Starting phenix.real_space_refine on Fri Feb 6 16:09:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ky7_62642/02_2026/9ky7_62642.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ky7_62642/02_2026/9ky7_62642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ky7_62642/02_2026/9ky7_62642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ky7_62642/02_2026/9ky7_62642.map" model { file = "/net/cci-nas-00/data/ceres_data/9ky7_62642/02_2026/9ky7_62642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ky7_62642/02_2026/9ky7_62642.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 10 5.21 5 S 130 5.16 5 C 16661 2.51 5 N 4470 2.21 5 O 5061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26362 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2292 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 1 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2330 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 14, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2355 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 14, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2379 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain breaks: 1 Chain: "E" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2377 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain breaks: 1 Chain: "F" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2377 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain breaks: 1 Chain: "G" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2377 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain breaks: 1 Chain: "H" Number of atoms: 2371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2371 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 14, 'TRANS': 286} Chain breaks: 1 Chain: "I" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2379 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain breaks: 1 Chain: "J" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2352 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Chain: "K" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2333 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "L" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: 5.92, per 1000 atoms: 0.22 Number of scatterers: 26362 At special positions: 0 Unit cell: (133.66, 138.99, 145.55, 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 130 16.00 P 30 15.00 Mg 10 11.99 O 5061 8.00 N 4470 7.00 C 16661 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: 2.20 Conformation dependent library (CDL) restraints added in 836.0 milliseconds 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6284 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 11 sheets defined 63.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.751A pdb=" N ALA A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A 66 " --> pdb=" O ALA A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 66' Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 96 through 113 removed outlier: 5.138A pdb=" N TYR A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.975A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 removed outlier: 3.624A pdb=" N ASP A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 294 through 319 removed outlier: 4.677A pdb=" N GLU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.754A pdb=" N PHE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.505A pdb=" N ALA B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 66 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.798A pdb=" N SER B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.529A pdb=" N TYR B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.607A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.947A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.518A pdb=" N ILE B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'C' and resid 43 through 61 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.557A pdb=" N ALA C 65 " --> pdb=" O PRO C 62 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU C 66 " --> pdb=" O ALA C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 77 Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 113 through 118 removed outlier: 3.703A pdb=" N TYR C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 removed outlier: 6.977A pdb=" N LEU C 122 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.976A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.551A pdb=" N ARG C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 319 removed outlier: 3.607A pdb=" N GLN C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.606A pdb=" N PHE C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 61 Processing helix chain 'D' and resid 62 through 67 removed outlier: 3.669A pdb=" N GLU D 66 " --> pdb=" O ALA D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 77 Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 116 through 124 removed outlier: 4.275A pdb=" N ASN D 119 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 120 " --> pdb=" O TYR D 117 " (cutoff:3.500A) Proline residue: D 121 - end of helix removed outlier: 3.946A pdb=" N GLN D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 124' Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.304A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 237 through 241 removed outlier: 3.557A pdb=" N ASP D 240 " --> pdb=" O ARG D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.753A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 321 removed outlier: 5.349A pdb=" N GLU D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TYR D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 347 removed outlier: 3.790A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 61 Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.561A pdb=" N ALA E 65 " --> pdb=" O PRO E 62 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU E 66 " --> pdb=" O ALA E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 77 Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 138 through 150 removed outlier: 3.534A pdb=" N SER E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.071A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 Processing helix chain 'E' and resid 294 through 310 Processing helix chain 'E' and resid 310 through 320 removed outlier: 3.716A pdb=" N GLN E 319 " --> pdb=" O LYS E 315 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU E 320 " --> pdb=" O GLN E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'F' and resid 39 through 42 removed outlier: 3.656A pdb=" N LYS F 42 " --> pdb=" O LEU F 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 39 through 42' Processing helix chain 'F' and resid 43 through 61 Processing helix chain 'F' and resid 62 through 66 removed outlier: 3.597A pdb=" N ALA F 65 " --> pdb=" O PRO F 62 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 66' Processing helix chain 'F' and resid 70 through 78 removed outlier: 3.720A pdb=" N SER F 78 " --> pdb=" O ARG F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 113 removed outlier: 5.270A pdb=" N TYR F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 113 through 118 removed outlier: 3.520A pdb=" N TYR F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 206 through 221 Processing helix chain 'F' and resid 237 through 241 Processing helix chain 'F' and resid 242 through 248 removed outlier: 3.676A pdb=" N ARG F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 282 through 290 removed outlier: 3.863A pdb=" N ILE F 286 " --> pdb=" O ASP F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 310 Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 340 through 348 removed outlier: 3.740A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 61 Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.619A pdb=" N ALA G 65 " --> pdb=" O PRO G 62 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU G 66 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 77 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 96 through 107 Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 113 through 118 removed outlier: 3.666A pdb=" N TYR G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 124 removed outlier: 6.873A pdb=" N LEU G 122 " --> pdb=" O ASN G 119 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN G 124 " --> pdb=" O PRO G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 158 through 163 Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.273A pdb=" N PHE G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 221 Processing helix chain 'G' and resid 242 through 248 removed outlier: 3.567A pdb=" N ARG G 248 " --> pdb=" O ALA G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 271 Processing helix chain 'G' and resid 282 through 290 Processing helix chain 'G' and resid 294 through 320 removed outlier: 5.312A pdb=" N GLU G 312 " --> pdb=" O ASP G 308 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N TYR G 313 " --> pdb=" O ALA G 309 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN G 319 " --> pdb=" O LYS G 315 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 320 " --> pdb=" O GLN G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 346 removed outlier: 4.014A pdb=" N PHE G 344 " --> pdb=" O LYS G 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 61 Processing helix chain 'H' and resid 62 through 67 removed outlier: 3.798A pdb=" N GLU H 66 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 89 through 93 removed outlier: 3.551A pdb=" N ILE H 93 " --> pdb=" O PHE H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 107 Processing helix chain 'H' and resid 107 through 113 Processing helix chain 'H' and resid 138 through 150 Processing helix chain 'H' and resid 168 through 184 Processing helix chain 'H' and resid 193 through 198 removed outlier: 4.328A pdb=" N PHE H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 221 Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 242 through 248 removed outlier: 3.564A pdb=" N ARG H 248 " --> pdb=" O ALA H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 271 Processing helix chain 'H' and resid 282 through 290 removed outlier: 3.839A pdb=" N ILE H 286 " --> pdb=" O ASP H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 310 Processing helix chain 'H' and resid 310 through 320 removed outlier: 3.621A pdb=" N LEU H 320 " --> pdb=" O GLN H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 348 removed outlier: 3.792A pdb=" N PHE H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS H 347 " --> pdb=" O ASP H 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 61 Processing helix chain 'I' and resid 62 through 67 removed outlier: 3.580A pdb=" N ALA I 65 " --> pdb=" O PRO I 62 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU I 66 " --> pdb=" O ALA I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 77 Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 89 through 93 Processing helix chain 'I' and resid 96 through 107 Processing helix chain 'I' and resid 107 through 113 Processing helix chain 'I' and resid 113 through 118 Processing helix chain 'I' and resid 138 through 150 Processing helix chain 'I' and resid 158 through 162 Processing helix chain 'I' and resid 168 through 184 removed outlier: 3.547A pdb=" N LYS I 172 " --> pdb=" O GLY I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 198 removed outlier: 4.261A pdb=" N PHE I 197 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 221 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 259 through 271 Processing helix chain 'I' and resid 283 through 290 Processing helix chain 'I' and resid 294 through 310 Processing helix chain 'I' and resid 310 through 321 removed outlier: 3.580A pdb=" N GLN I 319 " --> pdb=" O LYS I 315 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 346 Processing helix chain 'J' and resid 43 through 61 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 70 through 78 removed outlier: 3.704A pdb=" N SER J 78 " --> pdb=" O ARG J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 93 removed outlier: 3.513A pdb=" N ILE J 93 " --> pdb=" O PHE J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 113 removed outlier: 5.227A pdb=" N TYR J 109 " --> pdb=" O GLU J 105 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 113 through 118 removed outlier: 3.648A pdb=" N TYR J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 124 removed outlier: 6.889A pdb=" N LEU J 122 " --> pdb=" O ASN J 119 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN J 124 " --> pdb=" O PRO J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 150 Processing helix chain 'J' and resid 158 through 162 Processing helix chain 'J' and resid 169 through 184 Processing helix chain 'J' and resid 193 through 198 removed outlier: 4.133A pdb=" N PHE J 197 " --> pdb=" O GLN J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 221 Processing helix chain 'J' and resid 242 through 247 Processing helix chain 'J' and resid 259 through 271 Processing helix chain 'J' and resid 282 through 290 Processing helix chain 'J' and resid 294 through 310 Processing helix chain 'J' and resid 310 through 321 Processing helix chain 'J' and resid 340 through 346 removed outlier: 3.787A pdb=" N PHE J 344 " --> pdb=" O LYS J 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 61 Processing helix chain 'K' and resid 62 through 67 removed outlier: 3.848A pdb=" N GLU K 66 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 78 Processing helix chain 'K' and resid 82 through 86 Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'K' and resid 96 through 107 Processing helix chain 'K' and resid 107 through 113 Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'K' and resid 138 through 149 Processing helix chain 'K' and resid 158 through 163 Processing helix chain 'K' and resid 169 through 184 Processing helix chain 'K' and resid 193 through 198 removed outlier: 4.275A pdb=" N PHE K 197 " --> pdb=" O GLN K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 221 Processing helix chain 'K' and resid 242 through 247 Processing helix chain 'K' and resid 259 through 271 Processing helix chain 'K' and resid 282 through 290 Processing helix chain 'K' and resid 294 through 320 removed outlier: 5.268A pdb=" N GLU K 312 " --> pdb=" O ASP K 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TYR K 313 " --> pdb=" O ALA K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 removed outlier: 3.750A pdb=" N PHE K 344 " --> pdb=" O LYS K 340 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS K 347 " --> pdb=" O ASP K 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.866A pdb=" N PHE A 154 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ASP A 192 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N CYS A 187 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE A 232 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA A 234 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 191 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 4.136A pdb=" N PHE B 154 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS B 187 " --> pdb=" O MET B 230 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE B 232 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE B 189 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA B 234 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 191 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 156 removed outlier: 6.217A pdb=" N ASN C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE C 190 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASP C 192 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS C 187 " --> pdb=" O MET C 230 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE C 232 " --> pdb=" O CYS C 187 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE C 189 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA C 234 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE C 191 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 153 through 157 removed outlier: 6.255A pdb=" N ASN D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N PHE D 190 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASP D 192 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE D 157 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 removed outlier: 3.870A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 234 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 removed outlier: 4.207A pdb=" N PHE F 154 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 234 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL F 129 " --> pdb=" O GLY F 233 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N THR F 235 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU F 131 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 153 through 157 removed outlier: 6.257A pdb=" N ASN G 153 " --> pdb=" O ILE G 188 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N PHE G 190 " --> pdb=" O ASN G 153 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE G 155 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ASP G 192 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE G 157 " --> pdb=" O ASP G 192 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA G 234 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY G 128 " --> pdb=" O LYS G 251 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE G 253 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU G 130 " --> pdb=" O PHE G 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 80 through 81 removed outlier: 3.889A pdb=" N PHE H 154 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA H 234 " --> pdb=" O ILE H 191 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY H 128 " --> pdb=" O LYS H 251 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N PHE H 253 " --> pdb=" O GLY H 128 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU H 130 " --> pdb=" O PHE H 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 80 through 81 removed outlier: 4.045A pdb=" N PHE I 154 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN I 153 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE I 190 " --> pdb=" O ASN I 153 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE I 155 " --> pdb=" O PHE I 190 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASP I 192 " --> pdb=" O ILE I 155 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE I 157 " --> pdb=" O ASP I 192 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA I 234 " --> pdb=" O ILE I 191 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY I 128 " --> pdb=" O LYS I 251 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N PHE I 253 " --> pdb=" O GLY I 128 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU I 130 " --> pdb=" O PHE I 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 80 through 81 removed outlier: 4.173A pdb=" N PHE J 154 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA J 234 " --> pdb=" O ILE J 191 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY J 128 " --> pdb=" O LYS J 251 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N PHE J 253 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU J 130 " --> pdb=" O PHE J 253 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 80 through 81 removed outlier: 3.874A pdb=" N PHE K 154 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASN K 153 " --> pdb=" O ILE K 188 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N PHE K 190 " --> pdb=" O ASN K 153 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE K 155 " --> pdb=" O PHE K 190 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP K 192 " --> pdb=" O ILE K 155 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE K 157 " --> pdb=" O ASP K 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA K 234 " --> pdb=" O ILE K 191 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL K 129 " --> pdb=" O GLY K 233 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR K 235 " --> pdb=" O VAL K 129 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU K 131 " --> pdb=" O THR K 235 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY K 128 " --> pdb=" O LYS K 251 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE K 253 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU K 130 " --> pdb=" O PHE K 253 " (cutoff:3.500A) 1296 hydrogen bonds defined for protein. 3711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6152 1.33 - 1.45: 5015 1.45 - 1.58: 15342 1.58 - 1.70: 50 1.70 - 1.83: 227 Bond restraints: 26786 Sorted by residual: bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.60e+01 bond pdb=" C4 ATP K 401 " pdb=" C5 ATP K 401 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.44e+01 bond pdb=" C4 ATP H 401 " pdb=" C5 ATP H 401 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.43e+01 bond pdb=" C4 ATP E 401 " pdb=" C5 ATP E 401 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.43e+01 ... (remaining 26781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 35818 3.74 - 7.48: 266 7.48 - 11.21: 57 11.21 - 14.95: 12 14.95 - 18.69: 11 Bond angle restraints: 36164 Sorted by residual: angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 121.18 18.69 1.00e+00 1.00e+00 3.49e+02 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 121.74 18.13 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP I 401 " pdb=" O3B ATP I 401 " pdb=" PG ATP I 401 " ideal model delta sigma weight residual 139.87 122.38 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 122.98 16.89 1.00e+00 1.00e+00 2.85e+02 angle pdb=" PB ATP J 401 " pdb=" O3B ATP J 401 " pdb=" PG ATP J 401 " ideal model delta sigma weight residual 139.87 123.04 16.83 1.00e+00 1.00e+00 2.83e+02 ... (remaining 36159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14148 17.98 - 35.96: 1965 35.96 - 53.95: 565 53.95 - 71.93: 100 71.93 - 89.91: 51 Dihedral angle restraints: 16829 sinusoidal: 7178 harmonic: 9651 Sorted by residual: dihedral pdb=" CA LEU H 184 " pdb=" C LEU H 184 " pdb=" N GLN H 185 " pdb=" CA GLN H 185 " ideal model delta harmonic sigma weight residual -180.00 -157.14 -22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA LEU G 184 " pdb=" C LEU G 184 " pdb=" N GLN G 185 " pdb=" CA GLN G 185 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LEU E 184 " pdb=" C LEU E 184 " pdb=" N GLN E 185 " pdb=" CA GLN E 185 " ideal model delta harmonic sigma weight residual 180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 16826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3667 0.077 - 0.153: 432 0.153 - 0.230: 25 0.230 - 0.306: 13 0.306 - 0.383: 4 Chirality restraints: 4141 Sorted by residual: chirality pdb=" CA ASP B 273 " pdb=" N ASP B 273 " pdb=" C ASP B 273 " pdb=" CB ASP B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA UNK L 5 " pdb=" N UNK L 5 " pdb=" C UNK L 5 " pdb=" CB UNK L 5 " both_signs ideal model delta sigma weight residual False 2.52 2.19 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA LEU F 184 " pdb=" N LEU F 184 " pdb=" C LEU F 184 " pdb=" CB LEU F 184 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 4138 not shown) Planarity restraints: 4540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 196 " 0.016 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C SER F 196 " -0.052 2.00e-02 2.50e+03 pdb=" O SER F 196 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE F 197 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 337 " 0.050 5.00e-02 4.00e+02 7.42e-02 8.82e+00 pdb=" N PRO D 338 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 338 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 338 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 82 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO F 83 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 83 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 83 " -0.036 5.00e-02 4.00e+02 ... (remaining 4537 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 30 2.34 - 2.98: 11931 2.98 - 3.62: 41644 3.62 - 4.26: 65890 4.26 - 4.90: 110135 Nonbonded interactions: 229630 Sorted by model distance: nonbonded pdb=" O2G ATP E 401 " pdb="MG MG E 402 " model vdw 1.701 2.170 nonbonded pdb=" OG1 THR J 140 " pdb="MG MG J 402 " model vdw 1.703 2.170 nonbonded pdb=" O3G ATP D 401 " pdb="MG MG D 402 " model vdw 1.719 2.170 nonbonded pdb=" OG1 THR I 140 " pdb="MG MG I 402 " model vdw 1.724 2.170 nonbonded pdb=" O3G ATP I 401 " pdb="MG MG I 402 " model vdw 1.732 2.170 ... (remaining 229625 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 'A' selection = (chain 'B' and resid 43 through 349) selection = (chain 'C' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'D' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'E' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'F' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'G' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'H' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'I' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'J' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'K' and (resid 43 through 319 or resid 337 through 349)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.230 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.400 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 : 0.005 0.083 26786 Z= 0.341 Angle : 0.896 18.691 36164 Z= 0.603 Chirality : 0.049 0.383 4141 Planarity : 0.005 0.074 4540 Dihedral : 18.230 89.909 10545 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.21 % Allowed : 25.98 % Favored : 72.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.14), residues: 3245 helix: 0.83 (0.12), residues: 1747 sheet: 0.30 (0.29), residues: 328 loop : 1.01 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 337 TYR 0.023 0.001 TYR K 264 PHE 0.016 0.001 PHE E 154 TRP 0.007 0.001 TRP G 166 HIS 0.001 0.000 HIS I 206 Details of bonding type rmsd covalent geometry : bond 0.00469 (26786) covalent geometry : angle 0.89581 (36164) hydrogen bonds : bond 0.16087 ( 1296) hydrogen bonds : angle 5.74411 ( 3711) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 403 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 221 ASP cc_start: 0.7479 (t0) cc_final: 0.7076 (t70) REVERT: A 243 ASP cc_start: 0.7510 (m-30) cc_final: 0.6082 (t0) REVERT: C 197 PHE cc_start: 0.8914 (t80) cc_final: 0.8709 (t80) REVERT: D 82 THR cc_start: 0.8826 (p) cc_final: 0.8466 (p) REVERT: E 340 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8234 (mtmm) REVERT: H 74 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7278 (mtm-85) REVERT: J 47 LYS cc_start: 0.7436 (mtpp) cc_final: 0.6817 (mptt) outliers start: 35 outliers final: 25 residues processed: 435 average time/residue: 0.6533 time to fit residues: 328.5995 Evaluate side-chains 385 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 360 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 236 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.0170 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 10.0000 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN C 124 GLN E 124 GLN G 225 ASN H 171 ASN I 289 ASN K 153 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.156333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118680 restraints weight = 31088.523| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.72 r_work: 0.3020 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26786 Z= 0.119 Angle : 0.513 8.040 36164 Z= 0.256 Chirality : 0.041 0.140 4141 Planarity : 0.004 0.052 4540 Dihedral : 10.716 85.326 3921 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.11 % Allowed : 24.40 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.15), residues: 3245 helix: 1.55 (0.13), residues: 1738 sheet: 0.29 (0.29), residues: 329 loop : 1.30 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 248 TYR 0.012 0.001 TYR K 264 PHE 0.019 0.001 PHE B 293 TRP 0.005 0.001 TRP E 220 HIS 0.002 0.000 HIS K 104 Details of bonding type rmsd covalent geometry : bond 0.00268 (26786) covalent geometry : angle 0.51316 (36164) hydrogen bonds : bond 0.03619 ( 1296) hydrogen bonds : angle 4.54818 ( 3711) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 379 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6416 (tm-30) REVERT: A 70 ASP cc_start: 0.6025 (t0) cc_final: 0.5789 (t0) REVERT: A 139 LYS cc_start: 0.3112 (OUTLIER) cc_final: 0.2896 (mtmm) REVERT: A 207 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6413 (tm-30) REVERT: A 221 ASP cc_start: 0.7549 (t0) cc_final: 0.7072 (t70) REVERT: B 60 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8156 (tmm-80) REVERT: B 100 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7976 (mp) REVERT: B 104 HIS cc_start: 0.8225 (m-70) cc_final: 0.8019 (m-70) REVERT: E 299 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8440 (ttpm) REVERT: E 340 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8181 (mtmm) REVERT: F 221 ASP cc_start: 0.8311 (t0) cc_final: 0.8032 (t0) REVERT: G 289 ASN cc_start: 0.8886 (m110) cc_final: 0.8673 (m-40) REVERT: G 315 LYS cc_start: 0.7670 (pttp) cc_final: 0.7314 (mtmt) REVERT: H 60 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6707 (ttm-80) REVERT: H 74 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7250 (mtm-85) REVERT: H 184 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8339 (mt) REVERT: H 342 LYS cc_start: 0.7836 (pttp) cc_final: 0.7248 (pttm) REVERT: J 47 LYS cc_start: 0.7329 (mtpp) cc_final: 0.6626 (mptt) REVERT: J 55 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: K 115 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6182 (mp0) REVERT: K 215 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: K 219 LEU cc_start: 0.7939 (mm) cc_final: 0.7701 (mt) REVERT: K 228 ARG cc_start: 0.7357 (mpp80) cc_final: 0.7045 (mtp85) outliers start: 90 outliers final: 27 residues processed: 441 average time/residue: 0.6542 time to fit residues: 335.8861 Evaluate side-chains 393 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 355 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain H residue 60 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 149 GLU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain K residue 141 MET Chi-restraints excluded: chain K residue 215 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 153 optimal weight: 10.0000 chunk 271 optimal weight: 0.0870 chunk 138 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 225 ASN D 225 ASN G 225 ASN H 53 GLN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.153924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.115663 restraints weight = 31069.651| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.73 r_work: 0.2981 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26786 Z= 0.140 Angle : 0.502 9.145 36164 Z= 0.247 Chirality : 0.041 0.139 4141 Planarity : 0.003 0.047 4540 Dihedral : 10.626 86.046 3885 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.42 % Allowed : 24.67 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.15), residues: 3245 helix: 1.72 (0.13), residues: 1760 sheet: 0.20 (0.28), residues: 334 loop : 1.41 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 337 TYR 0.011 0.001 TYR I 167 PHE 0.015 0.001 PHE B 293 TRP 0.006 0.001 TRP E 220 HIS 0.001 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00328 (26786) covalent geometry : angle 0.50165 (36164) hydrogen bonds : bond 0.03126 ( 1296) hydrogen bonds : angle 4.40207 ( 3711) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 373 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6431 (tm-30) REVERT: A 70 ASP cc_start: 0.6115 (t0) cc_final: 0.5860 (t0) REVERT: A 139 LYS cc_start: 0.3091 (OUTLIER) cc_final: 0.2880 (mtmm) REVERT: A 221 ASP cc_start: 0.7565 (t0) cc_final: 0.7159 (t70) REVERT: B 100 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7955 (mp) REVERT: B 104 HIS cc_start: 0.8251 (m-70) cc_final: 0.8037 (m-70) REVERT: C 39 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6572 (mm) REVERT: C 307 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7641 (mp) REVERT: E 299 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8491 (tttm) REVERT: E 340 LYS cc_start: 0.8469 (mtmm) cc_final: 0.8211 (mtmm) REVERT: F 223 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8972 (mp) REVERT: F 312 GLU cc_start: 0.7370 (pm20) cc_final: 0.7140 (mp0) REVERT: G 61 SER cc_start: 0.8159 (m) cc_final: 0.7916 (p) REVERT: G 289 ASN cc_start: 0.8907 (m110) cc_final: 0.8691 (m-40) REVERT: G 314 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7957 (mp) REVERT: G 315 LYS cc_start: 0.7688 (pttp) cc_final: 0.7295 (mtmt) REVERT: H 60 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6673 (ttm-80) REVERT: H 74 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7270 (mtm-85) REVERT: H 184 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8294 (mt) REVERT: H 342 LYS cc_start: 0.7870 (pttp) cc_final: 0.7293 (pttm) REVERT: I 337 ARG cc_start: 0.8225 (ttp80) cc_final: 0.8004 (ttp80) REVERT: J 47 LYS cc_start: 0.7349 (mtpp) cc_final: 0.6614 (mptt) REVERT: J 55 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: J 89 THR cc_start: 0.8365 (m) cc_final: 0.8130 (t) REVERT: K 115 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: K 215 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6921 (tm-30) REVERT: K 219 LEU cc_start: 0.8026 (mm) cc_final: 0.7675 (mt) outliers start: 99 outliers final: 34 residues processed: 443 average time/residue: 0.6457 time to fit residues: 330.9809 Evaluate side-chains 402 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 355 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain H residue 60 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain K residue 141 MET Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 215 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 209 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 277 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 232 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS B 193 GLN B 225 ASN C 124 GLN D 225 ASN F 289 ASN G 225 ASN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 236 ASN ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 ASN K 153 ASN K 262 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.154887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116864 restraints weight = 30897.254| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.74 r_work: 0.3001 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26786 Z= 0.108 Angle : 0.477 8.585 36164 Z= 0.235 Chirality : 0.040 0.160 4141 Planarity : 0.003 0.047 4540 Dihedral : 10.447 89.395 3884 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.28 % Allowed : 24.60 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.15), residues: 3245 helix: 1.87 (0.13), residues: 1765 sheet: 0.09 (0.28), residues: 334 loop : 1.42 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 337 TYR 0.015 0.001 TYR K 264 PHE 0.012 0.001 PHE B 293 TRP 0.004 0.001 TRP E 220 HIS 0.001 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00248 (26786) covalent geometry : angle 0.47676 (36164) hydrogen bonds : bond 0.02816 ( 1296) hydrogen bonds : angle 4.30372 ( 3711) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 373 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6453 (tm-30) REVERT: A 57 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7380 (mp) REVERT: A 70 ASP cc_start: 0.6115 (t0) cc_final: 0.5899 (t0) REVERT: A 221 ASP cc_start: 0.7608 (t0) cc_final: 0.7164 (t70) REVERT: B 100 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8004 (mp) REVERT: B 104 HIS cc_start: 0.8268 (m-70) cc_final: 0.8015 (m-70) REVERT: C 39 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6502 (mm) REVERT: E 45 GLU cc_start: 0.8150 (tp30) cc_final: 0.7839 (tt0) REVERT: E 223 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8639 (mp) REVERT: E 299 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8501 (tttm) REVERT: E 340 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8220 (mtmm) REVERT: F 312 GLU cc_start: 0.7371 (pm20) cc_final: 0.7118 (mp0) REVERT: G 288 ASP cc_start: 0.8235 (m-30) cc_final: 0.7943 (m-30) REVERT: G 314 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7972 (mp) REVERT: G 315 LYS cc_start: 0.7691 (pttp) cc_final: 0.7308 (mtmt) REVERT: H 60 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6634 (ttm-80) REVERT: H 74 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7276 (mtm-85) REVERT: H 184 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8253 (mt) REVERT: H 342 LYS cc_start: 0.7838 (pttp) cc_final: 0.7260 (pttm) REVERT: I 68 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8344 (p) REVERT: J 47 LYS cc_start: 0.7326 (mtpp) cc_final: 0.6599 (mptt) REVERT: J 55 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: K 105 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: K 115 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: K 215 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7055 (tm-30) outliers start: 95 outliers final: 30 residues processed: 436 average time/residue: 0.6360 time to fit residues: 323.2058 Evaluate side-chains 399 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 355 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain H residue 60 ARG Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 247 ARG Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain K residue 141 MET Chi-restraints excluded: chain K residue 215 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 313 optimal weight: 0.9990 chunk 249 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 320 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 250 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 193 GLN B 225 ASN C 124 GLN D 225 ASN G 225 ASN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.155160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.117081 restraints weight = 30908.054| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.68 r_work: 0.3014 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 26786 Z= 0.107 Angle : 0.478 8.990 36164 Z= 0.235 Chirality : 0.040 0.169 4141 Planarity : 0.003 0.046 4540 Dihedral : 10.332 87.269 3884 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.28 % Allowed : 24.74 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.15), residues: 3245 helix: 1.97 (0.13), residues: 1759 sheet: 0.03 (0.28), residues: 335 loop : 1.47 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 337 TYR 0.011 0.001 TYR I 167 PHE 0.010 0.001 PHE B 293 TRP 0.006 0.001 TRP K 220 HIS 0.001 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00249 (26786) covalent geometry : angle 0.47808 (36164) hydrogen bonds : bond 0.02765 ( 1296) hydrogen bonds : angle 4.24534 ( 3711) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 377 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6481 (tm-30) REVERT: A 221 ASP cc_start: 0.7547 (t0) cc_final: 0.7162 (t70) REVERT: B 100 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7997 (mp) REVERT: B 104 HIS cc_start: 0.8259 (m-70) cc_final: 0.8017 (m-70) REVERT: C 39 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6531 (mm) REVERT: E 215 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: E 223 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8536 (mp) REVERT: E 299 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8417 (ttpm) REVERT: F 223 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8959 (mp) REVERT: F 312 GLU cc_start: 0.7365 (pm20) cc_final: 0.7095 (mp0) REVERT: G 288 ASP cc_start: 0.8225 (m-30) cc_final: 0.7971 (m-30) REVERT: G 314 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7974 (mp) REVERT: G 315 LYS cc_start: 0.7713 (pttp) cc_final: 0.7338 (mtmt) REVERT: H 60 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6563 (ttm-80) REVERT: H 74 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7236 (mtm-85) REVERT: H 184 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8228 (mt) REVERT: H 342 LYS cc_start: 0.7813 (pttp) cc_final: 0.7228 (pttm) REVERT: I 68 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8350 (p) REVERT: J 47 LYS cc_start: 0.7338 (mtpp) cc_final: 0.6608 (mptt) REVERT: J 55 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: J 89 THR cc_start: 0.8337 (m) cc_final: 0.8103 (t) REVERT: J 284 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8324 (tp-100) REVERT: K 105 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: K 115 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6107 (mp0) REVERT: K 201 ARG cc_start: 0.5551 (mmt90) cc_final: 0.5223 (mmt90) REVERT: K 215 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7677 (tm-30) outliers start: 95 outliers final: 34 residues processed: 442 average time/residue: 0.6928 time to fit residues: 354.4665 Evaluate side-chains 408 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 359 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain H residue 60 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 247 ARG Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain K residue 141 MET Chi-restraints excluded: chain K residue 215 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 171 optimal weight: 7.9990 chunk 184 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 326 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 298 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 225 ASN D 225 ASN E 53 GLN G 225 ASN G 236 ASN H 225 ASN ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 ASN K 53 GLN K 153 ASN K 262 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.150431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111576 restraints weight = 30868.482| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.66 r_work: 0.2994 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 26786 Z= 0.198 Angle : 0.554 9.294 36164 Z= 0.271 Chirality : 0.043 0.186 4141 Planarity : 0.004 0.047 4540 Dihedral : 10.516 86.530 3884 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.69 % Allowed : 24.15 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.15), residues: 3245 helix: 1.78 (0.13), residues: 1757 sheet: 0.02 (0.28), residues: 336 loop : 1.39 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 337 TYR 0.016 0.001 TYR G 167 PHE 0.011 0.001 PHE C 178 TRP 0.012 0.001 TRP E 220 HIS 0.002 0.001 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00481 (26786) covalent geometry : angle 0.55415 (36164) hydrogen bonds : bond 0.03226 ( 1296) hydrogen bonds : angle 4.44184 ( 3711) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 376 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: A 57 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7417 (mp) REVERT: A 221 ASP cc_start: 0.7653 (t0) cc_final: 0.7248 (t70) REVERT: B 100 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7991 (mp) REVERT: B 104 HIS cc_start: 0.8289 (m-70) cc_final: 0.8053 (m-70) REVERT: C 307 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7856 (mp) REVERT: E 215 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: E 223 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8696 (mp) REVERT: E 299 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8434 (ttpm) REVERT: F 55 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: F 223 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9061 (mp) REVERT: F 312 GLU cc_start: 0.7430 (pm20) cc_final: 0.7132 (mp0) REVERT: G 288 ASP cc_start: 0.8196 (m-30) cc_final: 0.7936 (m-30) REVERT: G 289 ASN cc_start: 0.8830 (m-40) cc_final: 0.8582 (t0) REVERT: G 312 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: G 314 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8011 (mp) REVERT: G 315 LYS cc_start: 0.7731 (pttp) cc_final: 0.7347 (mtmt) REVERT: H 60 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6593 (ttm-80) REVERT: H 74 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7281 (mtm-85) REVERT: H 124 GLN cc_start: 0.8953 (mt0) cc_final: 0.8652 (mm110) REVERT: H 184 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8382 (mt) REVERT: H 342 LYS cc_start: 0.7915 (pttp) cc_final: 0.7298 (pttm) REVERT: J 47 LYS cc_start: 0.7411 (mtpp) cc_final: 0.6672 (mptt) REVERT: J 55 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: J 89 THR cc_start: 0.8432 (m) cc_final: 0.8231 (t) REVERT: J 182 ASN cc_start: 0.9059 (m-40) cc_final: 0.8829 (m110) REVERT: J 284 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8259 (tp-100) REVERT: K 105 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: K 115 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6171 (mp0) outliers start: 107 outliers final: 39 residues processed: 447 average time/residue: 0.6976 time to fit residues: 359.3243 Evaluate side-chains 414 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 359 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 312 GLU Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain H residue 60 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 247 ARG Chi-restraints excluded: chain J residue 312 GLU Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain K residue 141 MET Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 109 optimal weight: 0.1980 chunk 296 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 252 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 318 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 225 ASN C 124 GLN E 53 GLN F 225 ASN F 289 ASN G 124 GLN G 225 ASN G 236 ASN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 ASN H 236 ASN I 87 ASN ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.155887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118042 restraints weight = 30677.626| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.60 r_work: 0.3071 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26786 Z= 0.102 Angle : 0.491 8.939 36164 Z= 0.244 Chirality : 0.040 0.173 4141 Planarity : 0.003 0.070 4540 Dihedral : 10.281 88.913 3884 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.59 % Allowed : 25.98 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.15), residues: 3245 helix: 1.97 (0.13), residues: 1748 sheet: -0.10 (0.28), residues: 338 loop : 1.43 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 337 TYR 0.014 0.001 TYR K 264 PHE 0.009 0.001 PHE K 197 TRP 0.005 0.001 TRP A 54 HIS 0.002 0.000 HIS I 206 Details of bonding type rmsd covalent geometry : bond 0.00232 (26786) covalent geometry : angle 0.49112 (36164) hydrogen bonds : bond 0.02771 ( 1296) hydrogen bonds : angle 4.31701 ( 3711) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 377 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6288 (tp30) REVERT: A 207 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6358 (tm-30) REVERT: A 221 ASP cc_start: 0.7493 (t0) cc_final: 0.7126 (t70) REVERT: B 100 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8012 (mp) REVERT: B 104 HIS cc_start: 0.8246 (m-70) cc_final: 0.8016 (m-70) REVERT: B 293 PHE cc_start: 0.5515 (OUTLIER) cc_final: 0.3411 (t80) REVERT: D 317 LYS cc_start: 0.7716 (mmmm) cc_final: 0.7429 (mmtm) REVERT: E 215 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: E 223 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8475 (mp) REVERT: E 299 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8509 (tttm) REVERT: F 312 GLU cc_start: 0.7341 (pm20) cc_final: 0.7061 (mp0) REVERT: G 288 ASP cc_start: 0.8163 (m-30) cc_final: 0.7826 (m-30) REVERT: G 289 ASN cc_start: 0.8799 (m-40) cc_final: 0.8508 (t0) REVERT: G 312 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: G 314 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7983 (mp) REVERT: G 315 LYS cc_start: 0.7690 (pttp) cc_final: 0.7318 (mtmt) REVERT: H 60 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6531 (ttm-80) REVERT: H 74 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7186 (mtm-85) REVERT: H 184 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8281 (mt) REVERT: H 275 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7599 (mptt) REVERT: H 342 LYS cc_start: 0.7816 (pttp) cc_final: 0.7249 (pttm) REVERT: J 47 LYS cc_start: 0.7345 (mtpp) cc_final: 0.6623 (mptt) REVERT: J 55 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: J 207 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: J 284 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8295 (tp-100) REVERT: K 105 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: K 115 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6073 (mp0) outliers start: 75 outliers final: 23 residues processed: 428 average time/residue: 0.7090 time to fit residues: 349.3847 Evaluate side-chains 401 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 362 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 312 GLU Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain H residue 60 ARG Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 275 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 247 ARG Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain K residue 141 MET Chi-restraints excluded: chain K residue 236 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 296 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 225 ASN C 124 GLN E 53 GLN F 289 ASN G 225 ASN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 ASN H 236 ASN ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.152409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113943 restraints weight = 30837.258| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.67 r_work: 0.3001 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26786 Z= 0.151 Angle : 0.522 9.001 36164 Z= 0.256 Chirality : 0.041 0.214 4141 Planarity : 0.004 0.065 4540 Dihedral : 10.306 88.437 3883 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.45 % Allowed : 26.02 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.15), residues: 3245 helix: 1.92 (0.13), residues: 1749 sheet: -0.09 (0.27), residues: 338 loop : 1.47 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 337 TYR 0.017 0.001 TYR D 264 PHE 0.010 0.001 PHE B 293 TRP 0.007 0.001 TRP E 220 HIS 0.001 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00362 (26786) covalent geometry : angle 0.52183 (36164) hydrogen bonds : bond 0.02932 ( 1296) hydrogen bonds : angle 4.34374 ( 3711) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 363 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6566 (tm-30) REVERT: A 57 LEU cc_start: 0.7842 (mp) cc_final: 0.7397 (mp) REVERT: A 105 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6544 (tp30) REVERT: A 207 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6396 (tm-30) REVERT: A 221 ASP cc_start: 0.7595 (t0) cc_final: 0.7211 (t70) REVERT: B 100 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 104 HIS cc_start: 0.8291 (m-70) cc_final: 0.8052 (m-70) REVERT: B 293 PHE cc_start: 0.5604 (OUTLIER) cc_final: 0.3538 (t80) REVERT: D 317 LYS cc_start: 0.7720 (mmmm) cc_final: 0.7442 (mmtm) REVERT: E 215 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: E 223 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8538 (mp) REVERT: E 299 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8523 (tttm) REVERT: F 223 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9028 (mp) REVERT: F 312 GLU cc_start: 0.7425 (pm20) cc_final: 0.7123 (mp0) REVERT: G 288 ASP cc_start: 0.8205 (m-30) cc_final: 0.7794 (m-30) REVERT: G 289 ASN cc_start: 0.8843 (m-40) cc_final: 0.8591 (m-40) REVERT: G 312 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: G 314 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8005 (mp) REVERT: G 315 LYS cc_start: 0.7709 (pttp) cc_final: 0.7329 (mtmt) REVERT: H 60 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6536 (ttm-80) REVERT: H 74 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7284 (mtm-85) REVERT: H 124 GLN cc_start: 0.8955 (mt0) cc_final: 0.8650 (mm110) REVERT: H 184 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8336 (mt) REVERT: H 275 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7638 (mptt) REVERT: H 342 LYS cc_start: 0.7842 (pttp) cc_final: 0.7283 (pttm) REVERT: I 337 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7977 (ttp80) REVERT: J 47 LYS cc_start: 0.7411 (mtpp) cc_final: 0.6680 (mptt) REVERT: J 55 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: J 207 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: J 284 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8290 (tp-100) REVERT: K 105 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: K 115 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6123 (mp0) outliers start: 71 outliers final: 31 residues processed: 405 average time/residue: 0.7349 time to fit residues: 342.1305 Evaluate side-chains 407 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 358 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 312 GLU Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 60 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 275 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 247 ARG Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain K residue 141 MET Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 236 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 282 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 182 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 28 optimal weight: 0.0070 chunk 82 optimal weight: 0.0010 chunk 150 optimal weight: 0.9980 chunk 241 optimal weight: 0.0060 chunk 163 optimal weight: 0.0050 overall best weight: 0.0434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 225 ASN C 124 GLN E 53 GLN F 119 ASN F 289 ASN G 225 ASN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 ASN H 236 ASN I 87 ASN I 316 GLN J 171 ASN J 182 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.159610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122936 restraints weight = 30827.304| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.61 r_work: 0.3111 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 26786 Z= 0.092 Angle : 0.484 11.401 36164 Z= 0.240 Chirality : 0.039 0.185 4141 Planarity : 0.003 0.059 4540 Dihedral : 9.966 89.659 3883 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 26.88 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.15), residues: 3245 helix: 2.08 (0.13), residues: 1755 sheet: -0.10 (0.28), residues: 337 loop : 1.56 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 337 TYR 0.013 0.001 TYR K 264 PHE 0.010 0.001 PHE K 197 TRP 0.008 0.001 TRP A 54 HIS 0.002 0.000 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00206 (26786) covalent geometry : angle 0.48444 (36164) hydrogen bonds : bond 0.02569 ( 1296) hydrogen bonds : angle 4.18194 ( 3711) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 377 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7211 (mp) REVERT: A 207 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6419 (tm-30) REVERT: A 221 ASP cc_start: 0.7386 (t0) cc_final: 0.7003 (t70) REVERT: B 100 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8080 (mp) REVERT: B 104 HIS cc_start: 0.8234 (m-70) cc_final: 0.7994 (m-70) REVERT: B 113 MET cc_start: 0.8735 (mtm) cc_final: 0.8507 (mpt) REVERT: B 293 PHE cc_start: 0.5400 (OUTLIER) cc_final: 0.3360 (t80) REVERT: C 45 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: C 113 MET cc_start: 0.8933 (mtp) cc_final: 0.8699 (mtt) REVERT: D 308 ASP cc_start: 0.8378 (m-30) cc_final: 0.8114 (m-30) REVERT: E 149 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7695 (mm-30) REVERT: F 312 GLU cc_start: 0.7355 (pm20) cc_final: 0.7070 (mp0) REVERT: G 288 ASP cc_start: 0.8138 (m-30) cc_final: 0.7910 (m-30) REVERT: G 289 ASN cc_start: 0.8792 (m-40) cc_final: 0.8549 (t0) REVERT: G 314 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7989 (mp) REVERT: G 315 LYS cc_start: 0.7717 (pttp) cc_final: 0.7337 (mtmt) REVERT: H 60 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6488 (ttm-80) REVERT: H 74 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7189 (mtm-85) REVERT: H 184 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8172 (mt) REVERT: H 275 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7659 (mptt) REVERT: H 342 LYS cc_start: 0.7761 (pttp) cc_final: 0.7193 (pttm) REVERT: I 262 GLN cc_start: 0.8585 (mt0) cc_final: 0.8290 (mt0) REVERT: I 337 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8187 (ttp80) REVERT: J 47 LYS cc_start: 0.7352 (mtpp) cc_final: 0.6636 (mptt) REVERT: J 55 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: J 284 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8289 (tp-100) REVERT: K 105 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: K 115 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6133 (mp0) outliers start: 54 outliers final: 11 residues processed: 413 average time/residue: 0.7106 time to fit residues: 337.9996 Evaluate side-chains 381 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 358 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain H residue 60 ARG Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 275 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 124 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 102 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 220 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 225 ASN C 124 GLN D 225 ASN G 225 ASN H 53 GLN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118290 restraints weight = 30655.960| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.62 r_work: 0.3075 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26786 Z= 0.122 Angle : 0.513 10.739 36164 Z= 0.251 Chirality : 0.041 0.208 4141 Planarity : 0.004 0.072 4540 Dihedral : 10.049 89.783 3883 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.28 % Allowed : 27.57 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.15), residues: 3245 helix: 2.08 (0.13), residues: 1754 sheet: -0.06 (0.28), residues: 339 loop : 1.60 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 337 TYR 0.018 0.001 TYR D 264 PHE 0.013 0.001 PHE I 197 TRP 0.006 0.001 TRP A 54 HIS 0.001 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00290 (26786) covalent geometry : angle 0.51268 (36164) hydrogen bonds : bond 0.02719 ( 1296) hydrogen bonds : angle 4.21818 ( 3711) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 362 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6385 (tm-30) REVERT: A 221 ASP cc_start: 0.7457 (t0) cc_final: 0.7084 (t70) REVERT: B 100 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8008 (mp) REVERT: B 104 HIS cc_start: 0.8251 (m-70) cc_final: 0.8034 (m-70) REVERT: B 293 PHE cc_start: 0.5453 (OUTLIER) cc_final: 0.3387 (t80) REVERT: C 45 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: D 308 ASP cc_start: 0.8396 (m-30) cc_final: 0.8138 (m-30) REVERT: E 149 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7821 (mm-30) REVERT: E 223 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8437 (mp) REVERT: F 312 GLU cc_start: 0.7386 (pm20) cc_final: 0.7101 (mp0) REVERT: G 115 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: G 288 ASP cc_start: 0.8120 (m-30) cc_final: 0.7805 (m-30) REVERT: G 289 ASN cc_start: 0.8804 (m-40) cc_final: 0.8573 (m-40) REVERT: G 314 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7990 (mp) REVERT: G 315 LYS cc_start: 0.7718 (pttp) cc_final: 0.7340 (mtmt) REVERT: H 60 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6474 (ttm-80) REVERT: H 74 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7176 (mtm-85) REVERT: H 184 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8228 (mt) REVERT: H 275 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7648 (mptt) REVERT: H 342 LYS cc_start: 0.7771 (pttp) cc_final: 0.7200 (pttm) REVERT: I 262 GLN cc_start: 0.8605 (mt0) cc_final: 0.8299 (mt0) REVERT: I 337 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8193 (ttp80) REVERT: J 47 LYS cc_start: 0.7360 (mtpp) cc_final: 0.6635 (mptt) REVERT: J 55 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: J 284 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8531 (tm-30) REVERT: K 105 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: K 115 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6139 (mp0) outliers start: 37 outliers final: 11 residues processed: 387 average time/residue: 0.7273 time to fit residues: 324.1351 Evaluate side-chains 376 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 352 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain H residue 60 ARG Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 275 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 124 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 39 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 291 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 87 optimal weight: 0.0030 chunk 256 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN C 124 GLN D 225 ASN G 225 ASN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 ASN K 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.156380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119173 restraints weight = 30743.003| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.60 r_work: 0.3043 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26786 Z= 0.112 Angle : 0.509 10.988 36164 Z= 0.250 Chirality : 0.040 0.216 4141 Planarity : 0.003 0.056 4540 Dihedral : 10.029 89.013 3883 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.21 % Allowed : 27.57 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.15), residues: 3245 helix: 2.08 (0.13), residues: 1754 sheet: -0.09 (0.27), residues: 343 loop : 1.64 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 337 TYR 0.012 0.001 TYR J 264 PHE 0.013 0.001 PHE I 197 TRP 0.005 0.001 TRP A 54 HIS 0.002 0.000 HIS J 206 Details of bonding type rmsd covalent geometry : bond 0.00264 (26786) covalent geometry : angle 0.50905 (36164) hydrogen bonds : bond 0.02669 ( 1296) hydrogen bonds : angle 4.22496 ( 3711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10925.12 seconds wall clock time: 186 minutes 47.57 seconds (11207.57 seconds total)