Starting phenix.real_space_refine on Mon Aug 25 07:57:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fd2_29000/08_2025/8fd2_29000.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fd2_29000/08_2025/8fd2_29000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fd2_29000/08_2025/8fd2_29000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fd2_29000/08_2025/8fd2_29000.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fd2_29000/08_2025/8fd2_29000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fd2_29000/08_2025/8fd2_29000.map" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 63 5.49 5 S 94 5.16 5 C 16320 2.51 5 N 4376 2.21 5 O 4944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25797 Number of models: 1 Model: "" Number of chains: 13 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} Time building chain proxies: 6.00, per 1000 atoms: 0.23 Number of scatterers: 25797 At special positions: 0 Unit cell: (102.238, 119.102, 196.044, 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 63 15.00 O 4944 8.00 N 4376 7.00 C 16320 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: 1.79 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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 2 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 3.43 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: 3.730A 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: 3.573A 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: 3.662A pdb=" N ASP C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.542A 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: 3.577A 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: 3.522A 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: 4.093A 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: 3.644A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.557A 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: 3.773A 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: 3.956A 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: 3.747A 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: 3.920A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 removed outlier: 3.603A 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: 3.538A 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: 3.667A 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: 3.835A 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: 5.965A 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: 3.525A 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: 3.816A pdb=" N VAL K 45 " --> pdb=" O ILE K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 73 removed outlier: 3.605A 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: 3.769A pdb=" N CYS L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.806A 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: 3.914A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 13.523A 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: 6.728A 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: 6.589A 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: 4.026A pdb=" N ARG B 19 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.693A 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: 9.343A 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: 9.119A 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: 4.994A 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: 5.658A 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: 5.658A 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: 4.558A 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: 3.662A 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: 3.546A 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: 6.569A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.401A 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: 6.569A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.401A 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: 4.653A 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 removed outlier: 3.512A pdb=" N GLY F 25 " --> pdb=" O THR F 178 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F 178 " --> pdb=" O GLY F 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 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: 5.521A 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: 5.521A 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: 3.535A 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: 4.585A 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: 6.705A 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: 3.570A 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: 6.521A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.242A 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: 6.614A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.256A 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 1109 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 6 hydrogen bonds 12 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 2.36 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: 7226 1.33 - 1.45: 5111 1.45 - 1.57: 13951 1.57 - 1.69: 125 1.69 - 1.81: 149 Bond restraints: 26562 Sorted by residual: bond pdb=" CA SER F 28 " pdb=" C SER F 28 " ideal model delta sigma weight residual 1.532 1.507 0.026 1.21e-02 6.83e+03 4.52e+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 -0.026 1.76e-02 3.23e+03 2.26e+00 bond pdb=" O5' U M 34 " pdb=" C5' U M 34 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.85e+00 bond pdb=" C3' G M 48 " pdb=" O3' G M 48 " ideal model delta sigma weight residual 1.427 1.447 -0.020 1.50e-02 4.44e+03 1.78e+00 ... (remaining 26557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 35794 2.36 - 4.72: 330 4.72 - 7.07: 39 7.07 - 9.43: 7 9.43 - 11.79: 2 Bond angle restraints: 36172 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 110.44 103.37 7.07 1.20e+00 6.94e-01 3.47e+01 angle pdb=" N LEU E 29 " pdb=" CA LEU E 29 " pdb=" C LEU E 29 " ideal model delta sigma weight residual 111.03 117.40 -6.37 1.11e+00 8.12e-01 3.30e+01 angle pdb=" N TYR H 244 " pdb=" CA TYR H 244 " pdb=" C TYR H 244 " ideal model delta sigma weight residual 114.56 108.29 6.27 1.27e+00 6.20e-01 2.44e+01 angle pdb=" C ARG E 35 " pdb=" CA ARG E 35 " pdb=" CB ARG E 35 " ideal model delta sigma weight residual 117.23 111.01 6.22 1.36e+00 5.41e-01 2.09e+01 angle pdb=" N SER I 260 " pdb=" CA SER I 260 " pdb=" C SER I 260 " ideal model delta sigma weight residual 113.61 107.25 6.36 1.50e+00 4.44e-01 1.80e+01 ... (remaining 36167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 15226 35.83 - 71.67: 643 71.67 - 107.50: 42 107.50 - 143.34: 1 143.34 - 179.17: 5 Dihedral angle restraints: 15917 sinusoidal: 7192 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 44.58 155.42 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 73.30 126.70 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 51.17 -179.17 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2770 0.036 - 0.072: 774 0.072 - 0.108: 250 0.108 - 0.145: 64 0.145 - 0.181: 11 Chirality restraints: 3869 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 8.16e-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 7.89e-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 7.57e-01 ... (remaining 3866 not shown) Planarity restraints: 4399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.019 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 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " -0.060 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO F 247 " 0.159 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=" C VAL B 209 " -0.042 5.00e-02 4.00e+02 6.46e-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 4396 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 785 2.69 - 3.24: 24850 3.24 - 3.79: 42277 3.79 - 4.35: 58691 4.35 - 4.90: 95244 Nonbonded interactions: 221847 Sorted by model distance: nonbonded pdb=" O LEU B 184 " pdb=" ND2 ASN B 185 " model vdw 2.136 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 221842 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 26.230 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 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 0.038 26562 Z= 0.131 Angle : 0.572 11.789 36172 Z= 0.309 Chirality : 0.040 0.181 3869 Planarity : 0.004 0.092 4399 Dihedral : 17.940 179.170 10327 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.40 % Favored : 94.26 % Rotamer: Outliers : 2.84 % Allowed : 20.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.16), residues: 2943 helix: 1.66 (0.17), residues: 1015 sheet: -0.68 (0.22), residues: 596 loop : -0.22 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 96 TYR 0.020 0.001 TYR I 334 PHE 0.016 0.001 PHE J 26 TRP 0.015 0.001 TRP I 488 HIS 0.005 0.001 HIS I 106 Details of bonding type rmsd covalent geometry : bond 0.00269 (26562) covalent geometry : angle 0.57165 (36172) hydrogen bonds : bond 0.16857 ( 1052) hydrogen bonds : angle 6.76402 ( 3117) *********************** 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 868 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 793 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1 MET cc_start: 0.3180 (mmm) cc_final: 0.2351 (tmm) REVERT: A 184 ASN cc_start: 0.5000 (m-40) cc_final: 0.2917 (m-40) REVERT: A 197 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6356 (mmm160) REVERT: B 61 ASN cc_start: 0.6906 (m-40) cc_final: 0.6613 (t0) REVERT: B 130 ASN cc_start: 0.8901 (m-40) cc_final: 0.8645 (m-40) REVERT: B 142 LEU cc_start: 0.7697 (mt) cc_final: 0.6685 (tt) REVERT: C 61 ARG cc_start: 0.6823 (mtt-85) cc_final: 0.6611 (ttm170) REVERT: C 245 CYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7305 (p) REVERT: D 15 TYR cc_start: 0.6014 (m-80) cc_final: 0.5622 (m-10) REVERT: F 57 SER cc_start: 0.6764 (OUTLIER) cc_final: 0.6409 (t) REVERT: G 57 SER cc_start: 0.7268 (p) cc_final: 0.6711 (t) REVERT: G 161 SER cc_start: 0.4287 (OUTLIER) cc_final: 0.3836 (m) REVERT: G 215 ASN cc_start: 0.7514 (p0) cc_final: 0.7227 (p0) REVERT: G 254 LEU cc_start: 0.8216 (tp) cc_final: 0.7990 (tp) REVERT: H 32 ASP cc_start: 0.5641 (t0) cc_final: 0.5223 (t0) REVERT: H 146 VAL cc_start: 0.8450 (m) cc_final: 0.8178 (p) REVERT: H 171 HIS cc_start: 0.6545 (p-80) cc_final: 0.6307 (p90) REVERT: H 242 PHE cc_start: 0.6630 (m-80) cc_final: 0.6401 (m-10) REVERT: H 248 LYS cc_start: 0.7911 (mttp) cc_final: 0.7340 (mttp) REVERT: I 109 ILE cc_start: 0.6496 (mt) cc_final: 0.6135 (tp) REVERT: I 261 SER cc_start: 0.5542 (OUTLIER) cc_final: 0.5311 (p) REVERT: I 321 VAL cc_start: 0.7563 (t) cc_final: 0.6878 (t) REVERT: I 482 TRP cc_start: 0.7030 (p-90) cc_final: 0.6653 (p-90) REVERT: J 26 PHE cc_start: 0.7836 (m-80) cc_final: 0.7135 (m-80) REVERT: K 6 GLU cc_start: 0.8210 (tp30) cc_final: 0.7858 (tp30) outliers start: 75 outliers final: 12 residues processed: 837 average time/residue: 0.2038 time to fit residues: 255.9999 Evaluate side-chains 482 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 465 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 261 SER Chi-restraints excluded: chain J residue 80 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 27 ASN B 96 GLN C 52 HIS ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 229 GLN E 232 ASN E 283 GLN F 30 ASN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 HIS F 256 GLN F 283 GLN ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 297 HIS I 88 HIS I 104 HIS I 149 HIS ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 GLN ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 ASN ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN L 20 GLN L 25 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.107007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.085596 restraints weight = 115608.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.087763 restraints weight = 71126.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.089282 restraints weight = 49461.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.090215 restraints weight = 38397.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.090755 restraints weight = 32485.964| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 26562 Z= 0.292 Angle : 0.807 10.841 36172 Z= 0.423 Chirality : 0.047 0.227 3869 Planarity : 0.006 0.087 4399 Dihedral : 15.125 179.510 4287 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.61 % Favored : 94.09 % Rotamer: Outliers : 5.97 % Allowed : 22.95 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2943 helix: 0.95 (0.16), residues: 1023 sheet: -0.68 (0.22), residues: 585 loop : -0.33 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 201 TYR 0.030 0.003 TYR I 399 PHE 0.038 0.003 PHE L 61 TRP 0.023 0.003 TRP I 363 HIS 0.016 0.002 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00628 (26562) covalent geometry : angle 0.80694 (36172) hydrogen bonds : bond 0.04904 ( 1052) hydrogen bonds : angle 5.46471 ( 3117) *********************** 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 639 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 481 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3875 (mmm) cc_final: 0.3462 (tmm) REVERT: A 14 THR cc_start: 0.8749 (p) cc_final: 0.8474 (t) REVERT: A 24 MET cc_start: 0.7217 (ttp) cc_final: 0.6906 (ttp) REVERT: A 39 MET cc_start: 0.8368 (tmm) cc_final: 0.8051 (tmm) REVERT: B 61 ASN cc_start: 0.6973 (m-40) cc_final: 0.6651 (t0) REVERT: B 64 GLU cc_start: 0.8972 (tp30) cc_final: 0.8542 (tm-30) REVERT: B 96 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6952 (tp-100) REVERT: B 142 LEU cc_start: 0.8478 (mt) cc_final: 0.7422 (tt) REVERT: B 177 PHE cc_start: 0.6044 (m-10) cc_final: 0.5837 (m-10) REVERT: B 183 GLU cc_start: 0.7956 (mp0) cc_final: 0.7641 (mp0) REVERT: C 46 TRP cc_start: 0.8641 (t-100) cc_final: 0.7906 (t-100) REVERT: C 94 ASP cc_start: 0.8777 (t0) cc_final: 0.7832 (t0) REVERT: C 96 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8098 (pp20) REVERT: D 24 TYR cc_start: 0.7845 (t80) cc_final: 0.7565 (t80) REVERT: D 45 TYR cc_start: 0.8363 (m-80) cc_final: 0.8017 (m-10) REVERT: D 143 ASN cc_start: 0.9115 (m-40) cc_final: 0.8892 (m-40) REVERT: D 144 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8087 (mtt) REVERT: E 38 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8356 (tttm) REVERT: E 54 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: E 64 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8920 (tp) REVERT: E 77 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8344 (ttp-170) REVERT: E 152 ASP cc_start: 0.8951 (p0) cc_final: 0.8324 (p0) REVERT: E 175 TYR cc_start: 0.8797 (p90) cc_final: 0.8502 (p90) REVERT: F 30 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7244 (t0) REVERT: F 57 SER cc_start: 0.8103 (p) cc_final: 0.5928 (t) REVERT: F 142 MET cc_start: 0.7614 (ttm) cc_final: 0.7402 (ttp) REVERT: F 272 LEU cc_start: 0.8840 (tp) cc_final: 0.8234 (mm) REVERT: G 135 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: G 218 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7662 (m-40) REVERT: H 43 LYS cc_start: 0.8522 (pttp) cc_final: 0.7938 (ptpp) REVERT: H 88 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7443 (tp) REVERT: H 234 PHE cc_start: 0.8177 (p90) cc_final: 0.7646 (p90) REVERT: H 240 TYR cc_start: 0.6285 (m-80) cc_final: 0.5939 (m-10) REVERT: H 248 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8405 (mptp) REVERT: H 249 SER cc_start: 0.7829 (OUTLIER) cc_final: 0.7399 (p) REVERT: H 280 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9161 (ptpt) REVERT: H 283 GLN cc_start: 0.9226 (mt0) cc_final: 0.8946 (mm-40) REVERT: I 26 MET cc_start: 0.7086 (mtt) cc_final: 0.6842 (mtt) REVERT: I 31 MET cc_start: 0.4954 (ttm) cc_final: 0.4674 (ttm) REVERT: I 204 PHE cc_start: 0.8418 (m-80) cc_final: 0.7924 (m-80) REVERT: I 295 LYS cc_start: 0.1094 (mtmt) cc_final: 0.0601 (pttm) REVERT: I 303 MET cc_start: 0.3096 (mmp) cc_final: 0.2685 (mmp) REVERT: I 320 GLN cc_start: 0.8565 (tm130) cc_final: 0.7966 (tm-30) REVERT: I 321 VAL cc_start: 0.8346 (t) cc_final: 0.8073 (t) REVERT: I 363 TRP cc_start: 0.7695 (t-100) cc_final: 0.7433 (t-100) REVERT: I 364 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: I 466 PHE cc_start: 0.7785 (t80) cc_final: 0.7433 (t80) REVERT: J 14 PHE cc_start: 0.8594 (t80) cc_final: 0.8386 (t80) REVERT: J 15 ILE cc_start: 0.8768 (mm) cc_final: 0.8552 (mm) REVERT: J 18 PHE cc_start: 0.9294 (t80) cc_final: 0.9088 (t80) REVERT: J 26 PHE cc_start: 0.7981 (m-80) cc_final: 0.7748 (m-80) REVERT: J 64 TYR cc_start: 0.7495 (t80) cc_final: 0.7186 (t80) REVERT: J 80 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7891 (pt0) REVERT: J 82 GLN cc_start: 0.8613 (mm110) cc_final: 0.8319 (mm110) REVERT: J 96 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8752 (mt-10) REVERT: J 100 TRP cc_start: 0.8513 (m-10) cc_final: 0.8094 (m-10) REVERT: J 108 TYR cc_start: 0.5455 (OUTLIER) cc_final: 0.3705 (t80) REVERT: K 10 GLN cc_start: 0.8508 (mt0) cc_final: 0.8004 (mt0) REVERT: K 18 PHE cc_start: 0.8806 (t80) cc_final: 0.8562 (t80) REVERT: K 34 GLU cc_start: 0.6903 (pm20) cc_final: 0.6692 (mm-30) REVERT: K 47 ARG cc_start: 0.9196 (mtp180) cc_final: 0.8905 (tpp-160) REVERT: K 100 TRP cc_start: 0.9149 (m-10) cc_final: 0.8845 (m-10) REVERT: L 96 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8931 (mp0) outliers start: 158 outliers final: 70 residues processed: 598 average time/residue: 0.2002 time to fit residues: 183.1543 Evaluate side-chains 488 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 402 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 135 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 261 SER Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 374 TYR Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 263 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 271 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 128 optimal weight: 0.3980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 90 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN F 232 ASN F 283 GLN G 181 GLN G 215 ASN G 218 ASN I 104 HIS I 250 GLN I 320 GLN ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN L 25 ASN L 79 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.107383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.085924 restraints weight = 115275.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.088095 restraints weight = 71189.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.089295 restraints weight = 49928.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.090437 restraints weight = 39631.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.090960 restraints weight = 33440.090| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26562 Z= 0.167 Angle : 0.695 10.886 36172 Z= 0.360 Chirality : 0.043 0.190 3869 Planarity : 0.005 0.087 4399 Dihedral : 14.977 178.912 4274 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.99 % Favored : 94.73 % Rotamer: Outliers : 4.35 % Allowed : 23.48 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.15), residues: 2943 helix: 0.85 (0.16), residues: 1016 sheet: -0.66 (0.22), residues: 588 loop : -0.38 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 34 TYR 0.027 0.002 TYR K 54 PHE 0.024 0.002 PHE I 338 TRP 0.037 0.002 TRP H 46 HIS 0.010 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00368 (26562) covalent geometry : angle 0.69531 (36172) hydrogen bonds : bond 0.04062 ( 1052) hydrogen bonds : angle 5.14663 ( 3117) *********************** 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 555 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 440 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4147 (mmm) cc_final: 0.3778 (tmm) REVERT: A 14 THR cc_start: 0.8810 (p) cc_final: 0.8541 (t) REVERT: A 41 LEU cc_start: 0.8605 (tp) cc_final: 0.8372 (mt) REVERT: A 69 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7555 (ttt180) REVERT: A 146 LYS cc_start: 0.5933 (tttt) cc_final: 0.5696 (tttp) REVERT: B 90 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8531 (tp-100) REVERT: B 131 PHE cc_start: 0.8474 (t80) cc_final: 0.8003 (m-80) REVERT: B 142 LEU cc_start: 0.8490 (mt) cc_final: 0.7497 (tt) REVERT: B 177 PHE cc_start: 0.5901 (m-10) cc_final: 0.5546 (m-10) REVERT: B 202 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7908 (ptpp) REVERT: C 46 TRP cc_start: 0.8601 (t-100) cc_final: 0.7872 (t-100) REVERT: C 94 ASP cc_start: 0.8829 (t0) cc_final: 0.8181 (t0) REVERT: C 96 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8149 (pp20) REVERT: C 190 HIS cc_start: 0.8801 (t-170) cc_final: 0.8558 (t-170) REVERT: D 24 TYR cc_start: 0.7887 (t80) cc_final: 0.7591 (t80) REVERT: D 45 TYR cc_start: 0.8254 (m-80) cc_final: 0.7875 (m-10) REVERT: D 143 ASN cc_start: 0.9023 (m-40) cc_final: 0.8817 (m-40) REVERT: D 205 MET cc_start: 0.8473 (mmm) cc_final: 0.8215 (mmm) REVERT: E 32 ASP cc_start: 0.8046 (t0) cc_final: 0.7830 (t0) REVERT: E 65 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7928 (mtp85) REVERT: E 152 ASP cc_start: 0.8733 (p0) cc_final: 0.7997 (p0) REVERT: E 175 TYR cc_start: 0.8720 (p90) cc_final: 0.8453 (p90) REVERT: F 30 ASN cc_start: 0.7332 (t0) cc_final: 0.6982 (t0) REVERT: F 57 SER cc_start: 0.8016 (OUTLIER) cc_final: 0.6278 (t) REVERT: F 75 VAL cc_start: 0.8878 (m) cc_final: 0.8648 (t) REVERT: F 175 TYR cc_start: 0.7599 (p90) cc_final: 0.6902 (p90) REVERT: F 272 LEU cc_start: 0.8841 (tp) cc_final: 0.8352 (mm) REVERT: G 35 ARG cc_start: 0.3668 (OUTLIER) cc_final: 0.3348 (tpp80) REVERT: G 61 ARG cc_start: 0.7519 (mtp180) cc_final: 0.7147 (mtp180) REVERT: G 218 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7849 (m-40) REVERT: H 43 LYS cc_start: 0.8414 (pttp) cc_final: 0.8063 (mtmm) REVERT: H 55 VAL cc_start: 0.8147 (t) cc_final: 0.7734 (t) REVERT: H 88 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7492 (tp) REVERT: H 104 PHE cc_start: 0.7924 (m-80) cc_final: 0.7628 (m-80) REVERT: H 180 TYR cc_start: 0.7030 (m-80) cc_final: 0.6587 (m-80) REVERT: H 221 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: H 234 PHE cc_start: 0.8072 (p90) cc_final: 0.7538 (p90) REVERT: H 244 TYR cc_start: 0.7015 (t80) cc_final: 0.6457 (t80) REVERT: H 248 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8226 (mptp) REVERT: H 249 SER cc_start: 0.7547 (OUTLIER) cc_final: 0.7026 (p) REVERT: H 283 GLN cc_start: 0.9223 (mt0) cc_final: 0.8951 (mm-40) REVERT: I 303 MET cc_start: 0.3225 (mmp) cc_final: 0.2981 (mmp) REVERT: I 320 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7998 (tm-30) REVERT: I 363 TRP cc_start: 0.7586 (t-100) cc_final: 0.7282 (t-100) REVERT: I 364 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8525 (pm20) REVERT: I 389 MET cc_start: 0.7740 (mmm) cc_final: 0.7496 (mmm) REVERT: I 451 GLU cc_start: 0.8994 (tt0) cc_final: 0.8482 (tm-30) REVERT: J 14 PHE cc_start: 0.8660 (t80) cc_final: 0.8361 (t80) REVERT: J 15 ILE cc_start: 0.8636 (mm) cc_final: 0.8385 (mm) REVERT: J 18 PHE cc_start: 0.9205 (t80) cc_final: 0.8744 (t80) REVERT: J 22 MET cc_start: 0.8636 (ppp) cc_final: 0.8223 (ppp) REVERT: J 26 PHE cc_start: 0.8174 (m-80) cc_final: 0.7946 (m-80) REVERT: J 80 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: J 100 TRP cc_start: 0.8605 (m-10) cc_final: 0.8047 (m-90) REVERT: J 108 TYR cc_start: 0.5486 (OUTLIER) cc_final: 0.4398 (t80) REVERT: K 18 PHE cc_start: 0.8958 (t80) cc_final: 0.8658 (t80) REVERT: K 47 ARG cc_start: 0.9178 (mtp180) cc_final: 0.8838 (tpp-160) REVERT: K 58 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: L 18 PHE cc_start: 0.8513 (t80) cc_final: 0.8302 (t80) REVERT: L 38 ASP cc_start: 0.6019 (OUTLIER) cc_final: 0.5804 (p0) REVERT: L 71 ARG cc_start: 0.8297 (ttm170) cc_final: 0.7873 (ttm110) outliers start: 115 outliers final: 55 residues processed: 529 average time/residue: 0.1666 time to fit residues: 136.7215 Evaluate side-chains 468 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 399 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 300 ARG Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER 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 58 GLU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 278 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 289 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS E 42 GLN E 256 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS F 181 GLN I 104 HIS I 227 HIS ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 GLN K 25 ASN K 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.103491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.082581 restraints weight = 116685.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.084608 restraints weight = 70797.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.086011 restraints weight = 49836.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.086712 restraints weight = 38950.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.087301 restraints weight = 33725.007| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26562 Z= 0.214 Angle : 0.714 13.580 36172 Z= 0.369 Chirality : 0.044 0.194 3869 Planarity : 0.005 0.089 4399 Dihedral : 15.048 179.276 4271 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.64 % Favored : 94.09 % Rotamer: Outliers : 4.84 % Allowed : 23.10 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.16), residues: 2943 helix: 0.80 (0.16), residues: 1019 sheet: -0.81 (0.22), residues: 586 loop : -0.43 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 300 TYR 0.028 0.002 TYR K 54 PHE 0.025 0.002 PHE I 119 TRP 0.045 0.002 TRP H 46 HIS 0.009 0.002 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00460 (26562) covalent geometry : angle 0.71448 (36172) hydrogen bonds : bond 0.04012 ( 1052) hydrogen bonds : angle 5.16602 ( 3117) *********************** 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 538 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 410 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3658 (mmm) cc_final: 0.3144 (ppp) REVERT: A 14 THR cc_start: 0.8920 (p) cc_final: 0.8697 (t) REVERT: A 20 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.7146 (t-90) REVERT: A 39 MET cc_start: 0.8758 (tmm) cc_final: 0.8111 (tmm) REVERT: A 202 ASP cc_start: 0.8559 (m-30) cc_final: 0.8058 (t0) REVERT: B 63 LEU cc_start: 0.5085 (OUTLIER) cc_final: 0.4606 (mt) REVERT: B 64 GLU cc_start: 0.9087 (tp30) cc_final: 0.8643 (tm-30) REVERT: B 131 PHE cc_start: 0.8508 (t80) cc_final: 0.8044 (m-80) REVERT: B 177 PHE cc_start: 0.5984 (m-10) cc_final: 0.5595 (m-10) REVERT: B 202 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8126 (ptpp) REVERT: C 55 VAL cc_start: 0.9240 (t) cc_final: 0.8592 (t) REVERT: D 24 TYR cc_start: 0.8004 (t80) cc_final: 0.7728 (t80) REVERT: D 143 ASN cc_start: 0.9084 (m-40) cc_final: 0.8775 (m-40) REVERT: D 205 MET cc_start: 0.8498 (mmm) cc_final: 0.8296 (mmm) REVERT: E 32 ASP cc_start: 0.8267 (t0) cc_final: 0.8012 (t0) REVERT: E 38 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8205 (tttm) REVERT: E 65 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7921 (mtp85) REVERT: E 152 ASP cc_start: 0.8833 (p0) cc_final: 0.8266 (p0) REVERT: E 175 TYR cc_start: 0.8707 (p90) cc_final: 0.8464 (p90) REVERT: F 30 ASN cc_start: 0.7554 (t0) cc_final: 0.7267 (t0) REVERT: F 57 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.7229 (m) REVERT: F 75 VAL cc_start: 0.8966 (m) cc_final: 0.8689 (t) REVERT: F 272 LEU cc_start: 0.8953 (tp) cc_final: 0.8365 (mm) REVERT: G 35 ARG cc_start: 0.4599 (OUTLIER) cc_final: 0.4192 (tpp80) REVERT: G 200 MET cc_start: 0.8202 (ptp) cc_final: 0.7893 (ptm) REVERT: H 88 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7579 (tp) REVERT: H 144 MET cc_start: 0.7367 (mmp) cc_final: 0.7003 (mmp) REVERT: H 175 TYR cc_start: 0.8458 (p90) cc_final: 0.8236 (p90) REVERT: H 180 TYR cc_start: 0.7225 (m-80) cc_final: 0.6469 (m-80) REVERT: H 221 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: H 248 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8178 (mptp) REVERT: H 249 SER cc_start: 0.7508 (OUTLIER) cc_final: 0.7221 (p) REVERT: H 283 GLN cc_start: 0.9303 (mt0) cc_final: 0.9062 (mm-40) REVERT: I 31 MET cc_start: 0.6653 (ttm) cc_final: 0.6163 (ttt) REVERT: I 89 LEU cc_start: 0.9195 (mp) cc_final: 0.8549 (tp) REVERT: I 247 TRP cc_start: 0.8664 (m-10) cc_final: 0.8195 (m-10) REVERT: I 363 TRP cc_start: 0.7794 (t-100) cc_final: 0.7316 (t-100) REVERT: I 364 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8321 (pm20) REVERT: I 449 PHE cc_start: 0.8104 (t80) cc_final: 0.7768 (t80) REVERT: J 14 PHE cc_start: 0.8879 (t80) cc_final: 0.8603 (t80) REVERT: J 15 ILE cc_start: 0.8642 (mm) cc_final: 0.8368 (mm) REVERT: J 18 PHE cc_start: 0.9313 (t80) cc_final: 0.8793 (t80) REVERT: J 22 MET cc_start: 0.8799 (ppp) cc_final: 0.8065 (ppp) REVERT: J 80 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: J 100 TRP cc_start: 0.8717 (m-10) cc_final: 0.8087 (m-90) REVERT: J 108 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.4382 (t80) REVERT: K 18 PHE cc_start: 0.9069 (t80) cc_final: 0.8832 (t80) REVERT: L 71 ARG cc_start: 0.8434 (ttm170) cc_final: 0.7959 (ttm110) REVERT: L 90 LYS cc_start: 0.8484 (tptp) cc_final: 0.8134 (tptt) REVERT: L 100 TRP cc_start: 0.8182 (m-10) cc_final: 0.7816 (m-10) outliers start: 128 outliers final: 76 residues processed: 499 average time/residue: 0.1907 time to fit residues: 147.8941 Evaluate side-chains 462 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 372 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 222 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 300 ARG Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER 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 58 GLU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 91 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 286 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN F 30 ASN G 215 ASN G 233 HIS H 52 HIS I 104 HIS ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 441 ASN ** I 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.104685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.083704 restraints weight = 115050.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.085802 restraints weight = 69715.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.087180 restraints weight = 49191.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.087962 restraints weight = 38684.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.088276 restraints weight = 33267.303| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26562 Z= 0.151 Angle : 0.674 14.952 36172 Z= 0.345 Chirality : 0.043 0.250 3869 Planarity : 0.005 0.089 4399 Dihedral : 15.019 178.354 4271 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.23 % Favored : 94.50 % Rotamer: Outliers : 4.57 % Allowed : 23.63 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.16), residues: 2943 helix: 0.80 (0.16), residues: 1022 sheet: -0.70 (0.22), residues: 575 loop : -0.43 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 163 TYR 0.034 0.002 TYR H 244 PHE 0.019 0.002 PHE E 217 TRP 0.057 0.002 TRP H 46 HIS 0.014 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00332 (26562) covalent geometry : angle 0.67422 (36172) hydrogen bonds : bond 0.03714 ( 1052) hydrogen bonds : angle 5.02887 ( 3117) *********************** 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 530 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 409 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3609 (mmm) cc_final: 0.2679 (ptt) REVERT: A 14 THR cc_start: 0.8894 (p) cc_final: 0.8657 (t) REVERT: A 20 HIS cc_start: 0.7318 (OUTLIER) cc_final: 0.7004 (t-90) REVERT: A 39 MET cc_start: 0.8786 (tmm) cc_final: 0.8290 (tmm) REVERT: A 69 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7400 (ttp80) REVERT: A 77 PHE cc_start: 0.6925 (m-80) cc_final: 0.6669 (m-80) REVERT: A 146 LYS cc_start: 0.6249 (tttm) cc_final: 0.5968 (mtpt) REVERT: A 202 ASP cc_start: 0.8563 (m-30) cc_final: 0.8061 (t0) REVERT: B 64 GLU cc_start: 0.9090 (tp30) cc_final: 0.8827 (tm-30) REVERT: B 131 PHE cc_start: 0.8462 (t80) cc_final: 0.8010 (m-80) REVERT: B 142 LEU cc_start: 0.8009 (mp) cc_final: 0.6877 (tt) REVERT: B 177 PHE cc_start: 0.5941 (m-10) cc_final: 0.5545 (m-10) REVERT: C 55 VAL cc_start: 0.9114 (t) cc_final: 0.8796 (t) REVERT: C 234 PHE cc_start: 0.7658 (m-10) cc_final: 0.7418 (m-10) REVERT: D 24 TYR cc_start: 0.7996 (t80) cc_final: 0.7726 (t80) REVERT: D 143 ASN cc_start: 0.9022 (t0) cc_final: 0.8770 (m-40) REVERT: D 152 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8400 (p0) REVERT: E 32 ASP cc_start: 0.8274 (t0) cc_final: 0.8031 (t0) REVERT: E 38 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8368 (tttm) REVERT: E 65 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7795 (mtp85) REVERT: E 152 ASP cc_start: 0.8787 (p0) cc_final: 0.8100 (p0) REVERT: E 175 TYR cc_start: 0.8442 (p90) cc_final: 0.8228 (p90) REVERT: F 30 ASN cc_start: 0.7535 (t0) cc_final: 0.7281 (t0) REVERT: F 57 SER cc_start: 0.8290 (p) cc_final: 0.7919 (m) REVERT: F 272 LEU cc_start: 0.8927 (tp) cc_final: 0.8390 (mm) REVERT: G 35 ARG cc_start: 0.4588 (OUTLIER) cc_final: 0.4157 (tpp80) REVERT: G 200 MET cc_start: 0.8134 (ptp) cc_final: 0.7884 (ptm) REVERT: H 43 LYS cc_start: 0.8379 (pttp) cc_final: 0.7993 (mtmm) REVERT: H 88 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7595 (tp) REVERT: H 175 TYR cc_start: 0.8411 (p90) cc_final: 0.8173 (p90) REVERT: H 180 TYR cc_start: 0.7277 (m-80) cc_final: 0.6518 (m-80) REVERT: H 183 TYR cc_start: 0.6440 (t80) cc_final: 0.5961 (t80) REVERT: H 221 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: H 234 PHE cc_start: 0.7986 (p90) cc_final: 0.7384 (p90) REVERT: H 248 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8092 (mptp) REVERT: H 249 SER cc_start: 0.7271 (OUTLIER) cc_final: 0.6766 (p) REVERT: I 89 LEU cc_start: 0.9096 (mp) cc_final: 0.8432 (tp) REVERT: I 247 TRP cc_start: 0.8675 (m-10) cc_final: 0.8311 (m-10) REVERT: I 363 TRP cc_start: 0.7791 (t-100) cc_final: 0.7402 (t-100) REVERT: I 364 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: I 449 PHE cc_start: 0.8169 (t80) cc_final: 0.7557 (t80) REVERT: I 465 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: I 482 TRP cc_start: 0.7660 (p-90) cc_final: 0.7061 (p-90) REVERT: J 14 PHE cc_start: 0.8823 (t80) cc_final: 0.8488 (t80) REVERT: J 15 ILE cc_start: 0.8663 (mm) cc_final: 0.8313 (mm) REVERT: J 18 PHE cc_start: 0.9419 (t80) cc_final: 0.9004 (t80) REVERT: J 22 MET cc_start: 0.8789 (ppp) cc_final: 0.8407 (ppp) REVERT: J 46 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7399 (pt0) REVERT: J 80 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: J 82 GLN cc_start: 0.8656 (mm110) cc_final: 0.8440 (mm110) REVERT: J 108 TYR cc_start: 0.6118 (OUTLIER) cc_final: 0.4306 (t80) REVERT: K 47 ARG cc_start: 0.9184 (tpp-160) cc_final: 0.8981 (tpp-160) REVERT: K 51 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7960 (mt-10) REVERT: K 58 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: L 71 ARG cc_start: 0.8454 (ttm170) cc_final: 0.7988 (ttm110) REVERT: L 90 LYS cc_start: 0.8355 (tptp) cc_final: 0.7926 (tptt) outliers start: 121 outliers final: 70 residues processed: 498 average time/residue: 0.1644 time to fit residues: 127.8269 Evaluate side-chains 459 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 375 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER 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 55 CYS Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 180 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 12 optimal weight: 0.0670 chunk 62 optimal weight: 3.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 136 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.103570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.082618 restraints weight = 117667.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.084603 restraints weight = 71673.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.086015 restraints weight = 50190.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.086892 restraints weight = 39004.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.087208 restraints weight = 33345.081| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26562 Z= 0.172 Angle : 0.698 15.154 36172 Z= 0.356 Chirality : 0.043 0.299 3869 Planarity : 0.005 0.090 4399 Dihedral : 15.042 178.522 4270 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.40 % Favored : 94.36 % Rotamer: Outliers : 4.69 % Allowed : 24.16 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.16), residues: 2943 helix: 0.65 (0.16), residues: 1022 sheet: -0.66 (0.22), residues: 574 loop : -0.45 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 302 TYR 0.029 0.002 TYR K 54 PHE 0.053 0.002 PHE J 26 TRP 0.066 0.002 TRP H 46 HIS 0.008 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00378 (26562) covalent geometry : angle 0.69811 (36172) hydrogen bonds : bond 0.03710 ( 1052) hydrogen bonds : angle 5.05990 ( 3117) *********************** 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 519 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 395 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3248 (mmm) cc_final: 0.2546 (ptt) REVERT: A 14 THR cc_start: 0.8811 (p) cc_final: 0.8592 (t) REVERT: A 20 HIS cc_start: 0.7168 (OUTLIER) cc_final: 0.6937 (t-90) REVERT: A 39 MET cc_start: 0.8720 (tmm) cc_final: 0.8223 (tmm) REVERT: A 41 LEU cc_start: 0.8658 (tp) cc_final: 0.8356 (mm) REVERT: A 69 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7400 (ttp80) REVERT: A 77 PHE cc_start: 0.7000 (m-80) cc_final: 0.6428 (m-10) REVERT: A 78 LYS cc_start: 0.7040 (mtmt) cc_final: 0.6798 (mtmt) REVERT: A 202 ASP cc_start: 0.8587 (m-30) cc_final: 0.8051 (t0) REVERT: B 64 GLU cc_start: 0.9054 (tp30) cc_final: 0.8784 (tm-30) REVERT: B 131 PHE cc_start: 0.8496 (t80) cc_final: 0.8065 (m-80) REVERT: B 177 PHE cc_start: 0.5827 (m-10) cc_final: 0.5516 (m-10) REVERT: C 55 VAL cc_start: 0.9104 (t) cc_final: 0.8886 (t) REVERT: C 234 PHE cc_start: 0.7932 (m-10) cc_final: 0.7660 (m-10) REVERT: D 24 TYR cc_start: 0.8073 (t80) cc_final: 0.7756 (t80) REVERT: D 143 ASN cc_start: 0.8921 (t0) cc_final: 0.8701 (m-40) REVERT: D 152 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8456 (p0) REVERT: E 32 ASP cc_start: 0.8320 (t0) cc_final: 0.8084 (t0) REVERT: F 30 ASN cc_start: 0.7641 (t0) cc_final: 0.7417 (t0) REVERT: F 57 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.8139 (m) REVERT: F 303 ASN cc_start: 0.9083 (m-40) cc_final: 0.8874 (p0) REVERT: G 35 ARG cc_start: 0.4790 (OUTLIER) cc_final: 0.4143 (tpm170) REVERT: G 200 MET cc_start: 0.8197 (ptp) cc_final: 0.7956 (ptm) REVERT: H 88 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7617 (tp) REVERT: H 144 MET cc_start: 0.7476 (mmp) cc_final: 0.7171 (mmp) REVERT: H 180 TYR cc_start: 0.7518 (m-80) cc_final: 0.6720 (m-80) REVERT: H 183 TYR cc_start: 0.6497 (t80) cc_final: 0.5975 (t80) REVERT: H 221 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: H 234 PHE cc_start: 0.7987 (p90) cc_final: 0.7349 (p90) REVERT: H 237 TYR cc_start: 0.3845 (OUTLIER) cc_final: 0.3452 (m-80) REVERT: H 248 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8161 (mptp) REVERT: H 249 SER cc_start: 0.7195 (OUTLIER) cc_final: 0.6975 (m) REVERT: I 89 LEU cc_start: 0.9037 (mp) cc_final: 0.8367 (tp) REVERT: I 247 TRP cc_start: 0.8534 (m-10) cc_final: 0.8278 (m-10) REVERT: I 363 TRP cc_start: 0.7885 (t-100) cc_final: 0.7419 (t-100) REVERT: I 364 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8197 (pm20) REVERT: I 449 PHE cc_start: 0.8228 (t80) cc_final: 0.7755 (t80) REVERT: I 451 GLU cc_start: 0.8983 (tt0) cc_final: 0.8528 (tm-30) REVERT: I 465 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6590 (m-80) REVERT: I 482 TRP cc_start: 0.7542 (p-90) cc_final: 0.7192 (p-90) REVERT: J 14 PHE cc_start: 0.8844 (t80) cc_final: 0.8505 (t80) REVERT: J 15 ILE cc_start: 0.8686 (mm) cc_final: 0.8319 (mm) REVERT: J 18 PHE cc_start: 0.9407 (t80) cc_final: 0.9038 (t80) REVERT: J 22 MET cc_start: 0.8835 (ppp) cc_final: 0.8553 (ppp) REVERT: J 80 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: J 108 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.4368 (t80) REVERT: K 19 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8441 (mp10) REVERT: K 22 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.6159 (ppp) REVERT: K 57 ASP cc_start: 0.6332 (t0) cc_final: 0.5667 (t0) REVERT: L 100 TRP cc_start: 0.8175 (m-10) cc_final: 0.7802 (m-10) outliers start: 124 outliers final: 81 residues processed: 484 average time/residue: 0.1728 time to fit residues: 131.4675 Evaluate side-chains 465 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 369 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 74 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 266 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 243 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 ASN G 256 GLN ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS I 117 ASN I 250 GLN ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 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 = 0.4251 r_free = 0.4251 target = 0.101983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.081334 restraints weight = 117176.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.083302 restraints weight = 71276.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.084463 restraints weight = 49882.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.085435 restraints weight = 39802.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.085877 restraints weight = 33833.816| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26562 Z= 0.190 Angle : 0.717 15.769 36172 Z= 0.366 Chirality : 0.044 0.327 3869 Planarity : 0.005 0.101 4399 Dihedral : 15.129 178.718 4270 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.64 % Favored : 94.12 % Rotamer: Outliers : 4.69 % Allowed : 24.50 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2943 helix: 0.54 (0.16), residues: 1024 sheet: -0.66 (0.22), residues: 588 loop : -0.60 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 61 TYR 0.038 0.002 TYR H 244 PHE 0.050 0.002 PHE J 26 TRP 0.068 0.002 TRP H 46 HIS 0.007 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00414 (26562) covalent geometry : angle 0.71723 (36172) hydrogen bonds : bond 0.03733 ( 1052) hydrogen bonds : angle 5.16006 ( 3117) *********************** 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 510 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 386 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3378 (mmm) cc_final: 0.3052 (ptm) REVERT: A 20 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6954 (t-90) REVERT: A 39 MET cc_start: 0.8737 (tmm) cc_final: 0.8321 (tmm) REVERT: A 69 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7346 (ttp80) REVERT: A 78 LYS cc_start: 0.7152 (mtmt) cc_final: 0.6901 (mtmt) REVERT: A 202 ASP cc_start: 0.8523 (m-30) cc_final: 0.8200 (t0) REVERT: B 63 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5640 (mt) REVERT: B 64 GLU cc_start: 0.9067 (tp30) cc_final: 0.8596 (tm-30) REVERT: B 142 LEU cc_start: 0.7561 (mp) cc_final: 0.6481 (tp) REVERT: C 94 ASP cc_start: 0.9119 (t0) cc_final: 0.8803 (p0) REVERT: D 24 TYR cc_start: 0.8175 (t80) cc_final: 0.7890 (t80) REVERT: D 143 ASN cc_start: 0.8897 (t0) cc_final: 0.8671 (m-40) REVERT: D 205 MET cc_start: 0.8596 (mmm) cc_final: 0.8396 (mmm) REVERT: E 32 ASP cc_start: 0.8320 (t0) cc_final: 0.8102 (t0) REVERT: E 38 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8149 (tttm) REVERT: F 30 ASN cc_start: 0.7728 (t0) cc_final: 0.7490 (t0) REVERT: F 57 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.7678 (m) REVERT: F 303 ASN cc_start: 0.9145 (m-40) cc_final: 0.8924 (p0) REVERT: H 88 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7639 (tp) REVERT: H 142 MET cc_start: 0.6821 (pmm) cc_final: 0.6235 (pmm) REVERT: H 144 MET cc_start: 0.7695 (mmp) cc_final: 0.7353 (mmp) REVERT: H 180 TYR cc_start: 0.7731 (m-80) cc_final: 0.6722 (m-80) REVERT: H 183 TYR cc_start: 0.6591 (t80) cc_final: 0.6074 (t80) REVERT: H 221 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.6966 (m-80) REVERT: H 234 PHE cc_start: 0.7902 (p90) cc_final: 0.7270 (p90) REVERT: H 237 TYR cc_start: 0.3839 (OUTLIER) cc_final: 0.3489 (m-80) REVERT: H 248 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8222 (mptp) REVERT: I 31 MET cc_start: 0.5406 (ttt) cc_final: 0.4871 (ttt) REVERT: I 363 TRP cc_start: 0.7942 (t-100) cc_final: 0.7505 (t-100) REVERT: I 364 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: I 449 PHE cc_start: 0.8212 (t80) cc_final: 0.7904 (t80) REVERT: I 451 GLU cc_start: 0.9009 (tt0) cc_final: 0.8546 (tm-30) REVERT: I 465 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: I 482 TRP cc_start: 0.7530 (p-90) cc_final: 0.7286 (p-90) REVERT: J 14 PHE cc_start: 0.8889 (t80) cc_final: 0.8569 (t80) REVERT: J 15 ILE cc_start: 0.8686 (mm) cc_final: 0.8368 (mm) REVERT: J 18 PHE cc_start: 0.9429 (t80) cc_final: 0.9059 (t80) REVERT: J 22 MET cc_start: 0.8875 (ppp) cc_final: 0.8434 (ppp) REVERT: J 80 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: J 100 TRP cc_start: 0.8749 (m-10) cc_final: 0.8151 (m-10) REVERT: J 108 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.4553 (t80) REVERT: K 19 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8494 (mp10) REVERT: K 96 GLU cc_start: 0.9108 (tt0) cc_final: 0.8897 (tt0) REVERT: L 66 SER cc_start: 0.9736 (m) cc_final: 0.9362 (t) REVERT: L 75 ASN cc_start: 0.8891 (t0) cc_final: 0.8335 (t0) outliers start: 124 outliers final: 88 residues processed: 483 average time/residue: 0.1613 time to fit residues: 123.5358 Evaluate side-chains 459 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 358 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 264 CYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 303 MET Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 350 ASP Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 55 CYS Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 242 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN B 27 ASN B 43 HIS ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN E 48 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 GLN ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 ASN ** 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 = 0.4252 r_free = 0.4252 target = 0.101898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.081306 restraints weight = 119018.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.083295 restraints weight = 73395.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.084409 restraints weight = 51009.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.085364 restraints weight = 40531.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.085929 restraints weight = 34730.368| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 26562 Z= 0.171 Angle : 0.720 16.330 36172 Z= 0.366 Chirality : 0.044 0.239 3869 Planarity : 0.005 0.093 4399 Dihedral : 15.135 179.986 4270 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.33 % Favored : 94.43 % Rotamer: Outliers : 4.27 % Allowed : 25.71 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.16), residues: 2943 helix: 0.43 (0.16), residues: 1018 sheet: -0.65 (0.22), residues: 572 loop : -0.61 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 49 TYR 0.041 0.002 TYR B 29 PHE 0.028 0.002 PHE L 61 TRP 0.019 0.002 TRP H 46 HIS 0.005 0.001 HIS I 104 Details of bonding type rmsd covalent geometry : bond 0.00379 (26562) covalent geometry : angle 0.72018 (36172) hydrogen bonds : bond 0.03781 ( 1052) hydrogen bonds : angle 5.17260 ( 3117) *********************** 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 491 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 378 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1 MET cc_start: 0.3577 (mmm) cc_final: 0.3343 (ptm) REVERT: A 20 HIS cc_start: 0.7418 (OUTLIER) cc_final: 0.7001 (t-90) REVERT: A 24 MET cc_start: 0.8610 (ttm) cc_final: 0.7706 (ttm) REVERT: A 48 ASN cc_start: 0.8208 (m-40) cc_final: 0.7743 (t0) REVERT: A 69 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7599 (ttp80) REVERT: A 78 LYS cc_start: 0.7203 (mtmt) cc_final: 0.6901 (mtmt) REVERT: A 202 ASP cc_start: 0.8646 (m-30) cc_final: 0.8217 (t0) REVERT: B 64 GLU cc_start: 0.9075 (tp30) cc_final: 0.8783 (tm-30) REVERT: C 55 VAL cc_start: 0.9071 (t) cc_final: 0.8860 (t) REVERT: C 94 ASP cc_start: 0.9231 (t0) cc_final: 0.8835 (p0) REVERT: D 24 TYR cc_start: 0.8196 (t80) cc_final: 0.7940 (t80) REVERT: E 32 ASP cc_start: 0.8418 (t0) cc_final: 0.8203 (t0) REVERT: E 38 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8132 (tttm) REVERT: F 30 ASN cc_start: 0.7750 (t0) cc_final: 0.7487 (t0) REVERT: F 40 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8402 (mm) REVERT: F 197 ILE cc_start: 0.8464 (tp) cc_final: 0.8131 (pt) REVERT: F 303 ASN cc_start: 0.9147 (m-40) cc_final: 0.8941 (p0) REVERT: H 43 LYS cc_start: 0.8263 (pttp) cc_final: 0.7970 (mttp) REVERT: H 88 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7666 (tp) REVERT: H 137 MET cc_start: 0.7937 (tpp) cc_final: 0.7352 (tpp) REVERT: H 183 TYR cc_start: 0.6308 (t80) cc_final: 0.5525 (t80) REVERT: H 221 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.6982 (m-80) REVERT: H 234 PHE cc_start: 0.7813 (p90) cc_final: 0.7222 (p90) REVERT: H 248 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8144 (mptp) REVERT: I 363 TRP cc_start: 0.7988 (t-100) cc_final: 0.7676 (t-100) REVERT: I 364 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8072 (pm20) REVERT: I 449 PHE cc_start: 0.8343 (t80) cc_final: 0.7569 (t80) REVERT: I 465 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: I 482 TRP cc_start: 0.7590 (p-90) cc_final: 0.7029 (p-90) REVERT: J 14 PHE cc_start: 0.8821 (t80) cc_final: 0.8503 (t80) REVERT: J 15 ILE cc_start: 0.8710 (mm) cc_final: 0.8390 (mm) REVERT: J 18 PHE cc_start: 0.9430 (t80) cc_final: 0.9081 (t80) REVERT: J 22 MET cc_start: 0.8960 (ppp) cc_final: 0.8509 (ppp) REVERT: J 46 GLU cc_start: 0.8641 (tm-30) cc_final: 0.7802 (pt0) REVERT: J 80 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: J 100 TRP cc_start: 0.8740 (m-10) cc_final: 0.8115 (m-10) REVERT: J 108 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.4966 (t80) REVERT: K 6 GLU cc_start: 0.8496 (pm20) cc_final: 0.7948 (tp30) REVERT: K 19 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8484 (mp10) REVERT: L 75 ASN cc_start: 0.8944 (t0) cc_final: 0.8413 (t0) REVERT: L 95 GLN cc_start: 0.9421 (mp10) cc_final: 0.9147 (mp10) outliers start: 113 outliers final: 77 residues processed: 458 average time/residue: 0.1640 time to fit residues: 119.6508 Evaluate side-chains 448 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 360 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 264 CYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 303 MET Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 350 ASP Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 81 HIS Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 232 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 264 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN F 171 HIS ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 GLN ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.100346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.079849 restraints weight = 119721.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.081789 restraints weight = 73207.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.082916 restraints weight = 51047.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.083863 restraints weight = 40579.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.084440 restraints weight = 34688.164| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.7513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 26562 Z= 0.206 Angle : 0.764 17.380 36172 Z= 0.388 Chirality : 0.045 0.407 3869 Planarity : 0.005 0.095 4399 Dihedral : 15.181 179.598 4270 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.81 % Favored : 93.95 % Rotamer: Outliers : 4.23 % Allowed : 26.20 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.15), residues: 2943 helix: 0.29 (0.16), residues: 1017 sheet: -0.70 (0.22), residues: 580 loop : -0.67 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 46 TYR 0.048 0.002 TYR H 244 PHE 0.026 0.002 PHE K 68 TRP 0.040 0.002 TRP H 230 HIS 0.006 0.001 HIS I 22 Details of bonding type rmsd covalent geometry : bond 0.00451 (26562) covalent geometry : angle 0.76392 (36172) hydrogen bonds : bond 0.03945 ( 1052) hydrogen bonds : angle 5.31671 ( 3117) *********************** 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 485 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 373 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3679 (mmm) cc_final: 0.2904 (pmm) REVERT: A 20 HIS cc_start: 0.7388 (OUTLIER) cc_final: 0.6978 (t-90) REVERT: A 24 MET cc_start: 0.8737 (ttm) cc_final: 0.8103 (ttm) REVERT: A 48 ASN cc_start: 0.8253 (m-40) cc_final: 0.7885 (t0) REVERT: A 77 PHE cc_start: 0.7101 (m-80) cc_final: 0.6548 (m-10) REVERT: A 78 LYS cc_start: 0.7319 (mtmt) cc_final: 0.7005 (mtmt) REVERT: A 202 ASP cc_start: 0.8684 (m-30) cc_final: 0.8193 (t0) REVERT: B 63 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6024 (mt) REVERT: B 64 GLU cc_start: 0.9172 (tp30) cc_final: 0.8709 (tm-30) REVERT: C 94 ASP cc_start: 0.9256 (t0) cc_final: 0.8775 (p0) REVERT: D 24 TYR cc_start: 0.8226 (t80) cc_final: 0.7952 (t80) REVERT: E 38 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8159 (tttm) REVERT: F 30 ASN cc_start: 0.7904 (t0) cc_final: 0.7624 (t0) REVERT: F 40 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8457 (mm) REVERT: F 272 LEU cc_start: 0.9011 (tp) cc_final: 0.8292 (mt) REVERT: H 43 LYS cc_start: 0.8318 (pttp) cc_final: 0.7936 (mttm) REVERT: H 88 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7728 (tp) REVERT: H 144 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6929 (mmp) REVERT: H 183 TYR cc_start: 0.6373 (t80) cc_final: 0.5570 (t80) REVERT: H 221 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7052 (m-80) REVERT: H 234 PHE cc_start: 0.7749 (p90) cc_final: 0.7184 (p90) REVERT: I 31 MET cc_start: 0.6004 (ttt) cc_final: 0.5649 (tpt) REVERT: I 363 TRP cc_start: 0.8050 (t-100) cc_final: 0.7563 (t-100) REVERT: I 449 PHE cc_start: 0.8370 (t80) cc_final: 0.7561 (t80) REVERT: I 465 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.6527 (m-80) REVERT: I 482 TRP cc_start: 0.7832 (p-90) cc_final: 0.6992 (p-90) REVERT: I 484 GLU cc_start: 0.9316 (mp0) cc_final: 0.9062 (pm20) REVERT: J 10 GLN cc_start: 0.8842 (mt0) cc_final: 0.8642 (mp10) REVERT: J 14 PHE cc_start: 0.8997 (t80) cc_final: 0.8713 (t80) REVERT: J 15 ILE cc_start: 0.8708 (mm) cc_final: 0.8388 (mm) REVERT: J 22 MET cc_start: 0.8913 (ppp) cc_final: 0.8533 (ppp) REVERT: J 46 GLU cc_start: 0.8656 (tm-30) cc_final: 0.7914 (pt0) REVERT: J 80 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8587 (mt-10) REVERT: J 100 TRP cc_start: 0.8771 (m-10) cc_final: 0.8152 (m-10) REVERT: J 108 TYR cc_start: 0.6380 (OUTLIER) cc_final: 0.4625 (t80) REVERT: K 19 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: K 22 MET cc_start: 0.6375 (ptm) cc_final: 0.6162 (ppp) REVERT: L 75 ASN cc_start: 0.8986 (t0) cc_final: 0.8445 (t0) outliers start: 112 outliers final: 85 residues processed: 456 average time/residue: 0.1840 time to fit residues: 133.4985 Evaluate side-chains 452 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 356 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 264 CYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 303 MET Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 350 ASP Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 81 HIS Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 62 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 63 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 264 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 chunk 195 optimal weight: 8.9990 chunk 236 optimal weight: 0.7980 chunk 223 optimal weight: 0.0010 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 136 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 HIS G 215 ASN H 287 ASN ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN L 10 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.103630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.083252 restraints weight = 117026.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.085351 restraints weight = 70648.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.086647 restraints weight = 48699.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.087577 restraints weight = 38069.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.088047 restraints weight = 32038.971| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26562 Z= 0.141 Angle : 0.775 17.904 36172 Z= 0.386 Chirality : 0.046 0.329 3869 Planarity : 0.005 0.095 4399 Dihedral : 15.110 178.402 4270 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.16 % Favored : 94.60 % Rotamer: Outliers : 3.25 % Allowed : 27.52 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.15), residues: 2943 helix: 0.38 (0.16), residues: 1009 sheet: -0.62 (0.23), residues: 546 loop : -0.60 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 49 TYR 0.050 0.002 TYR H 244 PHE 0.037 0.002 PHE K 26 TRP 0.042 0.002 TRP I 288 HIS 0.006 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00316 (26562) covalent geometry : angle 0.77510 (36172) hydrogen bonds : bond 0.03748 ( 1052) hydrogen bonds : angle 5.18311 ( 3117) ********************** 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 486 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 400 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1 MET cc_start: 0.3876 (mmm) cc_final: 0.3229 (pmm) REVERT: A 20 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.6980 (t-90) REVERT: A 24 MET cc_start: 0.8736 (ttm) cc_final: 0.7895 (ttm) REVERT: A 41 LEU cc_start: 0.8740 (pp) cc_final: 0.8096 (mt) REVERT: A 48 ASN cc_start: 0.8276 (m-40) cc_final: 0.7799 (t0) REVERT: A 69 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7697 (ttt180) REVERT: A 77 PHE cc_start: 0.7036 (m-80) cc_final: 0.6413 (m-10) REVERT: A 78 LYS cc_start: 0.7331 (mtmt) cc_final: 0.7016 (mtmt) REVERT: A 202 ASP cc_start: 0.8563 (m-30) cc_final: 0.8106 (t0) REVERT: B 63 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.5982 (mt) REVERT: B 64 GLU cc_start: 0.9157 (tp30) cc_final: 0.8704 (tm-30) REVERT: B 203 MET cc_start: 0.8451 (ptp) cc_final: 0.7775 (pmm) REVERT: D 157 LEU cc_start: 0.8857 (mm) cc_final: 0.8408 (mt) REVERT: D 305 MET cc_start: 0.7965 (ttm) cc_final: 0.7527 (ttt) REVERT: F 30 ASN cc_start: 0.7670 (t0) cc_final: 0.7431 (t0) REVERT: F 175 TYR cc_start: 0.7741 (p90) cc_final: 0.7024 (p90) REVERT: F 272 LEU cc_start: 0.8941 (tp) cc_final: 0.8556 (mm) REVERT: G 61 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7509 (mtp180) REVERT: G 305 MET cc_start: 0.7291 (ttt) cc_final: 0.7013 (ttt) REVERT: H 43 LYS cc_start: 0.8165 (pttp) cc_final: 0.7790 (mttm) REVERT: H 137 MET cc_start: 0.7719 (tpp) cc_final: 0.7108 (tpp) REVERT: H 144 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6574 (mmp) REVERT: H 180 TYR cc_start: 0.7669 (m-80) cc_final: 0.6654 (m-80) REVERT: H 183 TYR cc_start: 0.6137 (t80) cc_final: 0.5405 (t80) REVERT: H 221 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7023 (m-80) REVERT: I 31 MET cc_start: 0.5991 (ttt) cc_final: 0.5754 (tpt) REVERT: I 62 PHE cc_start: 0.0015 (OUTLIER) cc_final: -0.0456 (m-80) REVERT: I 363 TRP cc_start: 0.7938 (t-100) cc_final: 0.7499 (t-100) REVERT: I 410 MET cc_start: 0.7695 (ptm) cc_final: 0.7486 (ptt) REVERT: I 433 VAL cc_start: 0.8695 (t) cc_final: 0.8457 (p) REVERT: I 449 PHE cc_start: 0.8332 (t80) cc_final: 0.8019 (t80) REVERT: I 484 GLU cc_start: 0.9270 (mp0) cc_final: 0.9019 (pm20) REVERT: J 10 GLN cc_start: 0.8863 (mt0) cc_final: 0.8656 (mp10) REVERT: J 14 PHE cc_start: 0.8830 (t80) cc_final: 0.8606 (t80) REVERT: J 15 ILE cc_start: 0.8647 (mm) cc_final: 0.8236 (mm) REVERT: J 22 MET cc_start: 0.8971 (ppp) cc_final: 0.8605 (ppp) REVERT: J 34 GLU cc_start: 0.3599 (pm20) cc_final: 0.3165 (mp0) REVERT: J 58 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7838 (mp0) REVERT: J 64 TYR cc_start: 0.7623 (t80) cc_final: 0.7329 (t80) REVERT: J 80 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: J 108 TYR cc_start: 0.6621 (OUTLIER) cc_final: 0.5052 (t80) REVERT: K 6 GLU cc_start: 0.8543 (pm20) cc_final: 0.7882 (tp30) REVERT: K 78 PHE cc_start: 0.8079 (t80) cc_final: 0.7766 (t80) REVERT: L 53 ASN cc_start: 0.8708 (p0) cc_final: 0.8392 (t0) REVERT: L 75 ASN cc_start: 0.9050 (t0) cc_final: 0.8537 (t0) REVERT: L 81 HIS cc_start: 0.8376 (m90) cc_final: 0.8101 (m90) outliers start: 86 outliers final: 63 residues processed: 462 average time/residue: 0.1756 time to fit residues: 128.8854 Evaluate side-chains 438 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 368 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 264 CYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 101 SER 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 44 LYS Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 10 GLN Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 46 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 221 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 238 optimal weight: 0.0980 chunk 290 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN E 229 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 10 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.102778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.082592 restraints weight = 117780.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.084624 restraints weight = 70406.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.085813 restraints weight = 49115.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.086732 restraints weight = 38937.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.086935 restraints weight = 33123.198| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.7723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26562 Z= 0.151 Angle : 0.767 17.795 36172 Z= 0.385 Chirality : 0.045 0.304 3869 Planarity : 0.005 0.096 4399 Dihedral : 15.081 178.934 4269 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.33 % Favored : 94.46 % Rotamer: Outliers : 3.10 % Allowed : 27.75 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.16), residues: 2943 helix: 0.32 (0.16), residues: 1013 sheet: -0.65 (0.22), residues: 572 loop : -0.63 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 163 TYR 0.041 0.002 TYR B 29 PHE 0.038 0.002 PHE K 26 TRP 0.036 0.002 TRP I 288 HIS 0.004 0.001 HIS H 31 Details of bonding type rmsd covalent geometry : bond 0.00342 (26562) covalent geometry : angle 0.76672 (36172) hydrogen bonds : bond 0.03745 ( 1052) hydrogen bonds : angle 5.19572 ( 3117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5329.49 seconds wall clock time: 93 minutes 21.05 seconds (5601.05 seconds total)