131 GLN Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 408 ARG Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 69 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 155 optimal weight: 0.1980 chunk 231 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 ASN I 395 ASN ** I 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24058 Z= 0.321 Angle : 0.625 6.685 32762 Z= 0.336 Chirality : 0.048 0.315 3646 Planarity : 0.005 0.059 4126 Dihedral : 15.225 173.205 3888 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.08 % Rotamer: Outliers : 2.59 % Allowed : 14.21 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.16), residues: 2809 helix: 1.73 (0.17), residues: 942 sheet: 0.40 (0.22), residues: 524 loop : -1.02 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 57 HIS 0.006 0.001 HIS J 111 PHE 0.017 0.002 PHE I 593 TYR 0.016 0.002 TYR C 68 ARG 0.004 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 278 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6397 (tppp) cc_final: 0.6106 (mptp) REVERT: A 61 ARG cc_start: 0.7013 (mpp80) cc_final: 0.6741 (mtp180) REVERT: A 105 SER cc_start: 0.6863 (t) cc_final: 0.6454 (p) REVERT: A 140 LYS cc_start: 0.6853 (mmtm) cc_final: 0.6174 (tmmt) REVERT: A 199 ARG cc_start: 0.6102 (mpt-90) cc_final: 0.5334 (mtt-85) REVERT: A 207 LYS cc_start: 0.6871 (ptmm) cc_final: 0.6130 (tppt) REVERT: A 211 GLU cc_start: 0.6513 (pm20) cc_final: 0.5747 (tp30) REVERT: B 63 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5742 (tm-30) REVERT: B 123 MET cc_start: 0.7206 (mpp) cc_final: 0.6947 (mtm) REVERT: B 156 ARG cc_start: 0.6880 (ttp-170) cc_final: 0.6243 (ttp-170) REVERT: B 175 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7054 (tpp) REVERT: B 240 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7025 (mt0) REVERT: C 80 GLU cc_start: 0.5860 (mm-30) cc_final: 0.5065 (mt-10) REVERT: C 126 GLU cc_start: 0.6624 (tp30) cc_final: 0.6101 (mp0) REVERT: C 240 GLN cc_start: 0.7308 (tp40) cc_final: 0.6165 (tm-30) REVERT: C 256 LYS cc_start: 0.7484 (mtpp) cc_final: 0.7192 (mmtp) REVERT: C 287 LYS cc_start: 0.6390 (mtpp) cc_final: 0.5293 (tptm) REVERT: D 17 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6285 (mp0) REVERT: D 36 GLU cc_start: 0.6981 (mt-10) cc_final: 0.5920 (mt-10) REVERT: D 63 GLU cc_start: 0.7411 (tp30) cc_final: 0.6314 (tt0) REVERT: D 71 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6363 (tp30) REVERT: D 89 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6577 (mptt) REVERT: D 112 ASN cc_start: 0.7267 (m110) cc_final: 0.7020 (m110) REVERT: D 138 MET cc_start: 0.8304 (mtp) cc_final: 0.8006 (mtm) REVERT: D 157 MET cc_start: 0.7224 (ptm) cc_final: 0.6844 (ptm) REVERT: D 177 ARG cc_start: 0.7643 (ttm110) cc_final: 0.7291 (ttp-110) REVERT: D 256 LYS cc_start: 0.7705 (mmtm) cc_final: 0.6990 (mppt) REVERT: D 285 GLU cc_start: 0.7912 (tt0) cc_final: 0.7217 (tt0) REVERT: E 60 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7020 (mt-10) REVERT: E 63 GLU cc_start: 0.7109 (tt0) cc_final: 0.6763 (tt0) REVERT: E 191 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: E 221 ASP cc_start: 0.7837 (p0) cc_final: 0.7248 (p0) REVERT: E 250 LYS cc_start: 0.6621 (mtpp) cc_final: 0.6067 (tttm) REVERT: E 282 GLU cc_start: 0.6986 (tp30) cc_final: 0.6466 (tm-30) REVERT: F 133 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.4162 (tmm-80) REVERT: F 191 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7057 (m-80) REVERT: F 240 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.7018 (mt0) REVERT: F 287 LYS cc_start: 0.6512 (mtpt) cc_final: 0.6010 (mttt) REVERT: G 64 ARG cc_start: 0.6311 (mtm110) cc_final: 0.5815 (mtp85) REVERT: G 97 LYS cc_start: 0.7136 (mppt) cc_final: 0.6813 (mmmt) REVERT: G 153 SER cc_start: 0.6838 (OUTLIER) cc_final: 0.6363 (m) REVERT: G 157 MET cc_start: 0.6719 (ttm) cc_final: 0.6427 (mtt) REVERT: G 191 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.6558 (m-80) REVERT: G 245 ASN cc_start: 0.7826 (m-40) cc_final: 0.7588 (m110) REVERT: G 266 PRO cc_start: 0.7198 (Cg_exo) cc_final: 0.6879 (Cg_endo) REVERT: H 15 ASP cc_start: 0.5490 (m-30) cc_final: 0.4947 (p0) REVERT: H 94 LYS cc_start: 0.6345 (mttt) cc_final: 0.6093 (mtmm) REVERT: H 203 SER cc_start: 0.5776 (t) cc_final: 0.5390 (m) REVERT: H 256 LYS cc_start: 0.6932 (mtmm) cc_final: 0.6302 (mmtt) REVERT: H 259 ARG cc_start: 0.4856 (mtp180) cc_final: 0.4516 (mtt180) REVERT: H 289 MET cc_start: 0.7115 (mmm) cc_final: 0.6426 (mtt) REVERT: I 190 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7525 (ttm-80) REVERT: I 191 GLN cc_start: 0.6989 (mm-40) cc_final: 0.6662 (mt0) REVERT: I 202 LYS cc_start: 0.6374 (mtpp) cc_final: 0.5715 (mtmm) REVERT: I 241 GLU cc_start: 0.5225 (mm-30) cc_final: 0.4967 (tt0) REVERT: I 276 SER cc_start: 0.8177 (t) cc_final: 0.7861 (p) REVERT: I 337 LYS cc_start: 0.6267 (mmpt) cc_final: 0.5842 (mttt) REVERT: I 370 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: I 383 ARG cc_start: 0.5682 (mtp85) cc_final: 0.4864 (ttt180) REVERT: I 408 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.5988 (ttm170) REVERT: I 450 ARG cc_start: 0.6019 (ttm170) cc_final: 0.4949 (ttt180) REVERT: I 484 LYS cc_start: 0.7093 (mmtt) cc_final: 0.6861 (mptt) REVERT: I 539 VAL cc_start: 0.6534 (OUTLIER) cc_final: 0.6228 (p) REVERT: I 555 ARG cc_start: 0.5708 (ttm110) cc_final: 0.5375 (ttm-80) REVERT: I 568 GLU cc_start: 0.6321 (mm-30) cc_final: 0.5861 (mm-30) REVERT: I 570 MET cc_start: 0.6074 (mmt) cc_final: 0.5766 (mtp) REVERT: J 39 ARG cc_start: 0.6258 (mtm-85) cc_final: 0.5298 (mtp180) REVERT: J 92 ASP cc_start: 0.5919 (OUTLIER) cc_final: 0.5464 (m-30) REVERT: K 4 ASP cc_start: 0.6602 (t0) cc_final: 0.6023 (t0) REVERT: K 26 GLU cc_start: 0.5656 (tp30) cc_final: 0.4927 (mt-10) REVERT: K 80 GLU cc_start: 0.5409 (tp30) cc_final: 0.4840 (mt-10) REVERT: K 83 MET cc_start: 0.4466 (mtp) cc_final: 0.4118 (mtt) REVERT: K 99 SER cc_start: 0.6196 (p) cc_final: 0.5897 (p) outliers start: 62 outliers final: 35 residues processed: 313 average time/residue: 2.5465 time to fit residues: 910.9649 Evaluate side-chains 323 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 287 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 191 PHE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 131 GLN Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 266 ASP Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 408 ARG Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 579 SER Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 69 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** G 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 395 ASN ** I 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24058 Z= 0.211 Angle : 0.574 7.113 32762 Z= 0.305 Chirality : 0.045 0.280 3646 Planarity : 0.005 0.067 4126 Dihedral : 15.171 174.214 3888 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 2.26 % Allowed : 14.88 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2809 helix: 1.84 (0.17), residues: 954 sheet: 0.35 (0.22), residues: 529 loop : -0.96 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS E 249 PHE 0.013 0.001 PHE I 593 TYR 0.013 0.001 TYR C 68 ARG 0.008 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6282 (tppp) cc_final: 0.5992 (mptp) REVERT: A 61 ARG cc_start: 0.7019 (mpp80) cc_final: 0.6765 (mtp180) REVERT: A 105 SER cc_start: 0.6833 (t) cc_final: 0.6430 (p) REVERT: A 140 LYS cc_start: 0.6901 (mmtm) cc_final: 0.6252 (tmmt) REVERT: A 199 ARG cc_start: 0.6074 (mpt-90) cc_final: 0.5308 (mtt-85) REVERT: A 207 LYS cc_start: 0.6860 (ptmm) cc_final: 0.6124 (tppt) REVERT: A 211 GLU cc_start: 0.6398 (pm20) cc_final: 0.5619 (tp30) REVERT: B 63 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5750 (tm-30) REVERT: B 123 MET cc_start: 0.7080 (mpp) cc_final: 0.6836 (mtm) REVERT: B 156 ARG cc_start: 0.6895 (ttp-170) cc_final: 0.6281 (ttp-170) REVERT: B 175 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.7023 (tpp) REVERT: B 240 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7044 (mt0) REVERT: C 80 GLU cc_start: 0.5816 (mm-30) cc_final: 0.5022 (mt-10) REVERT: C 126 GLU cc_start: 0.6621 (tp30) cc_final: 0.6084 (mp0) REVERT: C 240 GLN cc_start: 0.7278 (tp40) cc_final: 0.6131 (tm-30) REVERT: C 256 LYS cc_start: 0.7489 (mtpp) cc_final: 0.6395 (mtmt) REVERT: C 287 LYS cc_start: 0.6434 (mtpp) cc_final: 0.5333 (tptm) REVERT: D 17 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6260 (mp0) REVERT: D 36 GLU cc_start: 0.6966 (mt-10) cc_final: 0.5890 (mt-10) REVERT: D 63 GLU cc_start: 0.7292 (tp30) cc_final: 0.6182 (tt0) REVERT: D 71 GLU cc_start: 0.6737 (tm-30) cc_final: 0.6356 (tp30) REVERT: D 89 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6521 (mptt) REVERT: D 112 ASN cc_start: 0.7247 (m110) cc_final: 0.6820 (m110) REVERT: D 157 MET cc_start: 0.7162 (ptm) cc_final: 0.6788 (ptm) REVERT: D 177 ARG cc_start: 0.7630 (ttm110) cc_final: 0.6355 (tpp-160) REVERT: D 226 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7635 (tpp80) REVERT: D 256 LYS cc_start: 0.7705 (mmtm) cc_final: 0.7000 (mppt) REVERT: D 285 GLU cc_start: 0.7900 (tt0) cc_final: 0.7315 (tt0) REVERT: E 60 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7027 (mt-10) REVERT: E 63 GLU cc_start: 0.7069 (tt0) cc_final: 0.6718 (tt0) REVERT: E 191 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: E 221 ASP cc_start: 0.7734 (p0) cc_final: 0.7236 (p0) REVERT: E 250 LYS cc_start: 0.6579 (mtpp) cc_final: 0.6053 (tttm) REVERT: E 282 GLU cc_start: 0.6923 (tp30) cc_final: 0.6530 (tm-30) REVERT: F 133 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.4232 (tmm-80) REVERT: F 191 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7036 (m-80) REVERT: F 240 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6962 (mt0) REVERT: F 287 LYS cc_start: 0.6566 (mtpt) cc_final: 0.5307 (tmtt) REVERT: F 289 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7599 (mmm) REVERT: G 64 ARG cc_start: 0.6226 (mtm110) cc_final: 0.5872 (mtp85) REVERT: G 97 LYS cc_start: 0.7109 (mppt) cc_final: 0.6807 (mmmt) REVERT: G 153 SER cc_start: 0.6835 (OUTLIER) cc_final: 0.6340 (m) REVERT: G 157 MET cc_start: 0.6702 (ttm) cc_final: 0.6421 (mtt) REVERT: G 177 ARG cc_start: 0.7100 (ptp90) cc_final: 0.6519 (ptt-90) REVERT: G 191 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.6582 (m-80) REVERT: G 245 ASN cc_start: 0.7801 (m-40) cc_final: 0.7563 (m110) REVERT: G 266 PRO cc_start: 0.7188 (Cg_exo) cc_final: 0.6920 (Cg_endo) REVERT: H 15 ASP cc_start: 0.5389 (m-30) cc_final: 0.4959 (p0) REVERT: H 94 LYS cc_start: 0.6376 (mttt) cc_final: 0.6136 (mtmm) REVERT: H 191 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.6290 (m-80) REVERT: H 203 SER cc_start: 0.5753 (t) cc_final: 0.5366 (m) REVERT: H 256 LYS cc_start: 0.6924 (mtmm) cc_final: 0.6276 (mmtt) REVERT: H 289 MET cc_start: 0.7107 (mmm) cc_final: 0.6437 (mtt) REVERT: I 190 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7526 (ttm-80) REVERT: I 191 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6623 (mt0) REVERT: I 202 LYS cc_start: 0.6341 (mtpp) cc_final: 0.5688 (mtmm) REVERT: I 241 GLU cc_start: 0.5338 (mm-30) cc_final: 0.5008 (tt0) REVERT: I 276 SER cc_start: 0.8165 (t) cc_final: 0.7845 (p) REVERT: I 337 LYS cc_start: 0.6291 (mmpt) cc_final: 0.5876 (mttt) REVERT: I 383 ARG cc_start: 0.5670 (mtp85) cc_final: 0.4858 (ttt180) REVERT: I 408 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.5963 (ttm170) REVERT: I 450 ARG cc_start: 0.6007 (ttm170) cc_final: 0.4950 (ttt180) REVERT: I 484 LYS cc_start: 0.7120 (mmtt) cc_final: 0.6903 (mptt) REVERT: I 539 VAL cc_start: 0.6471 (OUTLIER) cc_final: 0.6176 (p) REVERT: I 555 ARG cc_start: 0.5745 (ttm110) cc_final: 0.5352 (ttm-80) REVERT: I 568 GLU cc_start: 0.6317 (mm-30) cc_final: 0.5891 (mm-30) REVERT: I 570 MET cc_start: 0.6111 (mmt) cc_final: 0.5776 (mtp) REVERT: J 39 ARG cc_start: 0.6245 (mtm-85) cc_final: 0.5321 (mtp180) REVERT: J 92 ASP cc_start: 0.5920 (OUTLIER) cc_final: 0.5457 (m-30) REVERT: K 4 ASP cc_start: 0.6576 (t0) cc_final: 0.5983 (t0) REVERT: K 26 GLU cc_start: 0.5564 (tp30) cc_final: 0.4760 (mt-10) REVERT: K 80 GLU cc_start: 0.5379 (tp30) cc_final: 0.4819 (mt-10) REVERT: K 83 MET cc_start: 0.4501 (mtp) cc_final: 0.4120 (mtt) REVERT: K 99 SER cc_start: 0.6005 (p) cc_final: 0.5708 (p) outliers start: 54 outliers final: 29 residues processed: 312 average time/residue: 2.5870 time to fit residues: 921.9745 Evaluate side-chains 323 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 287 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 191 PHE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 131 GLN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 408 ARG Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 579 SER Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 69 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 0.6980 chunk 239 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 395 ASN ** I 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24058 Z= 0.235 Angle : 0.582 7.609 32762 Z= 0.309 Chirality : 0.046 0.280 3646 Planarity : 0.005 0.071 4126 Dihedral : 15.207 174.527 3888 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.13 % Allowed : 14.96 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.16), residues: 2809 helix: 1.91 (0.17), residues: 948 sheet: 0.35 (0.23), residues: 525 loop : -0.96 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 57 HIS 0.004 0.001 HIS E 249 PHE 0.015 0.001 PHE I 593 TYR 0.014 0.002 TYR C 68 ARG 0.011 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Evaluate side-chains 329 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 278 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6309 (tppp) cc_final: 0.6016 (mptp) REVERT: A 61 ARG cc_start: 0.7019 (mpp80) cc_final: 0.6758 (mtp180) REVERT: A 105 SER cc_start: 0.6864 (t) cc_final: 0.6451 (p) REVERT: A 199 ARG cc_start: 0.6137 (mpt-90) cc_final: 0.5385 (mtt-85) REVERT: A 207 LYS cc_start: 0.6862 (ptmm) cc_final: 0.6129 (tppt) REVERT: A 211 GLU cc_start: 0.6500 (pm20) cc_final: 0.5737 (tp30) REVERT: B 63 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5728 (tm-30) REVERT: B 123 MET cc_start: 0.7088 (mpp) cc_final: 0.6837 (mtm) REVERT: B 156 ARG cc_start: 0.6805 (ttp-170) cc_final: 0.6468 (ttp80) REVERT: B 175 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.7041 (tpp) REVERT: B 240 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7088 (mt0) REVERT: C 80 GLU cc_start: 0.5815 (mm-30) cc_final: 0.5026 (mt-10) REVERT: C 126 GLU cc_start: 0.6625 (tp30) cc_final: 0.6076 (mp0) REVERT: C 240 GLN cc_start: 0.7319 (tp40) cc_final: 0.6162 (tm-30) REVERT: C 256 LYS cc_start: 0.7463 (mtpp) cc_final: 0.6378 (mtmt) REVERT: C 287 LYS cc_start: 0.6474 (mtpp) cc_final: 0.5357 (tptm) REVERT: D 17 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6267 (mp0) REVERT: D 36 GLU cc_start: 0.6970 (mt-10) cc_final: 0.5903 (mt-10) REVERT: D 63 GLU cc_start: 0.7263 (tp30) cc_final: 0.6246 (tt0) REVERT: D 71 GLU cc_start: 0.6757 (tm-30) cc_final: 0.6369 (tp30) REVERT: D 89 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6519 (mptt) REVERT: D 112 ASN cc_start: 0.7241 (m110) cc_final: 0.6805 (m110) REVERT: D 138 MET cc_start: 0.8279 (mtp) cc_final: 0.8015 (mtm) REVERT: D 157 MET cc_start: 0.7162 (ptm) cc_final: 0.6784 (ptm) REVERT: D 177 ARG cc_start: 0.7665 (ttm110) cc_final: 0.6374 (tpp-160) REVERT: D 226 ARG cc_start: 0.7861 (tpp80) cc_final: 0.7638 (tpp80) REVERT: D 256 LYS cc_start: 0.7703 (mmtm) cc_final: 0.7007 (mppt) REVERT: D 285 GLU cc_start: 0.7910 (tt0) cc_final: 0.7327 (tt0) REVERT: E 60 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6960 (mt-10) REVERT: E 63 GLU cc_start: 0.7055 (tt0) cc_final: 0.6701 (tt0) REVERT: E 191 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: E 221 ASP cc_start: 0.7737 (p0) cc_final: 0.7238 (p0) REVERT: E 250 LYS cc_start: 0.6623 (mtpp) cc_final: 0.6055 (tttm) REVERT: E 282 GLU cc_start: 0.6915 (tp30) cc_final: 0.6504 (tm-30) REVERT: F 126 GLU cc_start: 0.6400 (mt-10) cc_final: 0.6033 (mm-30) REVERT: F 133 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.4155 (tmm-80) REVERT: F 191 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7028 (m-80) REVERT: F 240 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6968 (mt0) REVERT: F 287 LYS cc_start: 0.6585 (mtpt) cc_final: 0.5336 (tmtt) REVERT: F 289 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7545 (mmm) REVERT: G 64 ARG cc_start: 0.6236 (mtm110) cc_final: 0.5722 (mtp85) REVERT: G 97 LYS cc_start: 0.7110 (mppt) cc_final: 0.6804 (mmmt) REVERT: G 153 SER cc_start: 0.6841 (OUTLIER) cc_final: 0.6345 (m) REVERT: G 157 MET cc_start: 0.6642 (ttm) cc_final: 0.6392 (mtt) REVERT: G 177 ARG cc_start: 0.7175 (ptp90) cc_final: 0.6602 (ptt-90) REVERT: G 191 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.6587 (m-80) REVERT: G 245 ASN cc_start: 0.7773 (m-40) cc_final: 0.7539 (m110) REVERT: G 266 PRO cc_start: 0.7288 (Cg_exo) cc_final: 0.6969 (Cg_endo) REVERT: H 15 ASP cc_start: 0.5357 (m-30) cc_final: 0.4954 (p0) REVERT: H 91 GLU cc_start: 0.6952 (mm-30) cc_final: 0.5956 (mt-10) REVERT: H 94 LYS cc_start: 0.6390 (mttt) cc_final: 0.5985 (mtmm) REVERT: H 191 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.6304 (m-80) REVERT: H 203 SER cc_start: 0.5783 (t) cc_final: 0.5412 (m) REVERT: H 229 MET cc_start: 0.6099 (mtp) cc_final: 0.5895 (mtm) REVERT: H 256 LYS cc_start: 0.6927 (mtmm) cc_final: 0.6278 (mmtt) REVERT: H 289 MET cc_start: 0.7141 (mmm) cc_final: 0.6498 (mtt) REVERT: I 190 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7524 (ttm-80) REVERT: I 191 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6713 (mt0) REVERT: I 202 LYS cc_start: 0.6344 (mtpp) cc_final: 0.5659 (mtmm) REVERT: I 241 GLU cc_start: 0.5337 (mm-30) cc_final: 0.5011 (tt0) REVERT: I 266 ASP cc_start: 0.7322 (t70) cc_final: 0.7011 (t0) REVERT: I 276 SER cc_start: 0.8166 (t) cc_final: 0.7841 (p) REVERT: I 337 LYS cc_start: 0.6295 (mmpt) cc_final: 0.5894 (mttt) REVERT: I 370 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6340 (mp0) REVERT: I 383 ARG cc_start: 0.5688 (mtp85) cc_final: 0.4865 (ttt180) REVERT: I 408 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.5956 (ttm170) REVERT: I 450 ARG cc_start: 0.5946 (ttm170) cc_final: 0.4952 (ttt180) REVERT: I 484 LYS cc_start: 0.7120 (mmtt) cc_final: 0.6900 (mptt) REVERT: I 539 VAL cc_start: 0.6493 (OUTLIER) cc_final: 0.6196 (p) REVERT: I 555 ARG cc_start: 0.5735 (ttm110) cc_final: 0.5344 (ttm-80) REVERT: I 568 GLU cc_start: 0.6306 (mm-30) cc_final: 0.5882 (mm-30) REVERT: I 570 MET cc_start: 0.6055 (mmt) cc_final: 0.5720 (mtp) REVERT: J 39 ARG cc_start: 0.6244 (mtm-85) cc_final: 0.5306 (mtp180) REVERT: J 92 ASP cc_start: 0.5927 (OUTLIER) cc_final: 0.5467 (m-30) REVERT: K 4 ASP cc_start: 0.6579 (t0) cc_final: 0.5954 (t0) REVERT: K 26 GLU cc_start: 0.5662 (tp30) cc_final: 0.4801 (mt-10) REVERT: K 80 GLU cc_start: 0.5385 (tp30) cc_final: 0.4835 (mt-10) REVERT: K 83 MET cc_start: 0.4483 (mtp) cc_final: 0.4116 (mtt) REVERT: K 99 SER cc_start: 0.6012 (p) cc_final: 0.5719 (p) outliers start: 51 outliers final: 30 residues processed: 310 average time/residue: 2.6280 time to fit residues: 939.6694 Evaluate side-chains 323 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 287 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 191 PHE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 131 GLN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 408 ARG Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 579 SER Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 69 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN G 245 ASN I 395 ASN ** I 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24058 Z= 0.271 Angle : 0.601 7.514 32762 Z= 0.321 Chirality : 0.047 0.285 3646 Planarity : 0.005 0.077 4126 Dihedral : 15.280 175.322 3888 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.17 % Allowed : 15.00 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.16), residues: 2809 helix: 1.84 (0.17), residues: 948 sheet: 0.41 (0.22), residues: 524 loop : -1.01 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 57 HIS 0.005 0.001 HIS J 111 PHE 0.015 0.002 PHE I 593 TYR 0.015 0.002 TYR C 68 ARG 0.013 0.000 ARG F 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 280 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6414 (tppp) cc_final: 0.6121 (mptp) REVERT: A 61 ARG cc_start: 0.7021 (mpp80) cc_final: 0.6755 (mtp180) REVERT: A 105 SER cc_start: 0.6903 (t) cc_final: 0.6499 (p) REVERT: A 140 LYS cc_start: 0.6829 (mmtm) cc_final: 0.6144 (tmmt) REVERT: A 199 ARG cc_start: 0.6141 (mpt-90) cc_final: 0.5381 (mtt-85) REVERT: A 207 LYS cc_start: 0.6868 (ptmm) cc_final: 0.6145 (tppt) REVERT: A 211 GLU cc_start: 0.6502 (pm20) cc_final: 0.5752 (tp30) REVERT: B 63 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5722 (tm-30) REVERT: B 123 MET cc_start: 0.7159 (mpp) cc_final: 0.6932 (mtm) REVERT: B 156 ARG cc_start: 0.6850 (ttp-170) cc_final: 0.6502 (ttp80) REVERT: B 175 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.7060 (tpp) REVERT: B 240 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7036 (mt0) REVERT: C 80 GLU cc_start: 0.5793 (mm-30) cc_final: 0.4997 (mt-10) REVERT: C 126 GLU cc_start: 0.6596 (tp30) cc_final: 0.6071 (mp0) REVERT: C 240 GLN cc_start: 0.7308 (tp40) cc_final: 0.6155 (tm-30) REVERT: C 256 LYS cc_start: 0.7466 (mtpp) cc_final: 0.6382 (mtmt) REVERT: C 287 LYS cc_start: 0.6471 (mtpp) cc_final: 0.5355 (tptm) REVERT: D 17 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6259 (mp0) REVERT: D 36 GLU cc_start: 0.6978 (mt-10) cc_final: 0.5911 (mt-10) REVERT: D 63 GLU cc_start: 0.7315 (tp30) cc_final: 0.6201 (tt0) REVERT: D 71 GLU cc_start: 0.6778 (tm-30) cc_final: 0.6363 (tp30) REVERT: D 89 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6563 (mptt) REVERT: D 112 ASN cc_start: 0.7302 (m110) cc_final: 0.7045 (m110) REVERT: D 157 MET cc_start: 0.7174 (ptm) cc_final: 0.6817 (ptm) REVERT: D 177 ARG cc_start: 0.7597 (ttm110) cc_final: 0.6348 (tpp-160) REVERT: D 256 LYS cc_start: 0.7703 (mmtm) cc_final: 0.7007 (mppt) REVERT: D 285 GLU cc_start: 0.7924 (tt0) cc_final: 0.7297 (tt0) REVERT: E 60 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6937 (mt-10) REVERT: E 63 GLU cc_start: 0.7061 (tt0) cc_final: 0.6707 (tt0) REVERT: E 191 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: E 221 ASP cc_start: 0.7761 (p0) cc_final: 0.7306 (p0) REVERT: E 250 LYS cc_start: 0.6646 (mtpp) cc_final: 0.6071 (tttm) REVERT: E 282 GLU cc_start: 0.6913 (tp30) cc_final: 0.6535 (tm-30) REVERT: F 133 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.4178 (tmm-80) REVERT: F 191 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7050 (m-80) REVERT: F 240 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6978 (mt0) REVERT: F 287 LYS cc_start: 0.6564 (mtpt) cc_final: 0.5293 (tmtt) REVERT: F 289 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7596 (mmm) REVERT: G 64 ARG cc_start: 0.6237 (mtm110) cc_final: 0.5842 (mtp85) REVERT: G 97 LYS cc_start: 0.7316 (mppt) cc_final: 0.7010 (mmmt) REVERT: G 153 SER cc_start: 0.6831 (OUTLIER) cc_final: 0.6376 (m) REVERT: G 157 MET cc_start: 0.6593 (ttm) cc_final: 0.6345 (mtt) REVERT: G 177 ARG cc_start: 0.7174 (ptp90) cc_final: 0.6628 (ptt-90) REVERT: G 191 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: G 245 ASN cc_start: 0.7741 (m110) cc_final: 0.7495 (m110) REVERT: G 266 PRO cc_start: 0.7268 (Cg_exo) cc_final: 0.6943 (Cg_endo) REVERT: H 15 ASP cc_start: 0.5380 (m-30) cc_final: 0.4979 (p0) REVERT: H 91 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6019 (mt-10) REVERT: H 94 LYS cc_start: 0.6500 (mttt) cc_final: 0.6039 (mtmm) REVERT: H 191 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.6253 (m-80) REVERT: H 203 SER cc_start: 0.5777 (t) cc_final: 0.5420 (m) REVERT: H 229 MET cc_start: 0.6120 (mtp) cc_final: 0.5917 (mtm) REVERT: H 256 LYS cc_start: 0.6927 (mtmm) cc_final: 0.6273 (mmtt) REVERT: H 289 MET cc_start: 0.7102 (mmm) cc_final: 0.6506 (mtt) REVERT: I 190 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7517 (ttm-80) REVERT: I 191 GLN cc_start: 0.7105 (mm-40) cc_final: 0.6809 (mt0) REVERT: I 202 LYS cc_start: 0.6340 (mtpp) cc_final: 0.5660 (mtmm) REVERT: I 241 GLU cc_start: 0.5312 (mm-30) cc_final: 0.5051 (tt0) REVERT: I 266 ASP cc_start: 0.7229 (t70) cc_final: 0.6916 (t0) REVERT: I 276 SER cc_start: 0.8158 (t) cc_final: 0.7825 (p) REVERT: I 337 LYS cc_start: 0.6303 (mmpt) cc_final: 0.5889 (mttt) REVERT: I 370 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: I 383 ARG cc_start: 0.5701 (mtp85) cc_final: 0.4861 (ttt180) REVERT: I 408 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.5969 (ttm170) REVERT: I 450 ARG cc_start: 0.5947 (ttm170) cc_final: 0.4913 (ttt180) REVERT: I 484 LYS cc_start: 0.7124 (mmtt) cc_final: 0.6895 (mptt) REVERT: I 539 VAL cc_start: 0.6511 (OUTLIER) cc_final: 0.6216 (p) REVERT: I 555 ARG cc_start: 0.5740 (ttm110) cc_final: 0.5342 (ttm-80) REVERT: I 568 GLU cc_start: 0.6301 (mm-30) cc_final: 0.5868 (mm-30) REVERT: I 570 MET cc_start: 0.6005 (mmt) cc_final: 0.5659 (mtp) REVERT: J 39 ARG cc_start: 0.6271 (mtm-85) cc_final: 0.5305 (mtp180) REVERT: J 92 ASP cc_start: 0.5914 (OUTLIER) cc_final: 0.5460 (m-30) REVERT: K 4 ASP cc_start: 0.6581 (t0) cc_final: 0.5951 (t0) REVERT: K 26 GLU cc_start: 0.5631 (tp30) cc_final: 0.4942 (mt-10) REVERT: K 80 GLU cc_start: 0.5375 (tp30) cc_final: 0.4823 (mt-10) REVERT: K 83 MET cc_start: 0.4472 (mtp) cc_final: 0.4084 (mtt) REVERT: K 99 SER cc_start: 0.6154 (p) cc_final: 0.5857 (p) outliers start: 52 outliers final: 29 residues processed: 311 average time/residue: 2.5327 time to fit residues: 900.7866 Evaluate side-chains 322 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 287 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 191 PHE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 131 GLN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 408 ARG Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 579 SER Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 69 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 198 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 395 ASN ** I 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.153749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118108 restraints weight = 66563.392| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.51 r_work: 0.3152 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24058 Z= 0.193 Angle : 0.559 7.656 32762 Z= 0.295 Chirality : 0.045 0.260 3646 Planarity : 0.005 0.074 4126 Dihedral : 15.192 177.304 3888 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.88 % Allowed : 15.42 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.16), residues: 2809 helix: 1.99 (0.17), residues: 954 sheet: 0.38 (0.22), residues: 529 loop : -0.93 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS E 249 PHE 0.013 0.001 PHE I 593 TYR 0.013 0.001 TYR F 68 ARG 0.014 0.000 ARG F 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14527.49 seconds wall clock time: 248 minutes 39.86 seconds (14919.86 seconds total)