Starting phenix.real_space_refine on Sat Dec 28 05:23:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ff4_29039/12_2024/8ff4_29039_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ff4_29039/12_2024/8ff4_29039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ff4_29039/12_2024/8ff4_29039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ff4_29039/12_2024/8ff4_29039.map" model { file = "/net/cci-nas-00/data/ceres_data/8ff4_29039/12_2024/8ff4_29039_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ff4_29039/12_2024/8ff4_29039_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.113 sd= 0.968 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 859 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: 6 Type Number sf(0) Gaussians P 221 5.49 5 Mg 7 5.21 5 S 169 5.16 5 C 31473 2.51 5 N 8660 2.21 5 O 9792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 50322 Number of models: 1 Model: "" Number of chains: 30 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: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1702 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 199} 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: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2330 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} 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: 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: "H" 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: "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': 17, 'rna2p_pyr': 9, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 26, 'rna3p': 36} Chain: "N" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1734 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "O" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1070 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain breaks: 1 Chain: "P" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2618 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain: "Q" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2508 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "R" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "S" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "T" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "U" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "V" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "W" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.14, per 1000 atoms: 0.42 Number of scatterers: 50322 At special positions: 0 Unit cell: (135.966, 238.204, 254.014, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 169 16.00 P 221 15.00 Mg 7 11.99 O 9792 8.00 N 8660 7.00 C 31473 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: 10.54 Conformation dependent library (CDL) restraints added in 4.4 seconds 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10638 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 61 sheets defined 50.4% alpha, 14.0% beta 77 base pairs and 130 stacking pairs defined. Time for finding SS restraints: 13.84 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 40 through 44 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 142 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.634A 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: 3.617A 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 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' 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: 3.873A pdb=" N MET C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.897A 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 285 removed outlier: 3.610A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.535A pdb=" N MET C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) 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 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: 3.644A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.751A 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: 4.019A 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 removed outlier: 3.612A pdb=" N MET D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.586A 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: 3.772A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 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 285 removed outlier: 3.910A 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 removed outlier: 3.644A pdb=" N MET E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.634A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.554A 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: 3.932A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.801A 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: 3.716A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 removed outlier: 3.542A pdb=" N MET F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) 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 72 removed outlier: 3.749A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 104 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: 3.670A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.517A pdb=" N ILE G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) 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: 3.949A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 296 Processing helix chain 'G' and resid 301 through 317 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: 3.526A 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 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: 3.671A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.886A 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 284 removed outlier: 3.946A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 Processing helix chain 'H' and resid 301 through 318 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 42 through 46 Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.940A 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 152 through 157 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 238 through 250 Processing helix chain 'I' and resid 253 through 257 removed outlier: 3.572A pdb=" N PHE I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 253 through 257' Processing helix chain 'I' and resid 261 through 270 Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 removed outlier: 3.641A pdb=" N SER I 346 " --> pdb=" O ASN I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 367 Processing helix chain 'I' and resid 373 through 393 removed outlier: 3.957A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY I 385 " --> pdb=" O SER I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 421 removed outlier: 4.544A pdb=" N TYR I 399 " --> pdb=" O GLU I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 Processing helix chain 'I' and resid 445 through 461 removed outlier: 3.756A pdb=" N GLY I 461 " --> pdb=" O LEU I 457 " (cutoff:3.500A) 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 5 through 33 Processing helix chain 'J' and resid 41 through 54 Processing helix chain 'J' and resid 58 through 73 removed outlier: 6.086A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY J 73 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 81 Processing helix chain 'J' and resid 81 through 91 Processing helix chain 'J' and resid 93 through 108 Processing helix chain 'J' and resid 109 through 112 Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 41 through 54 Processing helix chain 'K' and resid 58 through 73 removed outlier: 6.029A pdb=" N TYR K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 81 removed outlier: 3.769A pdb=" N HIS K 81 " --> pdb=" O TYR K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 91 removed outlier: 4.059A pdb=" N ILE K 85 " --> pdb=" O HIS K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 109 removed outlier: 4.502A pdb=" N LYS K 109 " --> pdb=" O ILE K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.800A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 removed outlier: 3.549A pdb=" N HIS L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 92 Processing helix chain 'L' and resid 93 through 107 Processing helix chain 'P' and resid 36 through 48 Processing helix chain 'P' and resid 51 through 65 removed outlier: 4.670A pdb=" N ALA P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) Proline residue: P 62 - end of helix Processing helix chain 'P' and resid 69 through 74 Processing helix chain 'P' and resid 75 through 77 No H-bonds generated for 'chain 'P' and resid 75 through 77' Processing helix chain 'P' and resid 78 through 83 Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 95 through 110 Processing helix chain 'P' and resid 113 through 118 removed outlier: 3.603A pdb=" N THR P 118 " --> pdb=" O ARG P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 123 Processing helix chain 'P' and resid 139 through 149 Processing helix chain 'P' and resid 156 through 161 Processing helix chain 'P' and resid 214 through 235 removed outlier: 4.557A pdb=" N VAL P 219 " --> pdb=" O GLU P 215 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASN P 220 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR P 231 " --> pdb=" O LEU P 227 " (cutoff:3.500A) Proline residue: P 232 - end of helix removed outlier: 4.452A pdb=" N GLY P 235 " --> pdb=" O THR P 231 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 261 Processing helix chain 'P' and resid 263 through 281 removed outlier: 3.831A pdb=" N ASP P 267 " --> pdb=" O LYS P 263 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLY P 270 " --> pdb=" O GLY P 266 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE P 271 " --> pdb=" O ASP P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 292 through 300 Processing helix chain 'P' and resid 303 through 310 Processing helix chain 'P' and resid 311 through 323 Processing helix chain 'Q' and resid 8 through 13 removed outlier: 3.716A pdb=" N LEU Q 12 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 25 Processing helix chain 'Q' and resid 30 through 46 Processing helix chain 'Q' and resid 62 through 83 Proline residue: Q 80 - end of helix removed outlier: 4.384A pdb=" N GLU Q 83 " --> pdb=" O LEU Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 117 removed outlier: 3.787A pdb=" N TYR Q 109 " --> pdb=" O ASN Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 164 Processing helix chain 'Q' and resid 172 through 178 removed outlier: 3.534A pdb=" N LYS Q 178 " --> pdb=" O HIS Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 198 removed outlier: 4.237A pdb=" N GLN Q 186 " --> pdb=" O GLY Q 182 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU Q 189 " --> pdb=" O LEU Q 185 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET Q 198 " --> pdb=" O SER Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 208 through 214 removed outlier: 3.645A pdb=" N THR Q 213 " --> pdb=" O GLU Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 217 through 224 removed outlier: 3.904A pdb=" N LEU Q 221 " --> pdb=" O LEU Q 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG Q 224 " --> pdb=" O GLN Q 220 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 254 Processing helix chain 'Q' and resid 266 through 273 removed outlier: 3.575A pdb=" N ARG Q 273 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 295 Processing helix chain 'Q' and resid 301 through 308 removed outlier: 3.868A pdb=" N ARG Q 308 " --> pdb=" O ASP Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 311 through 330 Processing helix chain 'R' and resid 8 through 13 removed outlier: 3.595A pdb=" N LEU R 11 " --> pdb=" O PRO R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 26 removed outlier: 3.505A pdb=" N ARG R 19 " --> pdb=" O PRO R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 46 removed outlier: 3.560A pdb=" N GLU R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 85 Proline residue: R 80 - end of helix removed outlier: 3.634A pdb=" N SER R 84 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 118 Processing helix chain 'R' and resid 148 through 164 Processing helix chain 'R' and resid 172 through 178 removed outlier: 3.510A pdb=" N LYS R 178 " --> pdb=" O HIS R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 200 removed outlier: 3.528A pdb=" N ASP R 187 " --> pdb=" O TYR R 183 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 218 through 224 Processing helix chain 'R' and resid 237 through 254 removed outlier: 3.533A pdb=" N VAL R 241 " --> pdb=" O SER R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 275 Processing helix chain 'R' and resid 277 through 296 Processing helix chain 'R' and resid 301 through 308 removed outlier: 3.507A pdb=" N LEU R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG R 308 " --> pdb=" O ASP R 304 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 329 removed outlier: 3.849A pdb=" N GLN R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 343 removed outlier: 3.727A pdb=" N ASN R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU R 339 " --> pdb=" O ASP R 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 14 removed outlier: 3.660A pdb=" N LEU S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 26 removed outlier: 3.502A pdb=" N ARG S 19 " --> pdb=" O PRO S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.609A pdb=" N GLU S 46 " --> pdb=" O ARG S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 Proline residue: S 80 - end of helix Processing helix chain 'S' and resid 105 through 118 Processing helix chain 'S' and resid 148 through 164 Processing helix chain 'S' and resid 172 through 178 removed outlier: 3.568A pdb=" N LYS S 178 " --> pdb=" O HIS S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 200 removed outlier: 3.832A pdb=" N ASP S 187 " --> pdb=" O TYR S 183 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET S 198 " --> pdb=" O SER S 194 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR S 199 " --> pdb=" O LEU S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 215 Processing helix chain 'S' and resid 218 through 224 removed outlier: 3.734A pdb=" N ARG S 224 " --> pdb=" O GLN S 220 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 254 Processing helix chain 'S' and resid 266 through 275 Processing helix chain 'S' and resid 277 through 295 removed outlier: 3.540A pdb=" N LEU S 281 " --> pdb=" O CYS S 277 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 309 removed outlier: 3.611A pdb=" N ARG S 308 " --> pdb=" O ASP S 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 311 through 329 Processing helix chain 'S' and resid 332 through 343 removed outlier: 3.658A pdb=" N VAL S 336 " --> pdb=" O THR S 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 13 removed outlier: 3.511A pdb=" N LEU T 12 " --> pdb=" O LEU T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 26 removed outlier: 3.736A pdb=" N ARG T 19 " --> pdb=" O PRO T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 46 Processing helix chain 'T' and resid 62 through 85 Proline residue: T 80 - end of helix removed outlier: 4.017A pdb=" N SER T 84 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 118 removed outlier: 4.097A pdb=" N TYR T 109 " --> pdb=" O ASN T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 148 through 164 Processing helix chain 'T' and resid 172 through 178 removed outlier: 3.512A pdb=" N LYS T 178 " --> pdb=" O HIS T 175 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 200 removed outlier: 3.520A pdb=" N LEU T 185 " --> pdb=" O SER T 181 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN T 186 " --> pdb=" O GLY T 182 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU T 189 " --> pdb=" O LEU T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 208 through 215 removed outlier: 3.508A pdb=" N THR T 213 " --> pdb=" O GLU T 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 218 through 224 Processing helix chain 'T' and resid 237 through 254 Processing helix chain 'T' and resid 266 through 275 Processing helix chain 'T' and resid 277 through 296 Processing helix chain 'T' and resid 301 through 308 removed outlier: 3.550A pdb=" N ARG T 308 " --> pdb=" O ASP T 304 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 329 Processing helix chain 'T' and resid 332 through 343 removed outlier: 3.631A pdb=" N VAL T 336 " --> pdb=" O THR T 332 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 13 removed outlier: 3.574A pdb=" N LEU U 11 " --> pdb=" O PRO U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 26 removed outlier: 3.582A pdb=" N ARG U 19 " --> pdb=" O PRO U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 46 removed outlier: 3.590A pdb=" N GLU U 46 " --> pdb=" O ARG U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 85 Proline residue: U 80 - end of helix removed outlier: 3.539A pdb=" N SER U 84 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 118 Processing helix chain 'U' and resid 148 through 164 Processing helix chain 'U' and resid 172 through 178 Processing helix chain 'U' and resid 183 through 200 removed outlier: 3.726A pdb=" N ASP U 187 " --> pdb=" O TYR U 183 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET U 198 " --> pdb=" O SER U 194 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR U 199 " --> pdb=" O LEU U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 208 through 215 Processing helix chain 'U' and resid 218 through 224 Processing helix chain 'U' and resid 237 through 254 Processing helix chain 'U' and resid 263 through 265 No H-bonds generated for 'chain 'U' and resid 263 through 265' Processing helix chain 'U' and resid 266 through 275 removed outlier: 3.550A pdb=" N PHE U 270 " --> pdb=" O HIS U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 277 through 296 Processing helix chain 'U' and resid 301 through 308 removed outlier: 3.716A pdb=" N ARG U 308 " --> pdb=" O ASP U 304 " (cutoff:3.500A) Processing helix chain 'U' and resid 311 through 329 Processing helix chain 'U' and resid 332 through 344 removed outlier: 3.751A pdb=" N VAL U 336 " --> pdb=" O THR U 332 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 13 removed outlier: 3.545A pdb=" N LEU V 11 " --> pdb=" O PRO V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 26 Processing helix chain 'V' and resid 30 through 46 removed outlier: 4.118A pdb=" N GLU V 46 " --> pdb=" O ARG V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 78 Processing helix chain 'V' and resid 78 through 85 Processing helix chain 'V' and resid 105 through 118 Processing helix chain 'V' and resid 148 through 164 Processing helix chain 'V' and resid 173 through 178 removed outlier: 3.754A pdb=" N LYS V 178 " --> pdb=" O HIS V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 200 removed outlier: 4.014A pdb=" N LEU V 189 " --> pdb=" O LEU V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 208 through 215 Processing helix chain 'V' and resid 217 through 224 removed outlier: 4.009A pdb=" N LEU V 221 " --> pdb=" O LEU V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 237 through 254 Processing helix chain 'V' and resid 266 through 275 Processing helix chain 'V' and resid 277 through 295 removed outlier: 3.622A pdb=" N ARG V 295 " --> pdb=" O ASP V 291 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 308 removed outlier: 3.605A pdb=" N ARG V 308 " --> pdb=" O ASP V 304 " (cutoff:3.500A) Processing helix chain 'V' and resid 311 through 329 removed outlier: 3.846A pdb=" N LYS V 317 " --> pdb=" O ALA V 313 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE V 319 " --> pdb=" O CYS V 315 " (cutoff:3.500A) Processing helix chain 'V' and resid 332 through 344 Processing helix chain 'W' and resid 8 through 12 removed outlier: 3.635A pdb=" N LEU W 11 " --> pdb=" O PRO W 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU W 12 " --> pdb=" O LEU W 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 8 through 12' Processing helix chain 'W' and resid 15 through 26 Processing helix chain 'W' and resid 30 through 46 removed outlier: 3.646A pdb=" N GLU W 46 " --> pdb=" O ARG W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 83 removed outlier: 3.649A pdb=" N LEU W 79 " --> pdb=" O THR W 75 " (cutoff:3.500A) Proline residue: W 80 - end of helix Processing helix chain 'W' and resid 105 through 118 Processing helix chain 'W' and resid 148 through 164 Processing helix chain 'W' and resid 172 through 177 removed outlier: 3.783A pdb=" N HIS W 175 " --> pdb=" O GLU W 172 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY W 177 " --> pdb=" O GLN W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 200 Processing helix chain 'W' and resid 208 through 215 removed outlier: 3.550A pdb=" N THR W 213 " --> pdb=" O GLU W 210 " (cutoff:3.500A) Processing helix chain 'W' and resid 218 through 224 removed outlier: 3.606A pdb=" N ARG W 224 " --> pdb=" O GLN W 220 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 254 Processing helix chain 'W' and resid 263 through 265 No H-bonds generated for 'chain 'W' and resid 263 through 265' Processing helix chain 'W' and resid 266 through 275 Processing helix chain 'W' and resid 277 through 295 Processing helix chain 'W' and resid 301 through 308 removed outlier: 3.927A pdb=" N LEU W 305 " --> pdb=" O THR W 301 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN W 306 " --> pdb=" O LEU W 302 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG W 308 " --> pdb=" O ASP W 304 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 329 Processing helix chain 'W' and resid 332 through 343 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.984A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 160 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 6.915A 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: 6.994A pdb=" N ILE A 6 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TRP A 104 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR A 8 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 102 " --> pdb=" O TYR A 8 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP A 10 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 100 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.490A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.490A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (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: 6.294A pdb=" N PHE B 177 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 119 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.555A 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: 5.555A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.665A 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 Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB4, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.395A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.395A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 225 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 276 " --> pdb=" O TYR D 299 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AB7, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AB8, first strand: chain 'D' and resid 155 through 156 Processing sheet with id=AB9, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC1, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AC2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.620A pdb=" N SER E 225 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY E 276 " --> pdb=" O TYR E 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AC4, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.565A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'E' and resid 155 through 159 Processing sheet with id=AC7, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR F 182 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR F 15 " --> pdb=" O TRP F 230 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TRP F 230 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR F 17 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE F 228 " --> pdb=" O TYR F 17 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR F 19 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU F 226 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU F 21 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY F 276 " --> pdb=" O TYR F 299 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.689A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD3, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.398A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR G 183 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA G 145 " --> pdb=" O GLN G 181 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLN G 181 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 225 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 25 through 27 removed outlier: 3.782A pdb=" N GLY G 25 " --> pdb=" O THR G 178 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD6, first strand: chain 'G' and resid 77 through 80 Processing sheet with id=AD7, first strand: chain 'G' and resid 106 through 107 removed outlier: 4.048A pdb=" N PHE G 106 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD9, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.422A 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: 6.904A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE3, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AE4, first strand: chain 'I' and resid 9 through 12 removed outlier: 4.081A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 61 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 11 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AE6, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.591A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AE8, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.376A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 332 through 333 Processing sheet with id=AF1, first strand: chain 'P' and resid 7 through 8 removed outlier: 3.544A pdb=" N TRP P 8 " --> pdb=" O THR Q 27 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR Q 27 " --> pdb=" O TRP P 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'P' and resid 166 through 167 removed outlier: 3.612A pdb=" N GLN P 172 " --> pdb=" O CYS P 167 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 55 through 57 Processing sheet with id=AF4, first strand: chain 'Q' and resid 91 through 95 removed outlier: 6.646A pdb=" N VAL Q 92 " --> pdb=" O PHE Q 169 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP Q 171 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE Q 94 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE Q 168 " --> pdb=" O CYS Q 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'R' and resid 91 through 95 removed outlier: 3.571A pdb=" N VAL R 92 " --> pdb=" O VAL R 167 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE R 168 " --> pdb=" O CYS R 204 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU R 206 " --> pdb=" O PHE R 168 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL R 170 " --> pdb=" O LEU R 206 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE R 52 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE R 228 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE R 54 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE R 230 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR R 56 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 133 through 134 removed outlier: 3.791A pdb=" N SER R 134 " --> pdb=" O ASN R 142 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 91 through 95 removed outlier: 6.661A pdb=" N VAL S 92 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP S 171 " --> pdb=" O VAL S 92 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE S 94 " --> pdb=" O ASP S 171 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE S 53 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLY S 207 " --> pdb=" O ILE S 53 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL S 55 " --> pdb=" O GLY S 207 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE S 52 " --> pdb=" O VAL S 226 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE S 228 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE S 54 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE S 230 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR S 56 " --> pdb=" O PHE S 230 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 133 through 134 removed outlier: 3.550A pdb=" N SER S 134 " --> pdb=" O ASN S 142 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 91 through 95 removed outlier: 6.792A pdb=" N PHE T 52 " --> pdb=" O VAL T 226 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE T 228 " --> pdb=" O PHE T 52 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE T 54 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE T 230 " --> pdb=" O PHE T 54 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR T 56 " --> pdb=" O PHE T 230 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 133 through 134 Processing sheet with id=AG2, first strand: chain 'U' and resid 91 through 95 removed outlier: 6.951A pdb=" N VAL U 92 " --> pdb=" O PHE U 169 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP U 171 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE U 94 " --> pdb=" O ASP U 171 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE U 53 " --> pdb=" O LEU U 205 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 133 through 134 Processing sheet with id=AG4, first strand: chain 'V' and resid 92 through 95 removed outlier: 7.137A pdb=" N VAL V 92 " --> pdb=" O PHE V 169 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ASP V 171 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE V 94 " --> pdb=" O ASP V 171 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE V 53 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY V 207 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL V 55 " --> pdb=" O GLY V 207 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE V 52 " --> pdb=" O VAL V 226 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE V 228 " --> pdb=" O PHE V 52 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE V 54 " --> pdb=" O ILE V 228 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE V 230 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR V 56 " --> pdb=" O PHE V 230 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 133 through 134 removed outlier: 3.837A pdb=" N SER V 134 " --> pdb=" O ASN V 142 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 92 through 94 removed outlier: 7.142A pdb=" N VAL W 92 " --> pdb=" O PHE W 169 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE W 53 " --> pdb=" O LEU W 205 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLY W 207 " --> pdb=" O ILE W 53 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL W 55 " --> pdb=" O GLY W 207 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE W 52 " --> pdb=" O VAL W 226 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE W 228 " --> pdb=" O PHE W 52 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE W 54 " --> pdb=" O ILE W 228 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 133 through 135 2219 hydrogen bonds defined for protein. 6177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 187 hydrogen bonds 374 hydrogen bond angles 0 basepair planarities 77 basepair parallelities 130 stacking parallelities Total time for adding SS restraints: 18.16 Time building geometry restraints manager: 12.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 15392 1.34 - 1.46: 13510 1.46 - 1.59: 22312 1.59 - 1.71: 409 1.71 - 1.84: 253 Bond restraints: 51876 Sorted by residual: bond pdb=" N SER V 59 " pdb=" CA SER V 59 " ideal model delta sigma weight residual 1.463 1.433 0.030 1.30e-02 5.92e+03 5.23e+00 bond pdb=" CA VAL T 61 " pdb=" C VAL T 61 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.27e-02 6.20e+03 3.82e+00 bond pdb=" CA ASP D 246 " pdb=" C ASP D 246 " ideal model delta sigma weight residual 1.524 1.508 0.016 8.10e-03 1.52e+04 3.68e+00 bond pdb=" CA SER U 59 " pdb=" C SER U 59 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.30e-02 5.92e+03 3.49e+00 bond pdb=" O3' DC N 50 " pdb=" P DT N 51 " ideal model delta sigma weight residual 1.607 1.634 -0.027 1.50e-02 4.44e+03 3.34e+00 ... (remaining 51871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 69619 2.01 - 4.02: 1235 4.02 - 6.03: 156 6.03 - 8.05: 35 8.05 - 10.06: 10 Bond angle restraints: 71055 Sorted by residual: angle pdb=" N THR U 299 " pdb=" CA THR U 299 " pdb=" C THR U 299 " ideal model delta sigma weight residual 108.74 115.59 -6.85 1.38e+00 5.25e-01 2.46e+01 angle pdb=" N ALA U 58 " pdb=" CA ALA U 58 " pdb=" C ALA U 58 " ideal model delta sigma weight residual 110.41 116.25 -5.84 1.23e+00 6.61e-01 2.26e+01 angle pdb=" C VAL R 61 " pdb=" N GLY R 62 " pdb=" CA GLY R 62 " ideal model delta sigma weight residual 122.26 116.33 5.93 1.34e+00 5.57e-01 1.96e+01 angle pdb=" N TYR K 108 " pdb=" CA TYR K 108 " pdb=" C TYR K 108 " ideal model delta sigma weight residual 112.90 107.11 5.79 1.31e+00 5.83e-01 1.96e+01 angle pdb=" C TYR I 40 " pdb=" N PRO I 41 " pdb=" CA PRO I 41 " ideal model delta sigma weight residual 119.19 114.59 4.60 1.06e+00 8.90e-01 1.89e+01 ... (remaining 71050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 29243 35.81 - 71.62: 1614 71.62 - 107.43: 86 107.43 - 143.24: 3 143.24 - 179.05: 6 Dihedral angle restraints: 30952 sinusoidal: 14414 harmonic: 16538 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 20.95 179.05 1 1.50e+01 4.44e-03 8.53e+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 52.72 147.28 1 1.50e+01 4.44e-03 7.86e+01 dihedral pdb=" O4' U M 32 " pdb=" C1' U M 32 " pdb=" N1 U M 32 " pdb=" C2 U M 32 " ideal model delta sinusoidal sigma weight residual 232.00 66.54 165.46 1 1.70e+01 3.46e-03 6.54e+01 ... (remaining 30949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 6246 0.045 - 0.091: 1165 0.091 - 0.136: 335 0.136 - 0.182: 27 0.182 - 0.227: 6 Chirality restraints: 7779 Sorted by residual: chirality pdb=" C3' A M 38 " pdb=" C4' A M 38 " pdb=" O3' A M 38 " pdb=" C2' A M 38 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE J 13 " pdb=" CA ILE J 13 " pdb=" CG1 ILE J 13 " pdb=" CG2 ILE J 13 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE H 267 " pdb=" CA ILE H 267 " pdb=" CG1 ILE H 267 " pdb=" CG2 ILE H 267 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 7776 not shown) Planarity restraints: 8346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " -0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO F 247 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C PHE J 61 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE J 61 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 61 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C PHE K 61 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE K 61 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS K 62 " -0.018 2.00e-02 2.50e+03 ... (remaining 8343 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 571 2.57 - 3.15: 42049 3.15 - 3.73: 85161 3.73 - 4.32: 116089 4.32 - 4.90: 186466 Nonbonded interactions: 430336 Sorted by model distance: nonbonded pdb=" O3A ATP V 600 " pdb="MG MG V 601 " model vdw 1.983 2.170 nonbonded pdb=" O3B ATP T 600 " pdb="MG MG T 601 " model vdw 1.995 2.170 nonbonded pdb=" O3B ATP U 600 " pdb="MG MG U 601 " model vdw 2.000 2.170 nonbonded pdb=" O3B ATP Q 600 " pdb="MG MG Q 601 " model vdw 2.003 2.170 nonbonded pdb=" O3B ATP S 600 " pdb="MG MG S 601 " model vdw 2.005 2.170 ... (remaining 430331 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' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'Q' selection = (chain 'R' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'S' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'T' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'U' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'V' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'W' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) } 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.030 Extract box with map and model: 1.610 Check model and map are aligned: 0.270 Set scattering table: 0.360 Process input model: 94.270 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:1.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 0.059 51876 Z= 0.187 Angle : 0.643 10.058 71055 Z= 0.364 Chirality : 0.040 0.227 7779 Planarity : 0.004 0.088 8346 Dihedral : 19.458 179.052 20314 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.84 % Favored : 93.60 % Rotamer: Outliers : 0.71 % Allowed : 22.68 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.12), residues: 5598 helix: 1.17 (0.10), residues: 2570 sheet: -0.83 (0.18), residues: 800 loop : -0.86 (0.14), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP I 63 HIS 0.010 0.001 HIS W 162 PHE 0.047 0.001 PHE V 126 TYR 0.038 0.001 TYR C 244 ARG 0.011 0.000 ARG V 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 422 time to evaluate : 4.216 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: A 1 MET cc_start: 0.6465 (tpt) cc_final: 0.6155 (tpt) REVERT: A 116 LEU cc_start: 0.9228 (tp) cc_final: 0.8950 (tp) REVERT: A 209 GLN cc_start: 0.8860 (tt0) cc_final: 0.8573 (mt0) REVERT: B 118 ARG cc_start: 0.5287 (tmt170) cc_final: 0.4274 (ttt-90) REVERT: B 213 ARG cc_start: 0.4531 (tpp80) cc_final: 0.4012 (tpp80) REVERT: F 260 ASP cc_start: 0.9111 (t0) cc_final: 0.8903 (t0) REVERT: I 46 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7276 (mtt180) REVERT: I 358 TRP cc_start: 0.5740 (OUTLIER) cc_final: 0.5476 (p90) REVERT: J 87 LEU cc_start: 0.9249 (tp) cc_final: 0.9004 (tp) REVERT: P 40 TYR cc_start: 0.9251 (t80) cc_final: 0.8862 (t80) REVERT: P 99 GLU cc_start: 0.9395 (tp30) cc_final: 0.9156 (tp30) REVERT: P 272 MET cc_start: 0.8879 (ttm) cc_final: 0.8507 (ttm) REVERT: Q 191 CYS cc_start: 0.8268 (m) cc_final: 0.7975 (t) REVERT: S 9 LEU cc_start: 0.8215 (pt) cc_final: 0.7954 (mp) REVERT: T 61 VAL cc_start: 0.7330 (OUTLIER) cc_final: 0.6995 (m) REVERT: U 24 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7866 (mt-10) REVERT: U 86 ARG cc_start: 0.8396 (mmm160) cc_final: 0.7913 (mmm160) REVERT: W 61 VAL cc_start: 0.5589 (OUTLIER) cc_final: 0.5383 (m) REVERT: W 97 ILE cc_start: 0.7842 (pt) cc_final: 0.7549 (tt) REVERT: W 201 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7758 (mm) outliers start: 35 outliers final: 9 residues processed: 447 average time/residue: 0.4834 time to fit residues: 366.4668 Evaluate side-chains 384 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 370 time to evaluate : 4.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain I residue 46 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 291 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 485 optimal weight: 2.9990 chunk 435 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 450 optimal weight: 0.0970 chunk 174 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 522 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 195 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 ASN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 124 HIS ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 216 ASN T 197 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 51876 Z= 0.364 Angle : 0.649 10.825 71055 Z= 0.344 Chirality : 0.042 0.201 7779 Planarity : 0.005 0.094 8346 Dihedral : 18.495 175.694 9002 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.75 % Favored : 93.82 % Rotamer: Outliers : 3.10 % Allowed : 19.75 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.12), residues: 5598 helix: 1.24 (0.10), residues: 2639 sheet: -0.90 (0.19), residues: 779 loop : -0.86 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 52 HIS 0.008 0.001 HIS H 171 PHE 0.022 0.002 PHE G 234 TYR 0.020 0.002 TYR K 108 ARG 0.007 0.001 ARG J 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 383 time to evaluate : 4.359 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: A 1 MET cc_start: 0.6364 (tpt) cc_final: 0.6128 (tpt) REVERT: A 140 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6973 (tm-30) REVERT: A 202 ASP cc_start: 0.8299 (p0) cc_final: 0.7905 (p0) REVERT: B 213 ARG cc_start: 0.4599 (tpp80) cc_final: 0.3897 (tpp80) REVERT: D 136 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7340 (ttt90) REVERT: E 247 PRO cc_start: 0.7576 (Cg_exo) cc_final: 0.7322 (Cg_endo) REVERT: F 30 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.7968 (m110) REVERT: F 77 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8855 (ttp-170) REVERT: F 137 MET cc_start: 0.8463 (tpp) cc_final: 0.8207 (tpp) REVERT: F 260 ASP cc_start: 0.9185 (t0) cc_final: 0.8971 (t0) REVERT: G 77 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7893 (mtm-85) REVERT: H 181 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: I 62 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7127 (m-10) REVERT: I 303 MET cc_start: 0.8661 (mmp) cc_final: 0.8089 (mmm) REVERT: I 358 TRP cc_start: 0.5807 (OUTLIER) cc_final: 0.5567 (p90) REVERT: I 451 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8663 (tp30) REVERT: J 48 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9502 (tp) REVERT: J 63 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7942 (mp0) REVERT: P 99 GLU cc_start: 0.9373 (tp30) cc_final: 0.9172 (tp30) REVERT: Q 25 ASN cc_start: 0.8470 (m110) cc_final: 0.8266 (m110) REVERT: Q 191 CYS cc_start: 0.8278 (m) cc_final: 0.8060 (t) REVERT: Q 215 ARG cc_start: 0.6177 (OUTLIER) cc_final: 0.5618 (ptt90) REVERT: R 198 MET cc_start: 0.8264 (mtm) cc_final: 0.7732 (mtm) REVERT: S 9 LEU cc_start: 0.8362 (pt) cc_final: 0.8128 (mp) REVERT: S 102 ARG cc_start: 0.8454 (ttm110) cc_final: 0.7892 (ttm110) REVERT: S 105 ASN cc_start: 0.8769 (t0) cc_final: 0.8420 (t0) REVERT: S 324 GLU cc_start: 0.8069 (pp20) cc_final: 0.7600 (tm-30) REVERT: T 61 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7399 (m) REVERT: T 108 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8278 (tp30) REVERT: U 81 LYS cc_start: 0.8772 (tmtt) cc_final: 0.8501 (tmmt) REVERT: V 105 ASN cc_start: 0.9207 (t0) cc_final: 0.8981 (t0) REVERT: V 131 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7951 (mmm160) REVERT: W 97 ILE cc_start: 0.7928 (pt) cc_final: 0.7716 (tt) REVERT: W 105 ASN cc_start: 0.9127 (t0) cc_final: 0.8594 (t0) REVERT: W 198 MET cc_start: 0.7622 (mmm) cc_final: 0.6927 (mpp) REVERT: W 201 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8608 (mp) outliers start: 154 outliers final: 61 residues processed: 512 average time/residue: 0.4863 time to fit residues: 420.9784 Evaluate side-chains 414 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 340 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 303 LYS Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 321 GLU Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 105 ASN Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain U residue 320 LYS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 318 MET Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 290 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 434 optimal weight: 1.9990 chunk 355 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 523 optimal weight: 4.9990 chunk 565 optimal weight: 9.9990 chunk 465 optimal weight: 4.9990 chunk 518 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 419 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN R 105 ASN ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 216 ASN T 25 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 197 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 51876 Z= 0.384 Angle : 0.638 11.783 71055 Z= 0.337 Chirality : 0.042 0.209 7779 Planarity : 0.005 0.097 8346 Dihedral : 18.392 175.970 8989 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.95 % Favored : 93.60 % Rotamer: Outliers : 3.61 % Allowed : 18.99 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.12), residues: 5598 helix: 1.26 (0.10), residues: 2632 sheet: -0.99 (0.19), residues: 765 loop : -0.87 (0.14), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP I 52 HIS 0.010 0.001 HIS F 31 PHE 0.026 0.002 PHE V 126 TYR 0.022 0.002 TYR W 128 ARG 0.007 0.000 ARG J 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 379 time to evaluate : 4.216 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: A 140 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6956 (tm-30) REVERT: A 202 ASP cc_start: 0.8371 (p0) cc_final: 0.7971 (p0) REVERT: A 209 GLN cc_start: 0.8965 (tt0) cc_final: 0.8633 (mt0) REVERT: B 166 ASN cc_start: 0.8911 (m-40) cc_final: 0.8608 (p0) REVERT: B 213 ARG cc_start: 0.4661 (tpp80) cc_final: 0.3992 (mmm160) REVERT: C 244 TYR cc_start: 0.7316 (t80) cc_final: 0.6821 (t80) REVERT: E 152 ASP cc_start: 0.9131 (p0) cc_final: 0.8604 (p0) REVERT: E 181 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.8851 (pt0) REVERT: F 77 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8753 (ttp-170) REVERT: F 136 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7155 (mmm-85) REVERT: F 137 MET cc_start: 0.8458 (tpp) cc_final: 0.8081 (tpt) REVERT: F 260 ASP cc_start: 0.9208 (t0) cc_final: 0.8989 (t0) REVERT: G 77 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8002 (mtm-85) REVERT: G 229 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: I 62 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7240 (m-10) REVERT: I 358 TRP cc_start: 0.6022 (OUTLIER) cc_final: 0.5722 (p90) REVERT: I 451 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8545 (tp30) REVERT: J 37 LYS cc_start: 0.8052 (pttt) cc_final: 0.7825 (pttp) REVERT: J 48 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9491 (tp) REVERT: P 4 TYR cc_start: 0.8271 (m-80) cc_final: 0.7860 (m-80) REVERT: Q 56 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6874 (m-80) REVERT: Q 215 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.5698 (ptt90) REVERT: R 105 ASN cc_start: 0.8584 (t0) cc_final: 0.8235 (t0) REVERT: R 198 MET cc_start: 0.8100 (mtm) cc_final: 0.7519 (mpp) REVERT: S 9 LEU cc_start: 0.8386 (pt) cc_final: 0.8142 (mp) REVERT: S 102 ARG cc_start: 0.8489 (ttm110) cc_final: 0.7941 (ttm110) REVERT: S 128 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: S 251 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7578 (t80) REVERT: S 324 GLU cc_start: 0.8014 (pp20) cc_final: 0.7561 (tm-30) REVERT: V 105 ASN cc_start: 0.9186 (t0) cc_final: 0.8857 (t0) REVERT: V 131 ARG cc_start: 0.8273 (mmm160) cc_final: 0.7914 (mmm160) REVERT: W 102 ARG cc_start: 0.7901 (mmt-90) cc_final: 0.7377 (mmt180) REVERT: W 201 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8783 (mp) REVERT: W 285 LEU cc_start: 0.7748 (mt) cc_final: 0.7431 (tt) outliers start: 179 outliers final: 96 residues processed: 532 average time/residue: 0.5171 time to fit residues: 468.6660 Evaluate side-chains 450 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 340 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 282 ASN Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 303 LYS Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 321 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 190 ASP Chi-restraints excluded: chain W residue 201 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 516 optimal weight: 0.6980 chunk 393 optimal weight: 10.0000 chunk 271 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 524 optimal weight: 2.9990 chunk 555 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 chunk 497 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS S 25 ASN S 197 ASN T 25 ASN T 142 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 GLN V 314 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 51876 Z= 0.292 Angle : 0.598 13.197 71055 Z= 0.315 Chirality : 0.041 0.206 7779 Planarity : 0.004 0.099 8346 Dihedral : 18.249 176.238 8988 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.81 % Favored : 93.80 % Rotamer: Outliers : 3.73 % Allowed : 19.35 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.12), residues: 5598 helix: 1.43 (0.10), residues: 2614 sheet: -0.98 (0.19), residues: 762 loop : -0.78 (0.14), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 63 HIS 0.007 0.001 HIS H 171 PHE 0.025 0.001 PHE V 126 TYR 0.024 0.002 TYR A 37 ARG 0.007 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 376 time to evaluate : 5.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6517 (tpt) cc_final: 0.5740 (tpt) REVERT: A 140 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 146 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8116 (tttp) REVERT: A 202 ASP cc_start: 0.8346 (p0) cc_final: 0.7933 (p0) REVERT: B 187 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7630 (tm-30) REVERT: B 213 ARG cc_start: 0.4775 (tpp80) cc_final: 0.4375 (tpp80) REVERT: C 179 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8444 (ptp90) REVERT: C 244 TYR cc_start: 0.7305 (t80) cc_final: 0.6881 (t80) REVERT: E 152 ASP cc_start: 0.9064 (p0) cc_final: 0.8585 (p0) REVERT: E 181 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8819 (pt0) REVERT: E 247 PRO cc_start: 0.7965 (Cg_exo) cc_final: 0.7722 (Cg_endo) REVERT: F 137 MET cc_start: 0.8395 (tpp) cc_final: 0.8063 (tpt) REVERT: F 260 ASP cc_start: 0.9184 (t0) cc_final: 0.8950 (t0) REVERT: G 77 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8010 (mtm-85) REVERT: G 160 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8810 (mttp) REVERT: H 305 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8595 (tpp) REVERT: I 26 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8686 (mmm) REVERT: I 152 PHE cc_start: 0.8306 (t80) cc_final: 0.7977 (t80) REVERT: I 358 TRP cc_start: 0.5815 (OUTLIER) cc_final: 0.5596 (p90) REVERT: J 37 LYS cc_start: 0.8021 (pttt) cc_final: 0.7786 (pttp) REVERT: L 95 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8753 (mp10) REVERT: L 99 ILE cc_start: 0.9434 (mp) cc_final: 0.9229 (mp) REVERT: P 4 TYR cc_start: 0.8279 (m-80) cc_final: 0.7892 (m-80) REVERT: Q 100 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: Q 108 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8707 (tp30) REVERT: R 198 MET cc_start: 0.8021 (mtm) cc_final: 0.7545 (mpp) REVERT: R 303 LYS cc_start: 0.9225 (pttp) cc_final: 0.8768 (pptt) REVERT: S 9 LEU cc_start: 0.8498 (pt) cc_final: 0.8283 (mp) REVERT: S 102 ARG cc_start: 0.8493 (ttm110) cc_final: 0.7948 (ttm110) REVERT: S 128 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6842 (m-80) REVERT: S 251 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7640 (t80) REVERT: S 324 GLU cc_start: 0.7989 (pp20) cc_final: 0.7676 (tm-30) REVERT: U 95 GLU cc_start: 0.8451 (pm20) cc_final: 0.7759 (pm20) REVERT: V 102 ARG cc_start: 0.8050 (tmm160) cc_final: 0.7838 (tmm160) REVERT: V 105 ASN cc_start: 0.9197 (t0) cc_final: 0.8821 (t0) REVERT: V 128 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: V 131 ARG cc_start: 0.8330 (mmm160) cc_final: 0.8070 (mmm160) REVERT: V 198 MET cc_start: 0.7420 (mtt) cc_final: 0.7167 (mtt) REVERT: V 316 GLN cc_start: 0.9082 (pp30) cc_final: 0.8878 (pp30) REVERT: W 105 ASN cc_start: 0.9086 (t0) cc_final: 0.8834 (t0) REVERT: W 109 TYR cc_start: 0.8993 (t80) cc_final: 0.8172 (t80) REVERT: W 142 ASN cc_start: 0.8037 (t0) cc_final: 0.7824 (p0) REVERT: W 198 MET cc_start: 0.8096 (mmm) cc_final: 0.7886 (mmm) REVERT: W 284 TRP cc_start: 0.7508 (t60) cc_final: 0.7241 (t60) REVERT: W 285 LEU cc_start: 0.7673 (mt) cc_final: 0.7442 (tt) REVERT: W 326 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8397 (pt0) outliers start: 185 outliers final: 110 residues processed: 528 average time/residue: 0.4942 time to fit residues: 439.8558 Evaluate side-chains 476 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 351 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 284 SER Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 329 LEU Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 108 GLU Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain Q residue 301 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 234 CYS Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 197 ASN Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 314 GLN Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 190 ASP Chi-restraints excluded: chain W residue 304 ASP Chi-restraints excluded: chain W residue 326 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 462 optimal weight: 3.9990 chunk 315 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 413 optimal weight: 6.9990 chunk 229 optimal weight: 0.7980 chunk 474 optimal weight: 6.9990 chunk 384 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 chunk 498 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 HIS ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS S 25 ASN ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN T 142 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 GLN W 158 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 51876 Z= 0.221 Angle : 0.573 13.449 71055 Z= 0.301 Chirality : 0.040 0.198 7779 Planarity : 0.004 0.100 8346 Dihedral : 18.142 177.043 8986 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.56 % Favored : 94.05 % Rotamer: Outliers : 3.51 % Allowed : 20.14 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.12), residues: 5598 helix: 1.50 (0.10), residues: 2625 sheet: -0.95 (0.19), residues: 760 loop : -0.70 (0.14), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP I 73 HIS 0.016 0.001 HIS B 51 PHE 0.028 0.001 PHE G 234 TYR 0.028 0.001 TYR A 37 ARG 0.006 0.000 ARG J 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 384 time to evaluate : 4.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6398 (tpt) cc_final: 0.5744 (tpt) REVERT: A 116 LEU cc_start: 0.9311 (tp) cc_final: 0.9101 (tp) REVERT: A 140 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6990 (tm-30) REVERT: A 146 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8126 (tttp) REVERT: A 202 ASP cc_start: 0.8342 (p0) cc_final: 0.7914 (p0) REVERT: B 118 ARG cc_start: 0.4180 (tmt170) cc_final: 0.3182 (mmm-85) REVERT: B 187 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 213 ARG cc_start: 0.4698 (tpp80) cc_final: 0.3842 (tpp80) REVERT: C 179 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8450 (ptp90) REVERT: C 244 TYR cc_start: 0.7238 (t80) cc_final: 0.6842 (t80) REVERT: D 77 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8622 (mtm-85) REVERT: D 205 MET cc_start: 0.9142 (mmm) cc_final: 0.8931 (mmm) REVERT: E 152 ASP cc_start: 0.9074 (p0) cc_final: 0.8611 (p0) REVERT: F 30 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7806 (m110) REVERT: F 137 MET cc_start: 0.8354 (tpp) cc_final: 0.7862 (tpt) REVERT: F 260 ASP cc_start: 0.9160 (t0) cc_final: 0.8919 (t0) REVERT: G 77 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8001 (mtm-85) REVERT: G 152 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8646 (p0) REVERT: G 160 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8837 (mtmm) REVERT: H 216 ILE cc_start: 0.9277 (mm) cc_final: 0.9069 (mm) REVERT: I 26 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8556 (mmm) REVERT: I 62 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7194 (m-10) REVERT: I 244 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8273 (mm110) REVERT: I 358 TRP cc_start: 0.5902 (OUTLIER) cc_final: 0.5681 (p90) REVERT: I 451 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8583 (tp30) REVERT: J 37 LYS cc_start: 0.8020 (pttt) cc_final: 0.7793 (pttp) REVERT: J 107 SER cc_start: 0.8454 (m) cc_final: 0.8144 (p) REVERT: J 112 ASP cc_start: 0.5786 (OUTLIER) cc_final: 0.4476 (p0) REVERT: P 4 TYR cc_start: 0.8256 (m-80) cc_final: 0.7812 (m-80) REVERT: Q 56 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: Q 108 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8656 (tp30) REVERT: Q 215 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.5806 (ptt90) REVERT: R 105 ASN cc_start: 0.8509 (t0) cc_final: 0.8235 (t0) REVERT: R 198 MET cc_start: 0.8052 (mtm) cc_final: 0.7593 (mpp) REVERT: R 303 LYS cc_start: 0.9194 (pttp) cc_final: 0.8719 (pptt) REVERT: S 9 LEU cc_start: 0.8536 (pt) cc_final: 0.8313 (mp) REVERT: S 102 ARG cc_start: 0.8499 (ttm110) cc_final: 0.7951 (ttm110) REVERT: S 128 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: S 251 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7612 (t80) REVERT: S 324 GLU cc_start: 0.7947 (pp20) cc_final: 0.7685 (tm-30) REVERT: U 61 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7983 (m) REVERT: U 95 GLU cc_start: 0.8437 (pm20) cc_final: 0.7878 (pm20) REVERT: V 102 ARG cc_start: 0.8049 (tmm160) cc_final: 0.7846 (tmm160) REVERT: V 105 ASN cc_start: 0.9176 (t0) cc_final: 0.8942 (t0) REVERT: V 126 PHE cc_start: 0.7811 (t80) cc_final: 0.7100 (t80) REVERT: V 128 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: V 145 SER cc_start: 0.9462 (m) cc_final: 0.9053 (t) REVERT: V 198 MET cc_start: 0.7490 (mtt) cc_final: 0.7013 (mtt) REVERT: V 316 GLN cc_start: 0.9006 (pp30) cc_final: 0.8801 (pp30) REVERT: W 105 ASN cc_start: 0.9059 (t0) cc_final: 0.8818 (t0) REVERT: W 109 TYR cc_start: 0.8989 (t80) cc_final: 0.8249 (t80) REVERT: W 142 ASN cc_start: 0.8116 (t0) cc_final: 0.7797 (p0) REVERT: W 198 MET cc_start: 0.8058 (mmm) cc_final: 0.7852 (mmm) REVERT: W 201 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8914 (mp) REVERT: W 326 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8424 (pt0) outliers start: 174 outliers final: 100 residues processed: 527 average time/residue: 0.4813 time to fit residues: 427.5477 Evaluate side-chains 473 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 352 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 30 TYR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 284 SER Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 108 GLU Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain Q residue 301 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 326 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 186 optimal weight: 4.9990 chunk 500 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 326 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 556 optimal weight: 5.9990 chunk 461 optimal weight: 6.9990 chunk 257 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 184 optimal weight: 0.1980 chunk 292 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 ASN ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN T 142 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 51876 Z= 0.263 Angle : 0.590 16.757 71055 Z= 0.308 Chirality : 0.040 0.218 7779 Planarity : 0.004 0.153 8346 Dihedral : 18.063 177.702 8980 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.75 % Favored : 93.85 % Rotamer: Outliers : 3.43 % Allowed : 20.44 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.12), residues: 5598 helix: 1.53 (0.10), residues: 2630 sheet: -0.99 (0.19), residues: 763 loop : -0.67 (0.14), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 52 HIS 0.006 0.001 HIS H 171 PHE 0.026 0.001 PHE S 126 TYR 0.018 0.001 TYR L 11 ARG 0.008 0.000 ARG Q 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 368 time to evaluate : 4.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6413 (tpt) cc_final: 0.5759 (tpt) REVERT: A 116 LEU cc_start: 0.9312 (tp) cc_final: 0.9109 (tp) REVERT: A 202 ASP cc_start: 0.8363 (p0) cc_final: 0.7938 (p0) REVERT: A 209 GLN cc_start: 0.9050 (mt0) cc_final: 0.8807 (mt0) REVERT: B 118 ARG cc_start: 0.4201 (tmt170) cc_final: 0.3248 (mtp180) REVERT: B 187 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7576 (tm-30) REVERT: C 179 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8419 (ptp90) REVERT: C 244 TYR cc_start: 0.7300 (t80) cc_final: 0.6884 (t80) REVERT: D 156 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8888 (tptt) REVERT: E 152 ASP cc_start: 0.9083 (p0) cc_final: 0.8643 (p0) REVERT: E 181 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8767 (pt0) REVERT: F 136 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7152 (mmm-85) REVERT: F 137 MET cc_start: 0.8334 (tpp) cc_final: 0.7942 (tpt) REVERT: F 142 MET cc_start: 0.8666 (tpp) cc_final: 0.8453 (tpp) REVERT: F 234 PHE cc_start: 0.7970 (t80) cc_final: 0.7710 (t80) REVERT: F 247 PRO cc_start: 0.8951 (Cg_exo) cc_final: 0.8745 (Cg_endo) REVERT: F 260 ASP cc_start: 0.9173 (t0) cc_final: 0.8924 (t0) REVERT: G 77 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7996 (mtm-85) REVERT: G 135 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8781 (pm20) REVERT: G 160 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8844 (mtmm) REVERT: I 26 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8050 (mmm) REVERT: I 62 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7387 (m-10) REVERT: I 244 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8291 (mm110) REVERT: J 37 LYS cc_start: 0.8014 (pttt) cc_final: 0.7780 (pttp) REVERT: J 107 SER cc_start: 0.8494 (m) cc_final: 0.8210 (p) REVERT: J 112 ASP cc_start: 0.5792 (OUTLIER) cc_final: 0.4460 (p0) REVERT: L 95 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8810 (mp10) REVERT: P 4 TYR cc_start: 0.8273 (m-80) cc_final: 0.7840 (m-80) REVERT: Q 56 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6449 (m-80) REVERT: Q 215 ARG cc_start: 0.6491 (OUTLIER) cc_final: 0.5931 (ptt90) REVERT: R 198 MET cc_start: 0.8110 (mtm) cc_final: 0.7647 (mpp) REVERT: R 303 LYS cc_start: 0.9150 (pttp) cc_final: 0.8657 (pptt) REVERT: S 9 LEU cc_start: 0.8624 (pt) cc_final: 0.8404 (mp) REVERT: S 102 ARG cc_start: 0.8511 (ttm110) cc_final: 0.7969 (ttm110) REVERT: S 128 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: S 251 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7576 (t80) REVERT: S 324 GLU cc_start: 0.7961 (pp20) cc_final: 0.7700 (tm-30) REVERT: U 95 GLU cc_start: 0.8462 (pm20) cc_final: 0.7868 (pm20) REVERT: V 105 ASN cc_start: 0.9191 (t0) cc_final: 0.8944 (t0) REVERT: V 128 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: V 145 SER cc_start: 0.9461 (m) cc_final: 0.9052 (t) REVERT: V 198 MET cc_start: 0.7603 (mtt) cc_final: 0.7058 (mtt) REVERT: V 210 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: V 234 CYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7643 (t) REVERT: W 105 ASN cc_start: 0.9064 (t0) cc_final: 0.8852 (t0) REVERT: W 109 TYR cc_start: 0.9005 (t80) cc_final: 0.8319 (t80) REVERT: W 142 ASN cc_start: 0.8203 (t0) cc_final: 0.7836 (p0) REVERT: W 201 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8931 (mp) outliers start: 170 outliers final: 113 residues processed: 507 average time/residue: 0.4719 time to fit residues: 408.8156 Evaluate side-chains 483 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 351 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 135 GLN Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 284 SER Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 172 GLU Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 304 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 536 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 316 optimal weight: 0.5980 chunk 406 optimal weight: 0.1980 chunk 314 optimal weight: 5.9990 chunk 468 optimal weight: 10.0000 chunk 310 optimal weight: 0.9980 chunk 554 optimal weight: 8.9990 chunk 346 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 ASN ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN T 142 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 220 GLN U 266 HIS V 314 GLN V 316 GLN W 158 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 51876 Z= 0.256 Angle : 0.583 13.665 71055 Z= 0.305 Chirality : 0.040 0.201 7779 Planarity : 0.004 0.129 8346 Dihedral : 18.004 178.096 8977 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.59 % Favored : 94.02 % Rotamer: Outliers : 3.35 % Allowed : 20.62 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.12), residues: 5598 helix: 1.56 (0.10), residues: 2625 sheet: -0.91 (0.19), residues: 754 loop : -0.64 (0.14), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 63 HIS 0.007 0.001 HIS B 51 PHE 0.031 0.001 PHE G 234 TYR 0.034 0.001 TYR A 37 ARG 0.006 0.000 ARG H 302 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 367 time to evaluate : 5.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6569 (tpt) cc_final: 0.6003 (tpt) REVERT: A 202 ASP cc_start: 0.8363 (p0) cc_final: 0.7934 (p0) REVERT: B 118 ARG cc_start: 0.4239 (tmt170) cc_final: 0.3405 (mtp180) REVERT: B 187 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7568 (tm-30) REVERT: C 179 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8414 (ptp90) REVERT: C 244 TYR cc_start: 0.7307 (t80) cc_final: 0.6920 (t80) REVERT: D 77 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8562 (mtm-85) REVERT: D 156 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8889 (tptt) REVERT: E 152 ASP cc_start: 0.9081 (p0) cc_final: 0.8639 (p0) REVERT: E 181 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8754 (pt0) REVERT: F 32 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8110 (t70) REVERT: F 136 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7088 (mmm-85) REVERT: F 137 MET cc_start: 0.8302 (tpp) cc_final: 0.7933 (tpt) REVERT: F 142 MET cc_start: 0.8653 (tpp) cc_final: 0.8433 (tpp) REVERT: F 234 PHE cc_start: 0.8024 (t80) cc_final: 0.7738 (t80) REVERT: F 247 PRO cc_start: 0.8909 (Cg_exo) cc_final: 0.8700 (Cg_endo) REVERT: F 260 ASP cc_start: 0.9175 (t0) cc_final: 0.8914 (t0) REVERT: G 77 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8044 (mtm-85) REVERT: G 135 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8775 (pm20) REVERT: G 152 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8652 (p0) REVERT: G 160 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8840 (mtmm) REVERT: I 26 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8026 (mmm) REVERT: I 62 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: I 244 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8310 (mm110) REVERT: I 396 ASP cc_start: 0.7147 (t0) cc_final: 0.6470 (t70) REVERT: J 37 LYS cc_start: 0.7992 (pttt) cc_final: 0.7689 (pttp) REVERT: J 107 SER cc_start: 0.8476 (m) cc_final: 0.8188 (p) REVERT: J 112 ASP cc_start: 0.5784 (OUTLIER) cc_final: 0.4450 (p0) REVERT: L 95 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8774 (mp10) REVERT: P 4 TYR cc_start: 0.8244 (m-80) cc_final: 0.7805 (m-80) REVERT: P 163 ASP cc_start: 0.8541 (m-30) cc_final: 0.7763 (t0) REVERT: P 272 MET cc_start: 0.8926 (ttm) cc_final: 0.8447 (ttm) REVERT: Q 56 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: Q 215 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.6089 (ptt90) REVERT: Q 234 CYS cc_start: 0.8217 (t) cc_final: 0.7684 (p) REVERT: R 105 ASN cc_start: 0.8515 (t0) cc_final: 0.8257 (t0) REVERT: R 198 MET cc_start: 0.8119 (mtm) cc_final: 0.7610 (mpp) REVERT: R 303 LYS cc_start: 0.9148 (pttp) cc_final: 0.8655 (pptt) REVERT: S 97 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8326 (mm) REVERT: S 102 ARG cc_start: 0.8525 (ttm110) cc_final: 0.7990 (ttm110) REVERT: S 128 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: S 251 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7588 (t80) REVERT: S 324 GLU cc_start: 0.7978 (pp20) cc_final: 0.7715 (tm-30) REVERT: U 95 GLU cc_start: 0.8455 (pm20) cc_final: 0.7786 (pm20) REVERT: V 105 ASN cc_start: 0.9193 (t0) cc_final: 0.8939 (t0) REVERT: V 128 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: V 131 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7587 (mmm160) REVERT: V 145 SER cc_start: 0.9469 (m) cc_final: 0.9071 (t) REVERT: V 164 HIS cc_start: 0.8709 (t70) cc_final: 0.8470 (t70) REVERT: V 198 MET cc_start: 0.7687 (mtt) cc_final: 0.6988 (mtt) REVERT: V 210 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8536 (mp0) REVERT: V 234 CYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7702 (t) REVERT: W 105 ASN cc_start: 0.9083 (t0) cc_final: 0.8866 (t0) REVERT: W 109 TYR cc_start: 0.9001 (t80) cc_final: 0.8377 (t80) REVERT: W 142 ASN cc_start: 0.8246 (t0) cc_final: 0.7845 (p0) REVERT: W 198 MET cc_start: 0.8372 (mmm) cc_final: 0.7593 (mtm) REVERT: W 201 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8939 (mp) outliers start: 166 outliers final: 116 residues processed: 504 average time/residue: 0.4792 time to fit residues: 411.9593 Evaluate side-chains 490 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 351 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 135 GLN Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 329 LEU Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 186 GLN Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 234 CYS Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 172 GLU Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain U residue 266 HIS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 201 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 342 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 330 optimal weight: 0.7980 chunk 166 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 352 optimal weight: 8.9990 chunk 377 optimal weight: 5.9990 chunk 274 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 435 optimal weight: 10.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 ASN S 197 ASN ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN T 142 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 GLN ** V 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 158 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 51876 Z= 0.309 Angle : 0.604 13.410 71055 Z= 0.316 Chirality : 0.041 0.202 7779 Planarity : 0.004 0.119 8346 Dihedral : 18.001 178.342 8974 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.68 % Favored : 93.93 % Rotamer: Outliers : 3.29 % Allowed : 20.98 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.12), residues: 5598 helix: 1.55 (0.10), residues: 2624 sheet: -0.89 (0.20), residues: 754 loop : -0.66 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 63 HIS 0.011 0.001 HIS U 266 PHE 0.027 0.001 PHE G 234 TYR 0.021 0.001 TYR B 11 ARG 0.006 0.000 ARG H 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 356 time to evaluate : 4.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6550 (tpt) cc_final: 0.6030 (tpt) REVERT: A 202 ASP cc_start: 0.8394 (p0) cc_final: 0.7999 (p0) REVERT: B 118 ARG cc_start: 0.4331 (tmt170) cc_final: 0.3446 (mtp180) REVERT: B 187 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7605 (tm-30) REVERT: C 179 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8400 (ptp90) REVERT: C 244 TYR cc_start: 0.7441 (t80) cc_final: 0.6990 (t80) REVERT: D 77 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8541 (mtm-85) REVERT: D 156 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8902 (tptt) REVERT: E 152 ASP cc_start: 0.9108 (p0) cc_final: 0.8673 (p0) REVERT: E 181 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8781 (pt0) REVERT: F 137 MET cc_start: 0.8373 (tpp) cc_final: 0.7957 (tpt) REVERT: F 142 MET cc_start: 0.8658 (tpp) cc_final: 0.8448 (tpp) REVERT: F 234 PHE cc_start: 0.8031 (t80) cc_final: 0.7757 (t80) REVERT: F 260 ASP cc_start: 0.9180 (t0) cc_final: 0.8933 (t0) REVERT: G 77 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8032 (mtm-85) REVERT: G 135 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8800 (pm20) REVERT: G 152 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8665 (p0) REVERT: G 160 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8847 (mtmm) REVERT: I 26 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8044 (mmm) REVERT: I 62 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: I 244 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8344 (mm110) REVERT: I 396 ASP cc_start: 0.7159 (t0) cc_final: 0.6558 (t70) REVERT: I 451 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8537 (tp30) REVERT: J 37 LYS cc_start: 0.8022 (pttt) cc_final: 0.7715 (pttp) REVERT: J 107 SER cc_start: 0.8519 (m) cc_final: 0.8225 (p) REVERT: J 112 ASP cc_start: 0.5836 (OUTLIER) cc_final: 0.4465 (p0) REVERT: L 95 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8658 (mp10) REVERT: P 4 TYR cc_start: 0.8251 (m-80) cc_final: 0.7783 (m-80) REVERT: P 163 ASP cc_start: 0.8528 (m-30) cc_final: 0.7823 (t0) REVERT: P 272 MET cc_start: 0.8941 (ttm) cc_final: 0.8466 (ttm) REVERT: Q 56 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: Q 186 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8052 (pm20) REVERT: Q 215 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6211 (ptt90) REVERT: Q 234 CYS cc_start: 0.8227 (t) cc_final: 0.7703 (p) REVERT: R 105 ASN cc_start: 0.8533 (t0) cc_final: 0.8254 (t0) REVERT: R 198 MET cc_start: 0.8126 (mtm) cc_final: 0.7627 (mpp) REVERT: S 97 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8358 (mm) REVERT: S 102 ARG cc_start: 0.8526 (ttm110) cc_final: 0.7994 (ttm110) REVERT: S 324 GLU cc_start: 0.7981 (pp20) cc_final: 0.7719 (tm-30) REVERT: T 210 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: U 95 GLU cc_start: 0.8454 (pm20) cc_final: 0.7806 (pm20) REVERT: V 105 ASN cc_start: 0.9200 (t0) cc_final: 0.8939 (t0) REVERT: V 128 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: V 131 ARG cc_start: 0.7984 (mmm160) cc_final: 0.7671 (mmm160) REVERT: V 145 SER cc_start: 0.9479 (m) cc_final: 0.9076 (t) REVERT: V 164 HIS cc_start: 0.8716 (t70) cc_final: 0.8486 (t70) REVERT: V 198 MET cc_start: 0.7839 (mtt) cc_final: 0.7162 (mtt) REVERT: V 210 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: V 234 CYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7753 (t) REVERT: W 41 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7818 (mmm) REVERT: W 105 ASN cc_start: 0.9083 (t0) cc_final: 0.8860 (t0) REVERT: W 109 TYR cc_start: 0.8993 (t80) cc_final: 0.8363 (t80) REVERT: W 142 ASN cc_start: 0.8326 (t0) cc_final: 0.7872 (p0) REVERT: W 198 MET cc_start: 0.8383 (mmm) cc_final: 0.7624 (mtm) REVERT: W 201 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8918 (mp) outliers start: 163 outliers final: 125 residues processed: 488 average time/residue: 0.4716 time to fit residues: 392.0779 Evaluate side-chains 494 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 346 time to evaluate : 4.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 135 GLN Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 329 LEU Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 186 GLN Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 234 CYS Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 197 ASN Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 76 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 172 GLU Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 314 GLN Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 201 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 504 optimal weight: 0.6980 chunk 530 optimal weight: 1.9990 chunk 484 optimal weight: 6.9990 chunk 516 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 405 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 466 optimal weight: 0.0170 chunk 488 optimal weight: 3.9990 chunk 514 optimal weight: 3.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN S 25 ASN ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 ASN S 220 GLN ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN T 142 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 197 ASN U 266 HIS V 316 GLN W 158 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 51876 Z= 0.259 Angle : 0.594 18.961 71055 Z= 0.309 Chirality : 0.040 0.235 7779 Planarity : 0.004 0.162 8346 Dihedral : 17.980 178.504 8974 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.72 % Favored : 93.91 % Rotamer: Outliers : 3.41 % Allowed : 21.02 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.12), residues: 5598 helix: 1.56 (0.10), residues: 2622 sheet: -0.88 (0.20), residues: 754 loop : -0.66 (0.14), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 63 HIS 0.021 0.001 HIS B 51 PHE 0.034 0.001 PHE G 234 TYR 0.028 0.001 TYR A 37 ARG 0.005 0.000 ARG H 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 360 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6537 (tpt) cc_final: 0.6045 (tpt) REVERT: A 202 ASP cc_start: 0.8373 (p0) cc_final: 0.8004 (p0) REVERT: B 118 ARG cc_start: 0.4267 (tmt170) cc_final: 0.3403 (mtp180) REVERT: B 187 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7628 (tm-30) REVERT: C 33 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8460 (mm) REVERT: C 179 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8413 (ptp90) REVERT: C 244 TYR cc_start: 0.7419 (t80) cc_final: 0.7011 (t80) REVERT: D 77 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8577 (mtm-85) REVERT: D 156 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8892 (tptt) REVERT: E 152 ASP cc_start: 0.9082 (p0) cc_final: 0.8658 (p0) REVERT: E 181 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8755 (pt0) REVERT: F 137 MET cc_start: 0.8184 (tpp) cc_final: 0.7851 (tpt) REVERT: F 142 MET cc_start: 0.8640 (tpp) cc_final: 0.8423 (tpp) REVERT: F 234 PHE cc_start: 0.8024 (t80) cc_final: 0.7747 (t80) REVERT: F 260 ASP cc_start: 0.9175 (t0) cc_final: 0.8923 (t0) REVERT: G 77 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8079 (mtm-85) REVERT: G 135 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8762 (pm20) REVERT: G 152 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8653 (p0) REVERT: G 160 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8845 (mtmm) REVERT: I 26 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.7964 (mmm) REVERT: I 62 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7407 (m-10) REVERT: I 244 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8357 (mm110) REVERT: I 396 ASP cc_start: 0.7216 (t0) cc_final: 0.6580 (t70) REVERT: I 451 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8540 (tp30) REVERT: J 37 LYS cc_start: 0.8004 (pttt) cc_final: 0.7685 (pttp) REVERT: J 107 SER cc_start: 0.8497 (m) cc_final: 0.8201 (p) REVERT: J 112 ASP cc_start: 0.5850 (OUTLIER) cc_final: 0.4513 (p0) REVERT: L 95 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8754 (mp10) REVERT: P 4 TYR cc_start: 0.8160 (m-80) cc_final: 0.7728 (m-80) REVERT: P 163 ASP cc_start: 0.8524 (m-30) cc_final: 0.7739 (t0) REVERT: P 272 MET cc_start: 0.8922 (ttm) cc_final: 0.8435 (ttm) REVERT: Q 186 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: Q 215 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6348 (ptt90) REVERT: Q 234 CYS cc_start: 0.8216 (t) cc_final: 0.7699 (p) REVERT: R 198 MET cc_start: 0.8122 (mtm) cc_final: 0.7616 (mpp) REVERT: S 97 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8358 (mm) REVERT: S 102 ARG cc_start: 0.8522 (ttm110) cc_final: 0.8010 (ttm110) REVERT: S 324 GLU cc_start: 0.7982 (pp20) cc_final: 0.7723 (tm-30) REVERT: T 210 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: U 95 GLU cc_start: 0.8418 (pm20) cc_final: 0.7847 (pm20) REVERT: V 105 ASN cc_start: 0.9191 (t0) cc_final: 0.8931 (t0) REVERT: V 128 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: V 145 SER cc_start: 0.9486 (m) cc_final: 0.9079 (t) REVERT: V 164 HIS cc_start: 0.8734 (t70) cc_final: 0.8519 (t70) REVERT: V 198 MET cc_start: 0.7864 (mtt) cc_final: 0.7170 (mtt) REVERT: V 210 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: V 234 CYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7709 (t) REVERT: W 41 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7838 (mmm) REVERT: W 105 ASN cc_start: 0.9083 (t0) cc_final: 0.8853 (t0) REVERT: W 109 TYR cc_start: 0.8995 (t80) cc_final: 0.8456 (t80) REVERT: W 142 ASN cc_start: 0.8346 (t0) cc_final: 0.7875 (p0) REVERT: W 198 MET cc_start: 0.8410 (mmm) cc_final: 0.7656 (mtm) REVERT: W 201 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9027 (mp) outliers start: 169 outliers final: 124 residues processed: 494 average time/residue: 0.4786 time to fit residues: 403.8168 Evaluate side-chains 494 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 347 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 135 GLN Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 329 LEU Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 186 GLN Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 234 CYS Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 197 ASN Chi-restraints excluded: chain S residue 198 MET Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 76 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 172 GLU Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain U residue 266 HIS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 316 GLN Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 190 ASP Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 339 optimal weight: 2.9990 chunk 546 optimal weight: 0.1980 chunk 333 optimal weight: 4.9990 chunk 259 optimal weight: 0.9980 chunk 379 optimal weight: 9.9990 chunk 572 optimal weight: 9.9990 chunk 527 optimal weight: 3.9990 chunk 456 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 352 optimal weight: 8.9990 chunk 279 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 ASN S 25 ASN ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN T 142 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 197 ASN U 266 HIS W 158 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 51876 Z= 0.211 Angle : 0.588 15.133 71055 Z= 0.305 Chirality : 0.040 0.223 7779 Planarity : 0.004 0.147 8346 Dihedral : 17.940 178.942 8974 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.66 % Favored : 93.98 % Rotamer: Outliers : 2.90 % Allowed : 21.53 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.12), residues: 5598 helix: 1.59 (0.10), residues: 2622 sheet: -0.85 (0.20), residues: 754 loop : -0.64 (0.14), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 63 HIS 0.033 0.001 HIS B 51 PHE 0.029 0.001 PHE G 234 TYR 0.018 0.001 TYR L 11 ARG 0.005 0.000 ARG H 302 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 365 time to evaluate : 4.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6566 (tpt) cc_final: 0.5670 (tpt) REVERT: A 140 GLU cc_start: 0.7488 (tp30) cc_final: 0.7152 (tp30) REVERT: A 202 ASP cc_start: 0.8361 (p0) cc_final: 0.7985 (p0) REVERT: B 118 ARG cc_start: 0.4119 (tmt170) cc_final: 0.3404 (mtp180) REVERT: B 187 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7610 (tm-30) REVERT: C 33 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8398 (mm) REVERT: C 179 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8414 (ptp90) REVERT: C 244 TYR cc_start: 0.7401 (t80) cc_final: 0.6986 (t80) REVERT: D 77 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8354 (ttp-170) REVERT: D 144 MET cc_start: 0.9168 (ttp) cc_final: 0.8889 (ttp) REVERT: D 156 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8903 (tptt) REVERT: D 205 MET cc_start: 0.9187 (mmm) cc_final: 0.8930 (mmm) REVERT: E 152 ASP cc_start: 0.9025 (p0) cc_final: 0.8569 (p0) REVERT: E 181 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8738 (pt0) REVERT: F 137 MET cc_start: 0.8242 (tpp) cc_final: 0.7918 (tpp) REVERT: F 142 MET cc_start: 0.8626 (tpp) cc_final: 0.8404 (tpp) REVERT: F 234 PHE cc_start: 0.8004 (t80) cc_final: 0.7762 (t80) REVERT: F 247 PRO cc_start: 0.8936 (Cg_exo) cc_final: 0.8736 (Cg_endo) REVERT: F 260 ASP cc_start: 0.9142 (t0) cc_final: 0.8877 (t0) REVERT: G 50 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8348 (mtpp) REVERT: G 77 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8067 (mtm-85) REVERT: G 135 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8737 (pm20) REVERT: G 152 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8653 (p0) REVERT: G 160 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8863 (mtmm) REVERT: H 302 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8669 (mtt90) REVERT: I 26 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.7905 (mmm) REVERT: I 62 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7309 (m-10) REVERT: I 244 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8414 (mm-40) REVERT: I 396 ASP cc_start: 0.7221 (t0) cc_final: 0.6565 (t70) REVERT: I 451 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8543 (tp30) REVERT: J 37 LYS cc_start: 0.7981 (pttt) cc_final: 0.7734 (pttp) REVERT: J 107 SER cc_start: 0.8450 (m) cc_final: 0.8147 (p) REVERT: J 112 ASP cc_start: 0.5799 (OUTLIER) cc_final: 0.4499 (p0) REVERT: L 95 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8603 (mp10) REVERT: P 4 TYR cc_start: 0.8166 (m-80) cc_final: 0.7737 (m-80) REVERT: P 163 ASP cc_start: 0.8496 (m-30) cc_final: 0.7740 (t0) REVERT: P 272 MET cc_start: 0.8923 (ttm) cc_final: 0.8431 (ttm) REVERT: Q 186 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: Q 215 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6414 (ptt90) REVERT: Q 234 CYS cc_start: 0.8221 (t) cc_final: 0.7675 (p) REVERT: R 12 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8680 (mm) REVERT: R 198 MET cc_start: 0.8131 (mtm) cc_final: 0.7657 (mpp) REVERT: S 97 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8359 (mm) REVERT: S 102 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8006 (ttm110) REVERT: S 251 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7622 (t80) REVERT: S 324 GLU cc_start: 0.7955 (pp20) cc_final: 0.7713 (tm-30) REVERT: T 210 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: U 95 GLU cc_start: 0.8391 (pm20) cc_final: 0.7735 (pm20) REVERT: V 105 ASN cc_start: 0.9181 (t0) cc_final: 0.8911 (t0) REVERT: V 128 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: V 145 SER cc_start: 0.9485 (m) cc_final: 0.9079 (t) REVERT: V 164 HIS cc_start: 0.8736 (t70) cc_final: 0.8527 (t70) REVERT: V 198 MET cc_start: 0.7855 (mtt) cc_final: 0.7174 (mtt) REVERT: V 210 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: V 234 CYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7699 (t) REVERT: W 41 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7852 (mmm) REVERT: W 105 ASN cc_start: 0.9084 (t0) cc_final: 0.8853 (t0) REVERT: W 109 TYR cc_start: 0.8996 (t80) cc_final: 0.8465 (t80) REVERT: W 142 ASN cc_start: 0.8361 (t0) cc_final: 0.7917 (p0) REVERT: W 198 MET cc_start: 0.8415 (mmm) cc_final: 0.7664 (mtm) REVERT: W 201 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9046 (mp) outliers start: 144 outliers final: 106 residues processed: 479 average time/residue: 0.4880 time to fit residues: 397.0037 Evaluate side-chains 488 residues out of total 4961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 355 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 135 GLN Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 186 GLN Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 234 CYS Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 198 MET Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 76 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 172 GLU Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 362 optimal weight: 0.8980 chunk 485 optimal weight: 0.0670 chunk 139 optimal weight: 0.2980 chunk 420 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 456 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 469 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS B 193 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 HIS ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 ASN ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 ASN ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN T 142 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 266 HIS V 316 GLN W 158 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.084302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.061935 restraints weight = 172574.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.063800 restraints weight = 72218.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065028 restraints weight = 41904.009| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 51876 Z= 0.165 Angle : 0.569 12.143 71055 Z= 0.297 Chirality : 0.039 0.201 7779 Planarity : 0.004 0.104 8346 Dihedral : 17.867 179.792 8974 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.23 % Favored : 94.43 % Rotamer: Outliers : 2.42 % Allowed : 22.13 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.12), residues: 5598 helix: 1.65 (0.10), residues: 2620 sheet: -0.79 (0.20), residues: 751 loop : -0.62 (0.14), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 63 HIS 0.044 0.001 HIS B 51 PHE 0.030 0.001 PHE G 234 TYR 0.028 0.001 TYR A 37 ARG 0.005 0.000 ARG B 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8695.11 seconds wall clock time: 155 minutes 18.03 seconds (9318.03 seconds total)