Starting phenix.real_space_refine on Mon Jun 23 01:00:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fd3_29001/06_2025/8fd3_29001.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fd3_29001/06_2025/8fd3_29001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fd3_29001/06_2025/8fd3_29001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fd3_29001/06_2025/8fd3_29001.map" model { file = "/net/cci-nas-00/data/ceres_data/8fd3_29001/06_2025/8fd3_29001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fd3_29001/06_2025/8fd3_29001.cif" } resolution = 3.12 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= 0.013 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 408 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 85 5.49 5 S 94 5.16 5 C 16536 2.51 5 N 4460 2.21 5 O 5075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.49s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26250 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1745 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "B" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1727 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2345 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 10, 'TRANS': 277} Chain breaks: 1 Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2351 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Chain: "H" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2420 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 1 Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4147 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 10, 'rna3p_pur': 18, 'rna3p_pyr': 20} Link IDs: {'rna2p': 25, 'rna3p': 37} Chain: "N" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "O" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 15.03, per 1000 atoms: 0.57 Number of scatterers: 26250 At special positions: 0 Unit cell: (101.184, 115.94, 198.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 85 15.00 O 5075 8.00 N 4460 7.00 C 16536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 3.1 seconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5590 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 51 sheets defined 39.4% alpha, 23.4% beta 12 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 9.74 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.584A pdb=" N TRP A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 40 through 45 removed outlier: 4.325A pdb=" N GLU B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.817A pdb=" N MET B 204 " --> pdb=" O ARG B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.618A pdb=" N THR B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.729A pdb=" N ILE C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 196 through 206 removed outlier: 3.572A pdb=" N MET C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.645A pdb=" N SER C 214 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.552A pdb=" N GLY C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.661A pdb=" N ASP C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 318 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 56 through 71 removed outlier: 3.576A pdb=" N ILE D 60 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.522A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.784A pdb=" N GLY D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 277 through 284 removed outlier: 4.084A pdb=" N ASP D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.598A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.521A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.883A pdb=" N GLY E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 277 through 284 removed outlier: 4.092A pdb=" N ASP E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 301 through 318 Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.643A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.772A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.826A pdb=" N GLY F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.957A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 56 through 71 removed outlier: 3.748A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 105 Processing helix chain 'G' and resid 189 through 191 No H-bonds generated for 'chain 'G' and resid 189 through 191' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 206 removed outlier: 3.644A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 277 through 284 removed outlier: 4.009A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 318 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 56 through 71 removed outlier: 3.531A pdb=" N ILE H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 Processing helix chain 'H' and resid 109 through 112 Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 206 removed outlier: 3.573A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.679A pdb=" N GLY H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 270 No H-bonds generated for 'chain 'H' and resid 268 through 270' Processing helix chain 'H' and resid 277 through 285 removed outlier: 3.921A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 removed outlier: 3.604A pdb=" N LYS H 295 " --> pdb=" O PRO H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 317 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.747A pdb=" N ILE I 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.585A pdb=" N ALA I 70 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 113 Processing helix chain 'I' and resid 116 through 118 No H-bonds generated for 'chain 'I' and resid 116 through 118' Processing helix chain 'I' and resid 148 through 157 removed outlier: 5.400A pdb=" N ALA I 153 " --> pdb=" O HIS I 149 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU I 154 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 187 removed outlier: 3.505A pdb=" N GLN I 187 " --> pdb=" O ALA I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 238 through 250 Processing helix chain 'I' and resid 251 through 252 No H-bonds generated for 'chain 'I' and resid 251 through 252' Processing helix chain 'I' and resid 253 through 256 Processing helix chain 'I' and resid 261 through 270 removed outlier: 3.502A pdb=" N ALA I 265 " --> pdb=" O SER I 261 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR I 270 " --> pdb=" O GLY I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 Processing helix chain 'I' and resid 361 through 367 removed outlier: 3.668A pdb=" N LYS I 365 " --> pdb=" O ASN I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 382 removed outlier: 4.030A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU I 379 " --> pdb=" O LEU I 375 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE I 380 " --> pdb=" O PHE I 376 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER I 381 " --> pdb=" O ASN I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 392 Processing helix chain 'I' and resid 397 through 421 removed outlier: 3.686A pdb=" N ILE I 417 " --> pdb=" O ASN I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 removed outlier: 3.834A pdb=" N LYS I 432 " --> pdb=" O PRO I 428 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS I 443 " --> pdb=" O GLU I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 460 Processing helix chain 'I' and resid 463 through 469 Processing helix chain 'I' and resid 469 through 480 Processing helix chain 'I' and resid 481 through 495 Processing helix chain 'J' and resid 6 through 33 Processing helix chain 'J' and resid 41 through 53 Processing helix chain 'J' and resid 58 through 72 removed outlier: 5.964A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 81 Processing helix chain 'J' and resid 81 through 91 removed outlier: 3.716A pdb=" N ILE J 85 " --> pdb=" O HIS J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 107 Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.526A pdb=" N LYS J 111 " --> pdb=" O TYR J 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 41 through 54 removed outlier: 3.817A pdb=" N VAL K 45 " --> pdb=" O ILE K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 73 removed outlier: 3.604A pdb=" N GLY K 73 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 81 Processing helix chain 'K' and resid 82 through 91 Processing helix chain 'K' and resid 93 through 107 Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.768A pdb=" N CYS L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.805A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 Processing helix chain 'L' and resid 81 through 92 Processing helix chain 'L' and resid 93 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.913A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 13.522A pdb=" N LEU A 57 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N ARG A 165 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG A 186 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 150 removed outlier: 6.588A pdb=" N PHE A 13 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER A 97 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.025A pdb=" N ARG B 19 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 100 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.358A pdb=" N LEU B 109 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N GLU B 10 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N LYS B 107 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N VAL B 12 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N ASP B 105 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150 removed outlier: 5.582A pdb=" N VAL B 179 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG B 118 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 181 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR B 116 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.659A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.659A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR C 180 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR C 15 " --> pdb=" O TRP C 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP C 230 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR C 17 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE C 228 " --> pdb=" O TYR C 17 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 19 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU C 226 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 21 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 276 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.661A pdb=" N GLY C 25 " --> pdb=" O THR C 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB3, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB4, first strand: chain 'C' and resid 155 through 160 removed outlier: 3.545A pdb=" N SER C 169 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB6, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.648A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.648A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR D 180 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.541A pdb=" N GLY D 25 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.996A pdb=" N THR D 39 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AC2, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AC3, first strand: chain 'D' and resid 242 through 244 Processing sheet with id=AC4, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.451A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.451A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'E' and resid 106 through 107 Processing sheet with id=AC9, first strand: chain 'E' and resid 242 through 244 Processing sheet with id=AD1, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.720A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.720A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.531A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD6, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.520A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.520A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY G 276 " --> pdb=" O TYR G 299 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AD9, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AE1, first strand: chain 'G' and resid 77 through 80 removed outlier: 3.633A pdb=" N ILE G 85 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 106 through 107 removed outlier: 3.673A pdb=" N PHE G 106 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AE4, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.583A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.583A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR H 15 " --> pdb=" O TRP H 230 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TRP H 230 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE7, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AE8, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AE9, first strand: chain 'H' and resid 105 through 107 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.569A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AF3, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.476A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AF5, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.255A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 329 through 333 1110 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 10.10 Time building geometry restraints manager: 7.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7329 1.33 - 1.45: 5312 1.45 - 1.57: 14112 1.57 - 1.69: 167 1.69 - 1.81: 149 Bond restraints: 27069 Sorted by residual: bond pdb=" C1' DA O 12 " pdb=" N9 DA O 12 " ideal model delta sigma weight residual 1.460 1.403 0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" CA SER F 28 " pdb=" C SER F 28 " ideal model delta sigma weight residual 1.532 1.502 0.030 1.41e-02 5.03e+03 4.62e+00 bond pdb=" CA SER E 28 " pdb=" C SER E 28 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.61e-02 3.86e+03 2.33e+00 bond pdb=" CA LYS G 250 " pdb=" CB LYS G 250 " ideal model delta sigma weight residual 1.526 1.553 -0.027 1.76e-02 3.23e+03 2.27e+00 bond pdb=" O5' U M 34 " pdb=" C5' U M 34 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 1.91e+00 ... (remaining 27064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 36568 2.36 - 4.73: 333 4.73 - 7.09: 40 7.09 - 9.46: 7 9.46 - 11.82: 2 Bond angle restraints: 36950 Sorted by residual: angle pdb=" N SER E 28 " pdb=" CA SER E 28 " pdb=" C SER E 28 " ideal model delta sigma weight residual 110.44 103.41 7.03 1.20e+00 6.94e-01 3.43e+01 angle pdb=" N LEU E 29 " pdb=" CA LEU E 29 " pdb=" C LEU E 29 " ideal model delta sigma weight residual 111.03 117.42 -6.39 1.11e+00 8.12e-01 3.31e+01 angle pdb=" N TYR H 244 " pdb=" CA TYR H 244 " pdb=" C TYR H 244 " ideal model delta sigma weight residual 114.56 108.27 6.29 1.27e+00 6.20e-01 2.45e+01 angle pdb=" C ARG E 35 " pdb=" CA ARG E 35 " pdb=" CB ARG E 35 " ideal model delta sigma weight residual 117.23 111.04 6.19 1.36e+00 5.41e-01 2.07e+01 angle pdb=" N LEU A 198 " pdb=" CA LEU A 198 " pdb=" C LEU A 198 " ideal model delta sigma weight residual 111.40 106.13 5.27 1.22e+00 6.72e-01 1.86e+01 ... (remaining 36945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 15374 35.84 - 71.68: 737 71.68 - 107.52: 42 107.52 - 143.37: 1 143.37 - 179.21: 5 Dihedral angle restraints: 16159 sinusoidal: 7434 harmonic: 8725 Sorted by residual: dihedral pdb=" O4' U M 60 " pdb=" C1' U M 60 " pdb=" N1 U M 60 " pdb=" C2 U M 60 " ideal model delta sinusoidal sigma weight residual 200.00 44.62 155.38 1 1.50e+01 4.44e-03 8.15e+01 dihedral pdb=" O4' U M 20 " pdb=" C1' U M 20 " pdb=" N1 U M 20 " pdb=" C2 U M 20 " ideal model delta sinusoidal sigma weight residual 200.00 73.27 126.73 1 1.50e+01 4.44e-03 6.82e+01 dihedral pdb=" O4' C M 50 " pdb=" C1' C M 50 " pdb=" N1 C M 50 " pdb=" C2 C M 50 " ideal model delta sinusoidal sigma weight residual -128.00 51.21 -179.21 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2852 0.036 - 0.073: 779 0.073 - 0.109: 255 0.109 - 0.146: 59 0.146 - 0.182: 12 Chirality restraints: 3957 Sorted by residual: chirality pdb=" CA PRO F 247 " pdb=" N PRO F 247 " pdb=" C PRO F 247 " pdb=" CB PRO F 247 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA TYR I 334 " pdb=" N TYR I 334 " pdb=" C TYR I 334 " pdb=" CB TYR I 334 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" C1' U M 20 " pdb=" O4' U M 20 " pdb=" C2' U M 20 " pdb=" N1 U M 20 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 3954 not shown) Planarity restraints: 4421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " 0.060 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO F 247 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C PHE J 61 " -0.064 2.00e-02 2.50e+03 pdb=" O PHE J 61 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS J 62 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 209 " 0.042 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO B 210 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " 0.036 5.00e-02 4.00e+02 ... (remaining 4418 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 823 2.69 - 3.24: 25236 3.24 - 3.79: 43362 3.79 - 4.35: 59913 4.35 - 4.90: 96751 Nonbonded interactions: 226085 Sorted by model distance: nonbonded pdb=" O LEU B 184 " pdb=" ND2 ASN B 185 " model vdw 2.137 3.120 nonbonded pdb=" N GLU G 257 " pdb=" OE1 GLU G 257 " model vdw 2.194 3.120 nonbonded pdb=" OG1 THR A 15 " pdb=" NE2 GLN A 143 " model vdw 2.202 3.120 nonbonded pdb=" N GLU J 83 " pdb=" OE1 GLU J 83 " model vdw 2.206 3.120 nonbonded pdb=" OG1 THR E 19 " pdb=" O SER E 239 " model vdw 2.220 3.040 ... (remaining 226080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = (chain 'G' and (resid 12 through 109 or resid 133 through 319)) selection = (chain 'H' and (resid 12 through 109 or resid 133 through 319)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 64.820 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27069 Z= 0.137 Angle : 0.571 11.822 36950 Z= 0.310 Chirality : 0.040 0.182 3957 Planarity : 0.004 0.092 4421 Dihedral : 18.479 179.206 10569 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.40 % Favored : 94.29 % Rotamer: Outliers : 2.76 % Allowed : 20.76 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2943 helix: 1.67 (0.17), residues: 1013 sheet: -0.65 (0.22), residues: 596 loop : -0.22 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 488 HIS 0.004 0.001 HIS I 106 PHE 0.016 0.001 PHE J 26 TYR 0.020 0.001 TYR I 334 ARG 0.009 0.000 ARG I 96 Details of bonding type rmsd hydrogen bonds : bond 0.16765 ( 1077) hydrogen bonds : angle 6.71669 ( 3165) covalent geometry : bond 0.00277 (27069) covalent geometry : angle 0.57078 (36950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 457 time to evaluate : 3.190 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 39 MET cc_start: 0.5729 (tmm) cc_final: 0.5497 (tmm) REVERT: B 204 MET cc_start: 0.6695 (mtp) cc_final: 0.6236 (ptt) REVERT: C 42 GLN cc_start: 0.6925 (tt0) cc_final: 0.6538 (tt0) REVERT: C 71 GLN cc_start: 0.8218 (tp40) cc_final: 0.7780 (mm110) REVERT: C 84 HIS cc_start: 0.6689 (m90) cc_final: 0.5936 (t70) REVERT: D 134 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7793 (p0) REVERT: D 142 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7684 (ttp) REVERT: E 108 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6776 (tt) REVERT: E 305 MET cc_start: 0.7683 (ttp) cc_final: 0.7458 (ttt) REVERT: F 15 TYR cc_start: 0.7257 (m-80) cc_final: 0.6847 (m-80) REVERT: F 29 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6564 (mt) REVERT: F 187 ASP cc_start: 0.7583 (t0) cc_final: 0.7359 (t70) REVERT: G 78 VAL cc_start: 0.8948 (t) cc_final: 0.8716 (m) REVERT: G 137 MET cc_start: 0.7318 (tmm) cc_final: 0.6682 (tmm) REVERT: H 45 TYR cc_start: 0.6114 (m-80) cc_final: 0.5886 (m-80) REVERT: I 157 CYS cc_start: 0.3626 (m) cc_final: 0.2823 (m) REVERT: I 347 LEU cc_start: 0.3980 (OUTLIER) cc_final: 0.3671 (mt) REVERT: I 382 ASN cc_start: 0.3665 (m-40) cc_final: 0.3123 (m-40) REVERT: J 52 LEU cc_start: 0.8653 (mt) cc_final: 0.8417 (mm) REVERT: L 102 LEU cc_start: 0.7780 (mt) cc_final: 0.7550 (mt) outliers start: 73 outliers final: 20 residues processed: 515 average time/residue: 0.4526 time to fit residues: 356.1724 Evaluate side-chains 259 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain J residue 41 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 270 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN C 47 ASN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN E 256 GLN E 283 GLN F 30 ASN F 31 HIS F 76 ASN F 171 HIS F 181 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 GLN G 218 ASN G 283 GLN H 30 ASN H 84 HIS H 256 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 HIS ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.140805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.105581 restraints weight = 56607.696| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 3.37 r_work: 0.3526 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.152 27069 Z= 0.298 Angle : 0.748 23.031 36950 Z= 0.390 Chirality : 0.048 0.251 3957 Planarity : 0.006 0.083 4421 Dihedral : 16.884 178.918 4551 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.64 % Favored : 93.99 % Rotamer: Outliers : 4.20 % Allowed : 18.49 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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: -0.10 (0.16), residues: 2943 helix: 0.90 (0.16), residues: 1030 sheet: -0.70 (0.23), residues: 548 loop : -0.43 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 176 HIS 0.008 0.002 HIS H 52 PHE 0.017 0.002 PHE E 194 TYR 0.029 0.002 TYR I 40 ARG 0.028 0.001 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 1077) hydrogen bonds : angle 5.26998 ( 3165) covalent geometry : bond 0.00674 (27069) covalent geometry : angle 0.74782 (36950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 247 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7678 (tt0) cc_final: 0.7452 (tt0) REVERT: A 84 HIS cc_start: 0.8251 (t70) cc_final: 0.7694 (t-90) REVERT: B 123 LYS cc_start: 0.5449 (OUTLIER) cc_final: 0.4839 (mtpp) REVERT: C 42 GLN cc_start: 0.7362 (tt0) cc_final: 0.7081 (tt0) REVERT: C 261 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: D 261 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7952 (mm-30) REVERT: E 77 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8134 (ttp80) REVERT: E 83 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8319 (mp0) REVERT: E 137 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7491 (tmm) REVERT: E 261 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: E 305 MET cc_start: 0.8512 (ttp) cc_final: 0.8197 (ttt) REVERT: F 15 TYR cc_start: 0.8414 (m-80) cc_final: 0.8206 (m-80) REVERT: F 42 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: F 136 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7490 (mmm160) REVERT: G 33 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7643 (mp) REVERT: G 137 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7240 (tmm) REVERT: G 224 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8011 (t0) REVERT: H 142 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7608 (mtp) REVERT: H 248 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8045 (mptt) REVERT: H 251 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7755 (mt-10) REVERT: H 283 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: I 139 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6545 (t80) REVERT: I 157 CYS cc_start: 0.4120 (m) cc_final: 0.3559 (m) REVERT: I 303 MET cc_start: 0.8178 (mmm) cc_final: 0.7844 (mmm) REVERT: J 47 ARG cc_start: 0.8801 (ttm110) cc_final: 0.8347 (ttm110) REVERT: K 7 GLU cc_start: 0.7022 (pm20) cc_final: 0.6489 (pm20) REVERT: K 43 LYS cc_start: 0.7600 (pttm) cc_final: 0.7372 (mtpt) REVERT: K 95 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8141 (mp10) outliers start: 111 outliers final: 35 residues processed: 343 average time/residue: 0.4149 time to fit residues: 218.7780 Evaluate side-chains 248 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 212 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 162 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN D 283 GLN E 283 GLN F 30 ASN F 181 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN G 13 ASN G 42 GLN H 42 GLN H 134 ASN H 284 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.142504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.107511 restraints weight = 56772.347| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.23 r_work: 0.3584 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27069 Z= 0.129 Angle : 0.583 16.548 36950 Z= 0.306 Chirality : 0.041 0.210 3957 Planarity : 0.004 0.083 4421 Dihedral : 16.595 178.482 4520 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.06 % Favored : 94.67 % Rotamer: Outliers : 2.34 % Allowed : 19.21 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.16), residues: 2943 helix: 1.19 (0.16), residues: 1030 sheet: -0.66 (0.22), residues: 570 loop : -0.46 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 176 HIS 0.004 0.001 HIS F 176 PHE 0.016 0.001 PHE I 53 TYR 0.022 0.001 TYR F 244 ARG 0.007 0.000 ARG J 47 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 1077) hydrogen bonds : angle 4.81587 ( 3165) covalent geometry : bond 0.00282 (27069) covalent geometry : angle 0.58305 (36950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 224 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TRP cc_start: 0.5649 (t60) cc_final: 0.5390 (t60) REVERT: B 141 ASN cc_start: 0.6554 (m110) cc_final: 0.6183 (t0) REVERT: B 208 PHE cc_start: 0.5900 (m-80) cc_final: 0.5595 (m-80) REVERT: C 144 MET cc_start: 0.7760 (mtp) cc_final: 0.7399 (mtp) REVERT: C 221 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: C 261 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7852 (mm-30) REVERT: D 142 MET cc_start: 0.8702 (ttp) cc_final: 0.8280 (ttp) REVERT: D 261 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8192 (mm-30) REVERT: E 152 ASP cc_start: 0.7241 (p0) cc_final: 0.6775 (p0) REVERT: E 254 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8232 (mp) REVERT: E 305 MET cc_start: 0.8573 (ttp) cc_final: 0.8326 (ttt) REVERT: F 42 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: H 142 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7358 (mtp) REVERT: H 248 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7937 (mptt) REVERT: I 44 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7064 (mpt180) REVERT: I 139 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6533 (t80) REVERT: I 256 GLN cc_start: 0.7532 (mt0) cc_final: 0.6820 (tp40) REVERT: J 8 ASP cc_start: 0.8352 (m-30) cc_final: 0.7928 (p0) REVERT: J 47 ARG cc_start: 0.8684 (ttm110) cc_final: 0.8367 (ttm110) REVERT: K 8 ASP cc_start: 0.8470 (m-30) cc_final: 0.8200 (m-30) REVERT: K 43 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7210 (mtpt) REVERT: K 82 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7328 (mm-40) outliers start: 62 outliers final: 25 residues processed: 273 average time/residue: 0.3902 time to fit residues: 168.9203 Evaluate side-chains 232 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 284 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 217 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 209 optimal weight: 0.8980 chunk 297 optimal weight: 20.0000 chunk 35 optimal weight: 30.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 283 GLN F 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN H 284 GLN I 101 GLN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 GLN I 336 GLN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.137083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.102335 restraints weight = 57312.585| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.20 r_work: 0.3460 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27069 Z= 0.228 Angle : 0.659 19.581 36950 Z= 0.344 Chirality : 0.044 0.236 3957 Planarity : 0.005 0.084 4421 Dihedral : 16.544 175.697 4509 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.95 % Favored : 93.82 % Rotamer: Outliers : 3.52 % Allowed : 19.17 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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: -0.12 (0.15), residues: 2943 helix: 1.04 (0.16), residues: 1029 sheet: -0.78 (0.22), residues: 553 loop : -0.55 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP I 488 HIS 0.005 0.001 HIS I 258 PHE 0.024 0.002 PHE I 53 TYR 0.036 0.002 TYR L 54 ARG 0.006 0.001 ARG I 46 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 1077) hydrogen bonds : angle 4.88030 ( 3165) covalent geometry : bond 0.00515 (27069) covalent geometry : angle 0.65885 (36950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 218 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8379 (t-90) cc_final: 0.8061 (t-90) REVERT: A 142 ASP cc_start: 0.7872 (m-30) cc_final: 0.7564 (m-30) REVERT: A 176 TRP cc_start: 0.6206 (t-100) cc_final: 0.5707 (t60) REVERT: B 43 HIS cc_start: 0.7543 (t70) cc_final: 0.7204 (t-90) REVERT: B 77 HIS cc_start: 0.7682 (p90) cc_final: 0.7078 (p-80) REVERT: B 141 ASN cc_start: 0.6436 (m110) cc_final: 0.5983 (t0) REVERT: B 208 PHE cc_start: 0.5994 (m-80) cc_final: 0.5727 (m-80) REVERT: C 144 MET cc_start: 0.8397 (mtp) cc_final: 0.8146 (mtp) REVERT: C 221 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8165 (m-80) REVERT: C 261 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: E 152 ASP cc_start: 0.7642 (p0) cc_final: 0.7197 (p0) REVERT: E 254 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8434 (mp) REVERT: E 305 MET cc_start: 0.8635 (ttp) cc_final: 0.8287 (ttt) REVERT: F 42 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: F 64 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8015 (mt) REVERT: G 305 MET cc_start: 0.8533 (ttp) cc_final: 0.8324 (ttp) REVERT: H 75 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8142 (m) REVERT: H 87 ARG cc_start: 0.8769 (ttm110) cc_final: 0.8438 (ttm-80) REVERT: H 113 GLU cc_start: 0.8084 (pp20) cc_final: 0.7608 (pp20) REVERT: H 142 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7698 (mtt) REVERT: H 240 TYR cc_start: 0.7789 (m-80) cc_final: 0.7482 (m-80) REVERT: I 44 ARG cc_start: 0.7547 (mtp85) cc_final: 0.7043 (mpt180) REVERT: I 139 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6531 (t80) REVERT: J 47 ARG cc_start: 0.8676 (ttm110) cc_final: 0.8323 (ttm110) REVERT: K 7 GLU cc_start: 0.7094 (pm20) cc_final: 0.6744 (pm20) REVERT: K 43 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7227 (mtpt) REVERT: K 71 ARG cc_start: 0.8725 (mtp85) cc_final: 0.8079 (mtm-85) outliers start: 93 outliers final: 41 residues processed: 294 average time/residue: 0.3811 time to fit residues: 179.1943 Evaluate side-chains 244 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 284 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 4 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 276 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 269 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN F 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN H 284 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 ASN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 GLN J 4 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.138868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.103910 restraints weight = 57096.986| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 3.34 r_work: 0.3508 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27069 Z= 0.142 Angle : 0.572 15.723 36950 Z= 0.298 Chirality : 0.041 0.205 3957 Planarity : 0.004 0.086 4421 Dihedral : 16.415 179.102 4509 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.13 % Favored : 94.63 % Rotamer: Outliers : 3.10 % Allowed : 19.36 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2943 helix: 1.17 (0.16), residues: 1031 sheet: -0.83 (0.23), residues: 544 loop : -0.47 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP I 488 HIS 0.005 0.001 HIS I 210 PHE 0.021 0.001 PHE I 53 TYR 0.027 0.001 TYR I 324 ARG 0.005 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 1077) hydrogen bonds : angle 4.67002 ( 3165) covalent geometry : bond 0.00322 (27069) covalent geometry : angle 0.57172 (36950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 204 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8345 (t-90) cc_final: 0.8061 (t-90) REVERT: A 176 TRP cc_start: 0.6313 (t-100) cc_final: 0.5733 (t60) REVERT: B 43 HIS cc_start: 0.7421 (t70) cc_final: 0.7104 (t-90) REVERT: B 77 HIS cc_start: 0.7585 (p90) cc_final: 0.6895 (p-80) REVERT: B 141 ASN cc_start: 0.6388 (m110) cc_final: 0.6115 (t0) REVERT: C 144 MET cc_start: 0.8334 (mtp) cc_final: 0.8118 (mtp) REVERT: C 221 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: C 261 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: D 142 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8090 (ttp) REVERT: E 137 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7189 (tmm) REVERT: E 152 ASP cc_start: 0.7505 (p0) cc_final: 0.7022 (p0) REVERT: E 305 MET cc_start: 0.8598 (ttp) cc_final: 0.8329 (ttt) REVERT: F 42 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: G 179 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8517 (mtp180) REVERT: H 75 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8056 (m) REVERT: H 113 GLU cc_start: 0.8049 (pp20) cc_final: 0.7549 (pp20) REVERT: H 142 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7513 (mtp) REVERT: H 248 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8001 (mtmm) REVERT: I 44 ARG cc_start: 0.7535 (mtp85) cc_final: 0.6948 (mpt180) REVERT: I 139 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6547 (t80) REVERT: J 47 ARG cc_start: 0.8681 (ttm110) cc_final: 0.8314 (ttm110) REVERT: K 43 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7245 (mtpt) REVERT: K 82 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7248 (mt0) REVERT: K 98 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8825 (ttp80) outliers start: 82 outliers final: 44 residues processed: 265 average time/residue: 0.3806 time to fit residues: 160.8823 Evaluate side-chains 244 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 294 ASN Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 351 ASN Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 292 optimal weight: 7.9990 chunk 123 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 177 optimal weight: 0.2980 chunk 208 optimal weight: 0.2980 chunk 115 optimal weight: 0.0980 chunk 271 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 283 GLN E 42 GLN F 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN H 284 GLN I 336 GLN J 4 ASN K 20 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.138294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.103831 restraints weight = 56456.043| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.05 r_work: 0.3508 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27069 Z= 0.136 Angle : 0.563 14.819 36950 Z= 0.293 Chirality : 0.041 0.200 3957 Planarity : 0.004 0.087 4421 Dihedral : 16.356 179.193 4509 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.20 % Favored : 94.56 % Rotamer: Outliers : 2.80 % Allowed : 19.62 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2943 helix: 1.21 (0.16), residues: 1032 sheet: -0.71 (0.22), residues: 561 loop : -0.42 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP I 488 HIS 0.004 0.001 HIS I 469 PHE 0.014 0.001 PHE L 61 TYR 0.020 0.001 TYR L 54 ARG 0.005 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 1077) hydrogen bonds : angle 4.59790 ( 3165) covalent geometry : bond 0.00308 (27069) covalent geometry : angle 0.56313 (36950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 198 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8339 (t-90) cc_final: 0.7997 (t-170) REVERT: A 142 ASP cc_start: 0.7980 (m-30) cc_final: 0.7767 (m-30) REVERT: A 176 TRP cc_start: 0.6305 (t-100) cc_final: 0.5633 (t60) REVERT: B 43 HIS cc_start: 0.7481 (t70) cc_final: 0.7270 (t-90) REVERT: B 77 HIS cc_start: 0.7615 (p90) cc_final: 0.6926 (p-80) REVERT: B 141 ASN cc_start: 0.6447 (m110) cc_final: 0.6071 (t0) REVERT: C 144 MET cc_start: 0.8212 (mtp) cc_final: 0.7959 (mtp) REVERT: C 221 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: C 261 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: D 142 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8115 (ttp) REVERT: D 261 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: E 137 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7322 (tmm) REVERT: E 152 ASP cc_start: 0.7434 (p0) cc_final: 0.6947 (p0) REVERT: E 181 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: E 305 MET cc_start: 0.8619 (ttp) cc_final: 0.8357 (ttt) REVERT: F 42 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: F 64 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7879 (mt) REVERT: G 179 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8489 (mtp180) REVERT: H 113 GLU cc_start: 0.8014 (pp20) cc_final: 0.7519 (pp20) REVERT: H 142 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7383 (mtp) REVERT: H 248 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7963 (mtmm) REVERT: I 44 ARG cc_start: 0.7491 (mtp85) cc_final: 0.6879 (mpt180) REVERT: I 139 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6397 (t80) REVERT: I 251 GLN cc_start: 0.6806 (tm-30) cc_final: 0.6506 (pp30) REVERT: I 399 TYR cc_start: 0.6279 (OUTLIER) cc_final: 0.5427 (t80) REVERT: J 47 ARG cc_start: 0.8678 (ttm110) cc_final: 0.8303 (ttm110) REVERT: K 43 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7273 (mtpt) REVERT: K 71 ARG cc_start: 0.8738 (mtp85) cc_final: 0.8088 (mtm-85) outliers start: 74 outliers final: 54 residues processed: 251 average time/residue: 0.3777 time to fit residues: 152.4602 Evaluate side-chains 255 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 187 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 284 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 351 ASN Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 61 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 286 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN F 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN J 4 ASN K 20 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.137471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.103005 restraints weight = 56738.654| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.11 r_work: 0.3496 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27069 Z= 0.161 Angle : 0.570 15.202 36950 Z= 0.297 Chirality : 0.041 0.211 3957 Planarity : 0.004 0.089 4421 Dihedral : 16.335 177.456 4509 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.27 % Favored : 94.50 % Rotamer: Outliers : 3.25 % Allowed : 19.40 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2943 helix: 1.26 (0.16), residues: 1025 sheet: -0.79 (0.23), residues: 554 loop : -0.31 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP I 488 HIS 0.008 0.001 HIS F 31 PHE 0.015 0.001 PHE L 61 TYR 0.017 0.001 TYR F 244 ARG 0.004 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 1077) hydrogen bonds : angle 4.60164 ( 3165) covalent geometry : bond 0.00368 (27069) covalent geometry : angle 0.57047 (36950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 193 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8351 (t-90) cc_final: 0.7991 (t-170) REVERT: A 176 TRP cc_start: 0.6396 (t-100) cc_final: 0.5740 (t60) REVERT: B 43 HIS cc_start: 0.7436 (t70) cc_final: 0.7230 (t-90) REVERT: B 77 HIS cc_start: 0.7512 (p90) cc_final: 0.6775 (p-80) REVERT: B 141 ASN cc_start: 0.6488 (m110) cc_final: 0.6182 (t0) REVERT: C 221 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: C 261 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: D 142 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8071 (ttp) REVERT: D 261 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8087 (mm-30) REVERT: E 137 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7215 (tmm) REVERT: E 152 ASP cc_start: 0.7444 (p0) cc_final: 0.6958 (p0) REVERT: E 181 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8415 (pt0) REVERT: E 305 MET cc_start: 0.8560 (ttp) cc_final: 0.8297 (ttt) REVERT: F 42 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: F 64 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7923 (mt) REVERT: G 179 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8614 (mtp180) REVERT: H 75 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8150 (m) REVERT: H 113 GLU cc_start: 0.8041 (pp20) cc_final: 0.7554 (pp20) REVERT: H 142 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7400 (mtp) REVERT: H 248 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7986 (mtmm) REVERT: I 44 ARG cc_start: 0.7381 (mtp85) cc_final: 0.6820 (mpt180) REVERT: I 139 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.6477 (t80) REVERT: I 251 GLN cc_start: 0.6699 (tm-30) cc_final: 0.6402 (pp30) REVERT: I 399 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.5424 (t80) REVERT: J 47 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8228 (ttm110) REVERT: J 74 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6259 (mm) REVERT: K 43 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7339 (mtpt) REVERT: K 71 ARG cc_start: 0.8729 (mtp85) cc_final: 0.8104 (mtm-85) outliers start: 86 outliers final: 57 residues processed: 257 average time/residue: 0.3831 time to fit residues: 156.6297 Evaluate side-chains 258 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 185 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 284 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 351 ASN Chi-restraints excluded: chain I residue 362 PHE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 117 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 219 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN F 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN H 256 GLN H 284 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.136392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.101738 restraints weight = 56825.263| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.35 r_work: 0.3471 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27069 Z= 0.184 Angle : 0.586 16.036 36950 Z= 0.304 Chirality : 0.041 0.223 3957 Planarity : 0.004 0.091 4421 Dihedral : 16.334 176.115 4509 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.37 % Favored : 94.43 % Rotamer: Outliers : 3.18 % Allowed : 19.43 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2943 helix: 1.23 (0.16), residues: 1025 sheet: -0.81 (0.22), residues: 555 loop : -0.32 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP I 488 HIS 0.004 0.001 HIS D 171 PHE 0.016 0.001 PHE L 61 TYR 0.023 0.001 TYR L 54 ARG 0.005 0.000 ARG J 49 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 1077) hydrogen bonds : angle 4.63255 ( 3165) covalent geometry : bond 0.00421 (27069) covalent geometry : angle 0.58648 (36950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 187 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8460 (t-170) cc_final: 0.8107 (t-90) REVERT: A 176 TRP cc_start: 0.6404 (t-100) cc_final: 0.5731 (t60) REVERT: B 77 HIS cc_start: 0.7487 (p90) cc_final: 0.6615 (p-80) REVERT: B 141 ASN cc_start: 0.6484 (m110) cc_final: 0.6238 (t0) REVERT: C 221 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: C 261 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: E 137 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7266 (tmm) REVERT: E 152 ASP cc_start: 0.7411 (p0) cc_final: 0.6939 (p0) REVERT: E 181 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8393 (pt0) REVERT: F 42 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: F 64 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7953 (mt) REVERT: G 179 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8110 (mtp85) REVERT: H 113 GLU cc_start: 0.8047 (pp20) cc_final: 0.7571 (pp20) REVERT: H 248 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.8015 (mtmm) REVERT: I 44 ARG cc_start: 0.7474 (mtp85) cc_final: 0.6875 (mpt180) REVERT: I 139 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6537 (t80) REVERT: I 251 GLN cc_start: 0.6682 (tm-30) cc_final: 0.6416 (pp30) REVERT: I 399 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.5610 (t80) REVERT: J 7 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6885 (pp20) REVERT: J 47 ARG cc_start: 0.8646 (ttm110) cc_final: 0.8244 (ttm110) REVERT: K 43 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7381 (mtpt) REVERT: K 71 ARG cc_start: 0.8716 (mtp85) cc_final: 0.8095 (mtm-85) REVERT: K 82 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7264 (mt0) outliers start: 84 outliers final: 56 residues processed: 249 average time/residue: 0.4038 time to fit residues: 161.6448 Evaluate side-chains 247 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 179 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 294 ASN Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 351 ASN Chi-restraints excluded: chain I residue 362 PHE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 253 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 231 optimal weight: 0.4980 chunk 294 optimal weight: 50.0000 chunk 226 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 40.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN F 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN J 79 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.135712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.101001 restraints weight = 57049.466| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.34 r_work: 0.3462 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27069 Z= 0.198 Angle : 0.602 16.521 36950 Z= 0.311 Chirality : 0.042 0.226 3957 Planarity : 0.004 0.094 4421 Dihedral : 16.334 175.754 4509 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.40 % Favored : 94.39 % Rotamer: Outliers : 2.99 % Allowed : 19.47 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2943 helix: 1.19 (0.16), residues: 1026 sheet: -0.79 (0.23), residues: 553 loop : -0.39 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP I 488 HIS 0.004 0.001 HIS D 171 PHE 0.018 0.001 PHE L 61 TYR 0.019 0.002 TYR K 11 ARG 0.006 0.000 ARG I 437 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 1077) hydrogen bonds : angle 4.68511 ( 3165) covalent geometry : bond 0.00456 (27069) covalent geometry : angle 0.60215 (36950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 179 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8433 (t-170) cc_final: 0.8098 (t-90) REVERT: B 77 HIS cc_start: 0.7523 (p90) cc_final: 0.6665 (p-80) REVERT: B 141 ASN cc_start: 0.6544 (m110) cc_final: 0.6284 (t0) REVERT: C 200 MET cc_start: 0.7845 (mmp) cc_final: 0.6985 (mtt) REVERT: C 221 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: C 261 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: E 137 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7175 (tmm) REVERT: E 152 ASP cc_start: 0.7481 (p0) cc_final: 0.7011 (p0) REVERT: E 181 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: F 42 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: F 64 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7978 (mt) REVERT: G 179 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8005 (mtp85) REVERT: H 75 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8209 (m) REVERT: H 113 GLU cc_start: 0.8014 (pp20) cc_final: 0.7550 (pp20) REVERT: H 248 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8054 (mtmm) REVERT: I 44 ARG cc_start: 0.7469 (mtp85) cc_final: 0.6727 (mmm160) REVERT: I 139 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6501 (t80) REVERT: I 251 GLN cc_start: 0.6643 (tm-30) cc_final: 0.6392 (pp30) REVERT: I 399 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.5885 (t80) REVERT: I 486 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7841 (ptm160) REVERT: J 47 ARG cc_start: 0.8649 (ttm110) cc_final: 0.8242 (ttm110) REVERT: K 43 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7419 (mtpt) REVERT: K 71 ARG cc_start: 0.8725 (mtp85) cc_final: 0.8099 (mtm-85) REVERT: K 82 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7303 (mt0) outliers start: 79 outliers final: 52 residues processed: 240 average time/residue: 0.3848 time to fit residues: 147.4048 Evaluate side-chains 238 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 3.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 294 ASN Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 362 PHE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 158 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 chunk 124 optimal weight: 0.0870 chunk 196 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 164 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN F 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN H 256 GLN H 284 GLN K 20 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.136019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.101289 restraints weight = 56596.913| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.01 r_work: 0.3480 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27069 Z= 0.164 Angle : 0.592 15.605 36950 Z= 0.304 Chirality : 0.041 0.238 3957 Planarity : 0.004 0.095 4421 Dihedral : 16.294 176.394 4509 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.30 % Favored : 94.50 % Rotamer: Outliers : 2.68 % Allowed : 20.00 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.08 (0.16), residues: 2943 helix: 1.20 (0.16), residues: 1025 sheet: -0.74 (0.23), residues: 548 loop : -0.38 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP I 488 HIS 0.004 0.001 HIS D 171 PHE 0.030 0.001 PHE G 228 TYR 0.020 0.001 TYR F 244 ARG 0.007 0.000 ARG I 437 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 1077) hydrogen bonds : angle 4.64220 ( 3165) covalent geometry : bond 0.00374 (27069) covalent geometry : angle 0.59212 (36950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 186 time to evaluate : 4.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.6507 (tpp) cc_final: 0.5649 (tpt) REVERT: A 84 HIS cc_start: 0.8435 (t-170) cc_final: 0.8104 (t-90) REVERT: B 77 HIS cc_start: 0.7494 (p90) cc_final: 0.6626 (p-80) REVERT: B 141 ASN cc_start: 0.6487 (m110) cc_final: 0.6256 (t0) REVERT: C 71 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8589 (mm110) REVERT: C 200 MET cc_start: 0.7790 (mmp) cc_final: 0.7127 (mtt) REVERT: C 205 MET cc_start: 0.8490 (mmm) cc_final: 0.8051 (mmm) REVERT: C 221 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: C 261 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: E 137 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7229 (tmm) REVERT: E 152 ASP cc_start: 0.7400 (p0) cc_final: 0.6925 (p0) REVERT: E 181 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8364 (pt0) REVERT: E 305 MET cc_start: 0.8538 (ttp) cc_final: 0.8179 (ttt) REVERT: F 42 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: F 64 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7913 (mt) REVERT: G 179 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.7689 (mtp85) REVERT: H 75 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8163 (m) REVERT: H 113 GLU cc_start: 0.7925 (pp20) cc_final: 0.7455 (pp20) REVERT: H 251 GLU cc_start: 0.7884 (mp0) cc_final: 0.7652 (mt-10) REVERT: I 44 ARG cc_start: 0.7476 (mtp85) cc_final: 0.6719 (mmm160) REVERT: I 139 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.6592 (t80) REVERT: I 251 GLN cc_start: 0.6595 (tm-30) cc_final: 0.6364 (pp30) REVERT: I 399 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.5954 (t80) REVERT: I 486 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7834 (ptm160) REVERT: J 47 ARG cc_start: 0.8656 (ttm110) cc_final: 0.8251 (ttm110) REVERT: J 57 ASP cc_start: 0.6483 (t0) cc_final: 0.6263 (m-30) REVERT: K 22 MET cc_start: 0.8676 (ptm) cc_final: 0.8143 (ptm) REVERT: K 43 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7451 (mtpt) REVERT: K 71 ARG cc_start: 0.8705 (mtp85) cc_final: 0.8090 (mtm-85) REVERT: K 82 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7206 (mt0) outliers start: 71 outliers final: 48 residues processed: 240 average time/residue: 0.5726 time to fit residues: 221.6455 Evaluate side-chains 238 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 5.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 294 ASN Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 362 PHE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 204 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 206 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN G 13 ASN G 297 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.132264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.099317 restraints weight = 56133.800| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.86 r_work: 0.3469 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.7298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 27069 Z= 0.370 Angle : 0.750 19.791 36950 Z= 0.385 Chirality : 0.048 0.345 3957 Planarity : 0.005 0.100 4421 Dihedral : 16.485 174.819 4509 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.32 % Favored : 93.41 % Rotamer: Outliers : 2.50 % Allowed : 20.19 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.29 (0.16), residues: 2943 helix: 0.78 (0.16), residues: 1019 sheet: -0.66 (0.23), residues: 539 loop : -0.65 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP I 488 HIS 0.008 0.001 HIS H 31 PHE 0.027 0.002 PHE L 61 TYR 0.027 0.002 TYR K 11 ARG 0.009 0.001 ARG H 61 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 1077) hydrogen bonds : angle 5.09404 ( 3165) covalent geometry : bond 0.00859 (27069) covalent geometry : angle 0.75000 (36950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15955.99 seconds wall clock time: 281 minutes 49.89 seconds (16909.89 seconds total)