Starting phenix.real_space_refine on Sun Jun 15 13:58:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m5g_30085/06_2025/6m5g_30085.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m5g_30085/06_2025/6m5g_30085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m5g_30085/06_2025/6m5g_30085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m5g_30085/06_2025/6m5g_30085.map" model { file = "/net/cci-nas-00/data/ceres_data/6m5g_30085/06_2025/6m5g_30085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m5g_30085/06_2025/6m5g_30085.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 10 5.49 5 Mg 5 5.21 5 S 108 5.16 5 C 10948 2.51 5 N 2981 2.21 5 O 3311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17363 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2881 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2879 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2873 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2876 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "G" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.86, per 1000 atoms: 0.63 Number of scatterers: 17363 At special positions: 0 Unit cell: (129.72, 89.7, 194.58, 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 108 16.00 P 10 15.00 Mg 5 11.99 O 3311 8.00 N 2981 7.00 C 10948 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: 4.44 Conformation dependent library (CDL) restraints added in 2.1 seconds 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 34 sheets defined 50.3% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.713A pdb=" N LEU A 65 " --> pdb=" O ARG A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.853A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.042A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.625A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.722A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.610A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.690A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.739A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.860A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.914A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.041A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 202 through 217 removed outlier: 4.045A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.717A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.531A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.656A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.795A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.611A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 6.530A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.664A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.986A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.923A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 4.146A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.827A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 232 removed outlier: 4.233A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.904A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 255' Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.661A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.562A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 removed outlier: 3.972A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 307 removed outlier: 3.510A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Proline residue: C 307 - end of helix Processing helix chain 'C' and resid 308 through 319 removed outlier: 4.225A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.892A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.635A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 127 removed outlier: 3.931A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 4.171A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 removed outlier: 4.182A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 4.156A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 232 removed outlier: 3.687A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.135A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.517A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 removed outlier: 4.085A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.655A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Proline residue: D 307 - end of helix Processing helix chain 'D' and resid 308 through 319 removed outlier: 3.641A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.713A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.032A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.662A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.032A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 4.248A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.164A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.509A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.888A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 232 removed outlier: 3.691A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.553A pdb=" N THR E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 removed outlier: 4.250A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.592A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 319 removed outlier: 3.884A pdb=" N GLN E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.733A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'F' and resid 21 through 46 removed outlier: 3.787A pdb=" N ARG F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR F 36 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.847A pdb=" N LEU F 67 " --> pdb=" O GLY F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 103 Processing helix chain 'F' and resid 111 through 117 removed outlier: 3.885A pdb=" N ILE F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL F 116 " --> pdb=" O GLY F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 125 through 135 Processing helix chain 'G' and resid 21 through 46 removed outlier: 3.713A pdb=" N ARG G 25 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS G 29 " --> pdb=" O ARG G 25 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR G 36 " --> pdb=" O VAL G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 75 removed outlier: 3.517A pdb=" N GLU G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 102 Processing helix chain 'G' and resid 111 through 117 Processing helix chain 'G' and resid 119 through 124 Processing helix chain 'G' and resid 124 through 135 removed outlier: 3.734A pdb=" N TRP G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 46 removed outlier: 3.862A pdb=" N ARG H 25 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR H 36 " --> pdb=" O VAL H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 75 removed outlier: 3.982A pdb=" N LEU H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 103 Processing helix chain 'H' and resid 112 through 117 Processing helix chain 'H' and resid 119 through 124 Processing helix chain 'H' and resid 125 through 135 removed outlier: 3.647A pdb=" N TRP H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.572A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.756A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.169A pdb=" N ASP A 154 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 298 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.694A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 19 removed outlier: 3.674A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.740A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.710A pdb=" N GLN B 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.710A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AB5, first strand: chain 'B' and resid 297 through 298 Processing sheet with id=AB6, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.641A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 19 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB8, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.672A pdb=" N GLN C 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'C' and resid 150 through 155 removed outlier: 3.754A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 239 through 241 Processing sheet with id=AC3, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.055A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 8 through 9 removed outlier: 6.856A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.602A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AC7, first strand: chain 'D' and resid 71 through 72 removed outlier: 3.538A pdb=" N ILE D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 150 through 154 removed outlier: 3.561A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 240 through 241 Processing sheet with id=AD1, first strand: chain 'D' and resid 297 through 298 removed outlier: 6.033A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.690A pdb=" N VAL E 9 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AD4, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'E' and resid 150 through 154 removed outlier: 3.727A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP E 154 " --> pdb=" O HIS E 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 238 through 241 removed outlier: 3.724A pdb=" N LYS E 238 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 297 through 298 removed outlier: 6.116A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 696 hydrogen bonds defined for protein. 1896 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: 5.48 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5672 1.33 - 1.45: 2332 1.45 - 1.57: 9519 1.57 - 1.68: 15 1.68 - 1.80: 191 Bond restraints: 17729 Sorted by residual: bond pdb=" CA ARG E 335 " pdb=" C ARG E 335 " ideal model delta sigma weight residual 1.523 1.441 0.083 1.80e-02 3.09e+03 2.10e+01 bond pdb=" CA ALA C 310 " pdb=" C ALA C 310 " ideal model delta sigma weight residual 1.522 1.469 0.053 1.72e-02 3.38e+03 9.48e+00 bond pdb=" C GLN C 263 " pdb=" N PRO C 264 " ideal model delta sigma weight residual 1.334 1.310 0.023 8.40e-03 1.42e+04 7.70e+00 bond pdb=" C LEU D 171 " pdb=" N PRO D 172 " ideal model delta sigma weight residual 1.337 1.312 0.025 9.80e-03 1.04e+04 6.42e+00 bond pdb=" C TYR B 69 " pdb=" N PRO B 70 " ideal model delta sigma weight residual 1.336 1.310 0.026 1.20e-02 6.94e+03 4.73e+00 ... (remaining 17724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 22497 1.48 - 2.95: 1207 2.95 - 4.43: 261 4.43 - 5.90: 63 5.90 - 7.38: 16 Bond angle restraints: 24044 Sorted by residual: angle pdb=" C GLY B 308 " pdb=" N ILE B 309 " pdb=" CA ILE B 309 " ideal model delta sigma weight residual 121.97 129.35 -7.38 1.80e+00 3.09e-01 1.68e+01 angle pdb=" C GLY A 308 " pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta sigma weight residual 121.97 129.19 -7.22 1.80e+00 3.09e-01 1.61e+01 angle pdb=" N GLY E 268 " pdb=" CA GLY E 268 " pdb=" C GLY E 268 " ideal model delta sigma weight residual 114.95 110.30 4.65 1.41e+00 5.03e-01 1.09e+01 angle pdb=" N ARG B 335 " pdb=" CA ARG B 335 " pdb=" C ARG B 335 " ideal model delta sigma weight residual 113.21 109.78 3.43 1.15e+00 7.56e-01 8.92e+00 angle pdb=" C HIS A 161 " pdb=" CA HIS A 161 " pdb=" CB HIS A 161 " ideal model delta sigma weight residual 112.99 106.93 6.06 2.10e+00 2.27e-01 8.34e+00 ... (remaining 24039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 10150 25.51 - 51.02: 468 51.02 - 76.54: 40 76.54 - 102.05: 5 102.05 - 127.56: 2 Dihedral angle restraints: 10665 sinusoidal: 4315 harmonic: 6350 Sorted by residual: dihedral pdb=" C5' ADP C 402 " pdb=" O5' ADP C 402 " pdb=" PA ADP C 402 " pdb=" O2A ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 67.56 -127.56 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" C5' ADP B 402 " pdb=" O5' ADP B 402 " pdb=" PA ADP B 402 " pdb=" O2A ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 54.81 -114.80 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CA GLY A 308 " pdb=" C GLY A 308 " pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta harmonic sigma weight residual -180.00 -153.72 -26.28 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 10662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1484 0.039 - 0.077: 874 0.077 - 0.116: 283 0.116 - 0.154: 39 0.154 - 0.192: 11 Chirality restraints: 2691 Sorted by residual: chirality pdb=" C2' ADP B 402 " pdb=" C1' ADP B 402 " pdb=" C3' ADP B 402 " pdb=" O2' ADP B 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 2688 not shown) Planarity restraints: 3070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 306 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO C 307 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 181 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C ALA E 181 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA E 181 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY E 182 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 306 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 307 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " -0.025 5.00e-02 4.00e+02 ... (remaining 3067 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 183 2.54 - 3.13: 14624 3.13 - 3.72: 25617 3.72 - 4.31: 37456 4.31 - 4.90: 64163 Nonbonded interactions: 142043 Sorted by model distance: nonbonded pdb="MG MG E 401 " pdb=" O1B ADP E 402 " model vdw 1.951 2.170 nonbonded pdb="MG MG A 401 " pdb=" O1B ADP A 402 " model vdw 1.987 2.170 nonbonded pdb=" N ASP B 56 " pdb=" OD1 ASP B 56 " model vdw 2.127 3.120 nonbonded pdb=" N ASP A 56 " pdb=" OD1 ASP A 56 " model vdw 2.194 3.120 nonbonded pdb=" OG SER D 350 " pdb=" OE2 GLU F 81 " model vdw 2.199 3.040 ... (remaining 142038 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' and (resid 5 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 204 or (resid 205 and (name N or \ name CA or name C or name O or name CB )) or resid 206 through 212 or (resid 21 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 214 through \ 233 or (resid 234 and (name N or name CA or name C or name O or name CB )) or re \ sid 235 through 245 or (resid 246 and (name N or name CA or name C or name O or \ name CB )) or resid 247 through 374 or resid 401 through 402)) selection = (chain 'B' and (resid 5 through 204 or (resid 205 and (name N or name CA or name \ C or name O or name CB )) or resid 206 through 212 or (resid 213 and (name N or \ name CA or name C or name O or name CB )) or resid 214 through 233 or (resid 23 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 235 through \ 258 or (resid 259 and (name N or name CA or name C or name O or name CB )) or re \ sid 260 through 374 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 204 or (resid 205 and (name N or \ name CA or name C or name O or name CB )) or resid 206 through 212 or (resid 21 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 214 through \ 233 or (resid 234 and (name N or name CA or name C or name O or name CB )) or re \ sid 235 through 245 or (resid 246 and (name N or name CA or name C or name O or \ name CB )) or resid 247 through 258 or (resid 259 and (name N or name CA or name \ C or name O or name CB )) or resid 260 through 374 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 233 or (resid 234 and (name N or \ name CA or name C or name O or name CB )) or resid 235 through 245 or (resid 24 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 247 through \ 374 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 245 or (resid 246 and (name N or \ name CA or name C or name O or name CB )) or resid 247 through 258 or (resid 25 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 374 or resid 401 through 402)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 40.860 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 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 : 0.010 0.083 17729 Z= 0.451 Angle : 0.820 7.377 24044 Z= 0.430 Chirality : 0.050 0.192 2691 Planarity : 0.004 0.053 3070 Dihedral : 13.870 127.561 6591 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.41 % Favored : 90.40 % Rotamer: Outliers : 9.29 % Allowed : 10.58 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.15), residues: 2188 helix: -1.80 (0.15), residues: 923 sheet: -2.41 (0.30), residues: 265 loop : -3.00 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 340 HIS 0.006 0.001 HIS A 371 PHE 0.017 0.002 PHE B 262 TYR 0.012 0.002 TYR C 69 ARG 0.005 0.001 ARG B 254 Details of bonding type rmsd hydrogen bonds : bond 0.17912 ( 696) hydrogen bonds : angle 7.11317 ( 1896) covalent geometry : bond 0.01038 (17729) covalent geometry : angle 0.82039 (24044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 244 time to evaluate : 1.862 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9387 (pt) REVERT: A 44 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8262 (mtt) REVERT: A 119 MET cc_start: 0.8865 (ttm) cc_final: 0.8624 (ttm) REVERT: A 162 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8598 (m110) REVERT: A 227 MET cc_start: 0.8700 (mmm) cc_final: 0.8308 (mtp) REVERT: A 288 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8634 (m-30) REVERT: B 335 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8304 (ptt-90) REVERT: B 360 GLN cc_start: 0.8021 (tp40) cc_final: 0.7752 (tp-100) REVERT: C 50 LYS cc_start: 0.8074 (tptt) cc_final: 0.7848 (tptp) REVERT: C 176 MET cc_start: 0.8601 (mmm) cc_final: 0.8206 (mmt) REVERT: D 61 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8806 (mtmm) REVERT: D 92 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.8992 (m-40) REVERT: D 132 MET cc_start: 0.9235 (ppp) cc_final: 0.8918 (ptm) REVERT: D 249 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.9091 (p) REVERT: D 283 MET cc_start: 0.8831 (mmm) cc_final: 0.7794 (mmt) REVERT: F 31 ASP cc_start: 0.8179 (m-30) cc_final: 0.7833 (m-30) REVERT: F 34 LYS cc_start: 0.8874 (tttt) cc_final: 0.8663 (tttp) REVERT: F 64 ARG cc_start: 0.8457 (mtm110) cc_final: 0.8230 (mtm110) REVERT: F 86 ARG cc_start: 0.7754 (ttt-90) cc_final: 0.7487 (ttt-90) REVERT: F 94 ASN cc_start: 0.8411 (t0) cc_final: 0.8172 (t0) REVERT: F 98 GLN cc_start: 0.8311 (mt0) cc_final: 0.8011 (mt0) REVERT: F 119 ASN cc_start: 0.9017 (t0) cc_final: 0.8802 (t0) REVERT: F 121 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7784 (ttpt) REVERT: G 56 MET cc_start: 0.8853 (tpp) cc_final: 0.8464 (tpp) REVERT: G 71 GLU cc_start: 0.8864 (pt0) cc_final: 0.8182 (tt0) REVERT: G 81 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7522 (mm-30) REVERT: G 99 VAL cc_start: 0.9088 (m) cc_final: 0.8868 (p) REVERT: G 102 GLN cc_start: 0.8701 (mp10) cc_final: 0.8350 (mp10) REVERT: H 23 LYS cc_start: 0.8284 (mmmt) cc_final: 0.8009 (tppt) REVERT: H 24 SER cc_start: 0.9157 (m) cc_final: 0.8555 (p) REVERT: H 31 ASP cc_start: 0.8390 (m-30) cc_final: 0.8005 (m-30) REVERT: H 33 GLN cc_start: 0.8631 (mm110) cc_final: 0.8386 (mm-40) REVERT: H 60 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8719 (mp) REVERT: H 71 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8672 (tt0) outliers start: 174 outliers final: 117 residues processed: 407 average time/residue: 0.3058 time to fit residues: 184.9417 Evaluate side-chains 352 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 226 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 101 HIS A 162 ASN A 353 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 88 HIS B 92 ASN B 115 ASN B 162 ASN B 275 HIS ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 161 HIS C 162 ASN C 275 HIS D 40 HIS D 88 HIS D 161 HIS D 296 ASN E 88 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 275 HIS F 88 HIS F 120 HIS F 135 GLN G 33 GLN ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS H 29 HIS H 33 GLN H 88 HIS H 102 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.070457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.055474 restraints weight = 45585.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.057150 restraints weight = 21851.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.057772 restraints weight = 13366.339| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17729 Z= 0.121 Angle : 0.626 8.246 24044 Z= 0.310 Chirality : 0.043 0.186 2691 Planarity : 0.004 0.063 3070 Dihedral : 10.657 105.664 2679 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.93 % Allowed : 13.41 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.17), residues: 2188 helix: -0.62 (0.17), residues: 948 sheet: -2.04 (0.31), residues: 260 loop : -2.03 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 340 HIS 0.005 0.001 HIS G 133 PHE 0.011 0.001 PHE E 352 TYR 0.008 0.001 TYR A 362 ARG 0.010 0.001 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 696) hydrogen bonds : angle 5.12334 ( 1896) covalent geometry : bond 0.00270 (17729) covalent geometry : angle 0.62629 (24044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 249 time to evaluate : 1.924 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9252 (pt) REVERT: A 44 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7932 (mtt) REVERT: A 162 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8105 (m-40) REVERT: A 213 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9058 (tttt) REVERT: B 305 MET cc_start: 0.8543 (mtp) cc_final: 0.8284 (mtp) REVERT: B 335 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8395 (ptt-90) REVERT: C 14 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8699 (p) REVERT: C 50 LYS cc_start: 0.7972 (tptt) cc_final: 0.7675 (tptp) REVERT: C 254 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.7282 (mtm-85) REVERT: C 283 MET cc_start: 0.8676 (mmt) cc_final: 0.8389 (mmt) REVERT: D 192 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8832 (tp) REVERT: D 283 MET cc_start: 0.8785 (mmm) cc_final: 0.7856 (mmt) REVERT: D 355 MET cc_start: 0.8332 (mtt) cc_final: 0.8050 (mtm) REVERT: E 328 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7620 (ttpp) REVERT: F 23 LYS cc_start: 0.8258 (tppt) cc_final: 0.8039 (tppt) REVERT: F 34 LYS cc_start: 0.8947 (tttt) cc_final: 0.8744 (tttp) REVERT: F 56 MET cc_start: 0.8724 (tpp) cc_final: 0.8460 (tpp) REVERT: F 95 ARG cc_start: 0.8866 (tpp80) cc_final: 0.8297 (ttm110) REVERT: F 98 GLN cc_start: 0.8319 (mt0) cc_final: 0.7971 (pt0) REVERT: F 102 GLN cc_start: 0.9092 (mt0) cc_final: 0.8879 (mt0) REVERT: F 135 GLN cc_start: 0.6192 (tt0) cc_final: 0.5931 (tt0) REVERT: G 25 ARG cc_start: 0.8497 (tpp80) cc_final: 0.8171 (tpt170) REVERT: G 27 ASP cc_start: 0.7943 (m-30) cc_final: 0.7643 (m-30) REVERT: G 56 MET cc_start: 0.8994 (tpp) cc_final: 0.8725 (tpp) REVERT: G 71 GLU cc_start: 0.8767 (pt0) cc_final: 0.8309 (tt0) REVERT: G 81 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7562 (mm-30) REVERT: G 92 ASN cc_start: 0.8976 (m-40) cc_final: 0.8672 (m-40) REVERT: H 23 LYS cc_start: 0.8291 (mmmt) cc_final: 0.8042 (tppt) REVERT: H 24 SER cc_start: 0.9176 (m) cc_final: 0.8623 (p) REVERT: H 25 ARG cc_start: 0.7528 (tpp80) cc_final: 0.7060 (mmm-85) REVERT: H 31 ASP cc_start: 0.8526 (m-30) cc_final: 0.8119 (m-30) outliers start: 111 outliers final: 63 residues processed: 348 average time/residue: 0.2997 time to fit residues: 155.8341 Evaluate side-chains 307 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 235 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 135 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 10 optimal weight: 0.0270 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 12 ASN G 29 HIS ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN H 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.071479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.056304 restraints weight = 45278.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.058021 restraints weight = 21692.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.058621 restraints weight = 13640.283| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17729 Z= 0.111 Angle : 0.582 6.914 24044 Z= 0.286 Chirality : 0.043 0.277 2691 Planarity : 0.003 0.042 3070 Dihedral : 9.109 92.165 2559 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.75 % Allowed : 15.06 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 2188 helix: -0.19 (0.17), residues: 968 sheet: -2.13 (0.28), residues: 320 loop : -1.70 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.006 0.001 HIS G 133 PHE 0.019 0.001 PHE G 37 TYR 0.007 0.001 TYR C 166 ARG 0.004 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 696) hydrogen bonds : angle 4.83802 ( 1896) covalent geometry : bond 0.00244 (17729) covalent geometry : angle 0.58228 (24044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 252 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9224 (pt) REVERT: A 44 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8050 (mtt) REVERT: A 213 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9114 (ttpt) REVERT: B 335 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8333 (ptt-90) REVERT: C 50 LYS cc_start: 0.7934 (tptt) cc_final: 0.7636 (tptp) REVERT: C 254 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7182 (mtm-85) REVERT: C 283 MET cc_start: 0.8678 (mmt) cc_final: 0.8370 (mmt) REVERT: D 167 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7332 (mm-30) REVERT: D 192 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8787 (tp) REVERT: D 283 MET cc_start: 0.8682 (mmm) cc_final: 0.7650 (mmt) REVERT: F 34 LYS cc_start: 0.8990 (tttt) cc_final: 0.8770 (tttp) REVERT: F 56 MET cc_start: 0.8743 (tpp) cc_final: 0.8489 (tpp) REVERT: F 62 ASP cc_start: 0.7960 (p0) cc_final: 0.7703 (p0) REVERT: F 98 GLN cc_start: 0.8307 (mt0) cc_final: 0.7923 (pt0) REVERT: F 102 GLN cc_start: 0.9080 (mt0) cc_final: 0.8797 (mt0) REVERT: G 25 ARG cc_start: 0.8478 (tpp80) cc_final: 0.8254 (tpt-90) REVERT: G 27 ASP cc_start: 0.7977 (m-30) cc_final: 0.7615 (m-30) REVERT: G 56 MET cc_start: 0.8974 (tpp) cc_final: 0.8575 (tpp) REVERT: G 71 GLU cc_start: 0.8737 (pt0) cc_final: 0.8267 (tt0) REVERT: G 81 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7580 (mm-30) REVERT: G 92 ASN cc_start: 0.9049 (m-40) cc_final: 0.8774 (m-40) REVERT: H 23 LYS cc_start: 0.8305 (mmmt) cc_final: 0.8062 (tppt) REVERT: H 24 SER cc_start: 0.9149 (m) cc_final: 0.8660 (p) REVERT: H 25 ARG cc_start: 0.7501 (tpp80) cc_final: 0.7228 (mmm-85) REVERT: H 31 ASP cc_start: 0.8482 (m-30) cc_final: 0.8087 (m-30) REVERT: H 71 GLU cc_start: 0.8463 (tt0) cc_final: 0.8258 (tt0) outliers start: 89 outliers final: 62 residues processed: 330 average time/residue: 0.3070 time to fit residues: 151.1002 Evaluate side-chains 309 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 240 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 135 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 154 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 HIS F 120 HIS F 135 GLN G 42 ASN G 88 HIS G 98 GLN H 101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.070367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.055242 restraints weight = 45408.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.056751 restraints weight = 22167.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.057376 restraints weight = 14030.072| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17729 Z= 0.168 Angle : 0.601 7.106 24044 Z= 0.294 Chirality : 0.044 0.241 2691 Planarity : 0.003 0.042 3070 Dihedral : 8.676 91.801 2532 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.29 % Allowed : 15.49 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2188 helix: 0.04 (0.17), residues: 948 sheet: -2.04 (0.28), residues: 320 loop : -1.50 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.006 0.001 HIS H 101 PHE 0.012 0.001 PHE G 37 TYR 0.007 0.001 TYR C 69 ARG 0.004 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 696) hydrogen bonds : angle 4.82387 ( 1896) covalent geometry : bond 0.00395 (17729) covalent geometry : angle 0.60101 (24044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 243 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9230 (pt) REVERT: A 44 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8149 (mtt) REVERT: A 213 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9073 (tttt) REVERT: C 14 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8755 (p) REVERT: C 132 MET cc_start: 0.8910 (ptm) cc_final: 0.8588 (ptm) REVERT: C 283 MET cc_start: 0.8659 (mmt) cc_final: 0.8351 (mmt) REVERT: D 167 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: D 192 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8828 (tp) REVERT: D 283 MET cc_start: 0.8680 (mmm) cc_final: 0.7626 (mmt) REVERT: F 23 LYS cc_start: 0.8620 (tppt) cc_final: 0.8347 (tppt) REVERT: F 34 LYS cc_start: 0.9011 (tttt) cc_final: 0.8790 (tttp) REVERT: F 56 MET cc_start: 0.8746 (tpp) cc_final: 0.8121 (tpp) REVERT: F 71 GLU cc_start: 0.8937 (tt0) cc_final: 0.8428 (tt0) REVERT: F 95 ARG cc_start: 0.8408 (ttm110) cc_final: 0.7976 (ttm110) REVERT: F 98 GLN cc_start: 0.8355 (mt0) cc_final: 0.7893 (pt0) REVERT: F 102 GLN cc_start: 0.9103 (mt0) cc_final: 0.8777 (mt0) REVERT: G 25 ARG cc_start: 0.8360 (tpp80) cc_final: 0.8055 (tpp80) REVERT: G 27 ASP cc_start: 0.8105 (m-30) cc_final: 0.7757 (m-30) REVERT: G 56 MET cc_start: 0.8994 (tpp) cc_final: 0.8622 (tpp) REVERT: G 71 GLU cc_start: 0.8747 (pt0) cc_final: 0.8250 (tt0) REVERT: H 23 LYS cc_start: 0.8310 (mmmt) cc_final: 0.8090 (tppt) REVERT: H 24 SER cc_start: 0.9169 (m) cc_final: 0.8626 (p) REVERT: H 25 ARG cc_start: 0.7497 (tpp80) cc_final: 0.7240 (mmm-85) REVERT: H 31 ASP cc_start: 0.8489 (m-30) cc_final: 0.8091 (m-30) REVERT: H 98 GLN cc_start: 0.8605 (mt0) cc_final: 0.8295 (mt0) outliers start: 99 outliers final: 74 residues processed: 325 average time/residue: 0.2869 time to fit residues: 140.8368 Evaluate side-chains 317 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 237 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 135 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN F 120 HIS G 42 ASN G 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.070610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.055475 restraints weight = 45706.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.056903 restraints weight = 22761.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.057578 restraints weight = 14604.240| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17729 Z= 0.155 Angle : 0.587 7.014 24044 Z= 0.286 Chirality : 0.043 0.214 2691 Planarity : 0.003 0.042 3070 Dihedral : 8.453 88.561 2525 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.45 % Allowed : 15.71 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.18), residues: 2188 helix: 0.22 (0.18), residues: 943 sheet: -1.97 (0.28), residues: 320 loop : -1.33 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.005 0.001 HIS G 133 PHE 0.008 0.001 PHE D 255 TYR 0.007 0.001 TYR C 166 ARG 0.005 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 696) hydrogen bonds : angle 4.74008 ( 1896) covalent geometry : bond 0.00363 (17729) covalent geometry : angle 0.58651 (24044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 239 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9231 (pt) REVERT: A 44 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8113 (mtt) REVERT: A 132 MET cc_start: 0.9138 (tmm) cc_final: 0.8903 (tmm) REVERT: A 213 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9090 (tttt) REVERT: B 47 MET cc_start: 0.8767 (mmm) cc_final: 0.8483 (mmm) REVERT: C 14 SER cc_start: 0.9102 (OUTLIER) cc_final: 0.8775 (p) REVERT: C 132 MET cc_start: 0.8931 (ptm) cc_final: 0.8632 (ptm) REVERT: C 254 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7157 (mtm-85) REVERT: C 283 MET cc_start: 0.8638 (mmt) cc_final: 0.8300 (mmt) REVERT: D 167 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7430 (mm-30) REVERT: D 192 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8857 (tp) REVERT: D 283 MET cc_start: 0.8659 (mmm) cc_final: 0.7616 (mmt) REVERT: F 23 LYS cc_start: 0.8558 (tppt) cc_final: 0.8321 (tppt) REVERT: F 34 LYS cc_start: 0.9009 (tttt) cc_final: 0.8737 (tttp) REVERT: F 56 MET cc_start: 0.8763 (tpp) cc_final: 0.7833 (tpp) REVERT: F 71 GLU cc_start: 0.8948 (tt0) cc_final: 0.8675 (tt0) REVERT: F 95 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8052 (ttm110) REVERT: F 98 GLN cc_start: 0.8360 (mt0) cc_final: 0.7913 (pt0) REVERT: F 102 GLN cc_start: 0.9102 (mt0) cc_final: 0.8768 (mt0) REVERT: G 25 ARG cc_start: 0.8342 (tpp80) cc_final: 0.8054 (tpp80) REVERT: G 27 ASP cc_start: 0.8120 (m-30) cc_final: 0.7785 (m-30) REVERT: G 56 MET cc_start: 0.8987 (tpp) cc_final: 0.8599 (tpp) REVERT: G 62 ASP cc_start: 0.8555 (p0) cc_final: 0.8344 (p0) REVERT: G 68 ASP cc_start: 0.8094 (p0) cc_final: 0.7864 (p0) REVERT: G 71 GLU cc_start: 0.8743 (pt0) cc_final: 0.8209 (tt0) REVERT: G 81 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7450 (mm-30) REVERT: H 23 LYS cc_start: 0.8305 (mmmt) cc_final: 0.8089 (tppt) REVERT: H 24 SER cc_start: 0.9171 (m) cc_final: 0.8627 (p) REVERT: H 25 ARG cc_start: 0.7489 (tpp80) cc_final: 0.7227 (mmm-85) REVERT: H 31 ASP cc_start: 0.8463 (m-30) cc_final: 0.8096 (m-30) outliers start: 102 outliers final: 77 residues processed: 324 average time/residue: 0.3068 time to fit residues: 148.6624 Evaluate side-chains 320 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 236 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 197 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS E 162 ASN F 120 HIS G 42 ASN H 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.072067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.056998 restraints weight = 45329.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.058460 restraints weight = 22139.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.059095 restraints weight = 14258.160| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17729 Z= 0.100 Angle : 0.553 6.763 24044 Z= 0.268 Chirality : 0.042 0.178 2691 Planarity : 0.003 0.050 3070 Dihedral : 8.015 76.675 2524 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.59 % Allowed : 17.04 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2188 helix: 0.36 (0.18), residues: 963 sheet: -1.84 (0.28), residues: 320 loop : -1.22 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.006 0.001 HIS E 161 PHE 0.011 0.001 PHE B 31 TYR 0.007 0.001 TYR A 53 ARG 0.005 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.02865 ( 696) hydrogen bonds : angle 4.57831 ( 1896) covalent geometry : bond 0.00229 (17729) covalent geometry : angle 0.55320 (24044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 246 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9164 (pt) REVERT: A 132 MET cc_start: 0.9159 (tmm) cc_final: 0.8877 (tmm) REVERT: A 213 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9122 (tttt) REVERT: B 47 MET cc_start: 0.8798 (mmm) cc_final: 0.8463 (mmm) REVERT: B 305 MET cc_start: 0.8211 (mtp) cc_final: 0.7973 (mmm) REVERT: C 14 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8943 (p) REVERT: C 132 MET cc_start: 0.8892 (ptm) cc_final: 0.8587 (ptm) REVERT: C 180 LEU cc_start: 0.8925 (tp) cc_final: 0.8685 (tp) REVERT: C 254 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7343 (mtm-85) REVERT: C 283 MET cc_start: 0.8612 (mmt) cc_final: 0.8267 (mmt) REVERT: D 167 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7406 (mm-30) REVERT: D 192 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8840 (tp) REVERT: D 283 MET cc_start: 0.8595 (mmm) cc_final: 0.7426 (mmt) REVERT: F 23 LYS cc_start: 0.8534 (tppt) cc_final: 0.8220 (tppt) REVERT: F 34 LYS cc_start: 0.8995 (tttt) cc_final: 0.8723 (tttp) REVERT: F 40 TRP cc_start: 0.8388 (t60) cc_final: 0.8176 (t60) REVERT: F 56 MET cc_start: 0.8715 (tpp) cc_final: 0.7854 (tpp) REVERT: F 62 ASP cc_start: 0.7656 (p0) cc_final: 0.7343 (p0) REVERT: F 64 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7878 (mtm110) REVERT: F 71 GLU cc_start: 0.8958 (tt0) cc_final: 0.8661 (tt0) REVERT: F 95 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8011 (ttm110) REVERT: F 98 GLN cc_start: 0.8358 (mt0) cc_final: 0.7892 (pt0) REVERT: F 102 GLN cc_start: 0.9083 (mt0) cc_final: 0.8749 (mt0) REVERT: G 25 ARG cc_start: 0.8286 (tpp80) cc_final: 0.8016 (tpt170) REVERT: G 27 ASP cc_start: 0.8133 (m-30) cc_final: 0.7777 (m-30) REVERT: G 56 MET cc_start: 0.8966 (tpp) cc_final: 0.8612 (tpp) REVERT: G 62 ASP cc_start: 0.8552 (p0) cc_final: 0.8330 (p0) REVERT: G 71 GLU cc_start: 0.8730 (pt0) cc_final: 0.8197 (tt0) REVERT: G 92 ASN cc_start: 0.8965 (m-40) cc_final: 0.8559 (m-40) REVERT: H 23 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7980 (tppt) REVERT: H 25 ARG cc_start: 0.7452 (tpp80) cc_final: 0.7072 (mmm-85) REVERT: H 28 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7009 (pp20) REVERT: H 31 ASP cc_start: 0.8456 (m-30) cc_final: 0.8104 (m-30) REVERT: H 98 GLN cc_start: 0.8528 (mt0) cc_final: 0.8295 (mt0) REVERT: H 103 ASN cc_start: 0.8356 (m-40) cc_final: 0.7798 (t0) outliers start: 86 outliers final: 69 residues processed: 317 average time/residue: 0.3454 time to fit residues: 163.1953 Evaluate side-chains 311 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 235 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS G 42 ASN H 92 ASN H 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.070015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.055110 restraints weight = 45419.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.056572 restraints weight = 22801.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.057089 restraints weight = 15525.174| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17729 Z= 0.212 Angle : 0.620 7.319 24044 Z= 0.303 Chirality : 0.045 0.176 2691 Planarity : 0.004 0.045 3070 Dihedral : 7.961 84.361 2513 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.24 % Allowed : 16.83 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2188 helix: 0.35 (0.18), residues: 943 sheet: -1.88 (0.28), residues: 320 loop : -1.16 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.005 0.001 HIS E 161 PHE 0.010 0.001 PHE B 262 TYR 0.008 0.001 TYR C 69 ARG 0.005 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 696) hydrogen bonds : angle 4.75680 ( 1896) covalent geometry : bond 0.00498 (17729) covalent geometry : angle 0.61962 (24044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 234 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9241 (pt) REVERT: A 213 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.9092 (tttt) REVERT: B 47 MET cc_start: 0.8825 (mmm) cc_final: 0.8508 (mmm) REVERT: B 305 MET cc_start: 0.8311 (mtp) cc_final: 0.8089 (mmm) REVERT: C 14 SER cc_start: 0.9134 (OUTLIER) cc_final: 0.8833 (p) REVERT: C 132 MET cc_start: 0.8928 (ptm) cc_final: 0.8633 (ptm) REVERT: C 254 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.7210 (mtm-85) REVERT: C 283 MET cc_start: 0.8656 (mmt) cc_final: 0.8365 (mmt) REVERT: D 167 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: D 192 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8927 (tp) REVERT: D 283 MET cc_start: 0.8648 (mmm) cc_final: 0.7581 (mmt) REVERT: F 56 MET cc_start: 0.8668 (tpp) cc_final: 0.8421 (tpp) REVERT: F 62 ASP cc_start: 0.7717 (p0) cc_final: 0.7121 (p0) REVERT: F 64 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7857 (ttm110) REVERT: F 71 GLU cc_start: 0.8967 (tt0) cc_final: 0.8661 (tt0) REVERT: F 95 ARG cc_start: 0.8419 (ttm110) cc_final: 0.8057 (ttm110) REVERT: F 98 GLN cc_start: 0.8380 (mt0) cc_final: 0.7889 (pt0) REVERT: F 102 GLN cc_start: 0.9105 (mt0) cc_final: 0.8708 (mt0) REVERT: F 103 ASN cc_start: 0.8388 (m-40) cc_final: 0.7635 (t0) REVERT: G 25 ARG cc_start: 0.8232 (tpp80) cc_final: 0.7972 (tpt170) REVERT: G 56 MET cc_start: 0.9018 (tpp) cc_final: 0.8557 (tpp) REVERT: G 62 ASP cc_start: 0.8483 (p0) cc_final: 0.8182 (p0) REVERT: G 71 GLU cc_start: 0.8749 (pt0) cc_final: 0.8211 (tt0) REVERT: G 81 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6994 (mm-30) REVERT: G 92 ASN cc_start: 0.8917 (m-40) cc_final: 0.8659 (m-40) REVERT: H 23 LYS cc_start: 0.8312 (mmmt) cc_final: 0.8042 (tppt) REVERT: H 25 ARG cc_start: 0.7530 (tpp80) cc_final: 0.7176 (mmm-85) REVERT: H 28 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7089 (pp20) REVERT: H 31 ASP cc_start: 0.8457 (m-30) cc_final: 0.8103 (m-30) REVERT: H 103 ASN cc_start: 0.8372 (m-40) cc_final: 0.7918 (t0) outliers start: 98 outliers final: 78 residues processed: 315 average time/residue: 0.3117 time to fit residues: 148.0919 Evaluate side-chains 317 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 232 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 135 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 206 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN G 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.072114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.057199 restraints weight = 45006.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.058684 restraints weight = 21724.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.059368 restraints weight = 14050.055| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17729 Z= 0.102 Angle : 0.560 7.820 24044 Z= 0.273 Chirality : 0.042 0.166 2691 Planarity : 0.003 0.049 3070 Dihedral : 7.491 72.933 2511 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.27 % Allowed : 17.68 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 2188 helix: 0.50 (0.18), residues: 945 sheet: -1.70 (0.28), residues: 320 loop : -1.02 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 356 HIS 0.005 0.001 HIS E 161 PHE 0.008 0.001 PHE B 31 TYR 0.007 0.001 TYR B 53 ARG 0.006 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.02871 ( 696) hydrogen bonds : angle 4.56317 ( 1896) covalent geometry : bond 0.00235 (17729) covalent geometry : angle 0.56036 (24044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 236 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9163 (pt) REVERT: A 213 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9112 (tttt) REVERT: B 47 MET cc_start: 0.8803 (mmm) cc_final: 0.8490 (mmm) REVERT: C 14 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8946 (p) REVERT: C 132 MET cc_start: 0.8879 (ptm) cc_final: 0.8604 (ptm) REVERT: C 180 LEU cc_start: 0.8914 (tp) cc_final: 0.8712 (tp) REVERT: C 254 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7281 (mtm-85) REVERT: C 283 MET cc_start: 0.8614 (mmt) cc_final: 0.8273 (mmt) REVERT: D 167 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7382 (mm-30) REVERT: D 192 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8833 (tp) REVERT: D 283 MET cc_start: 0.8632 (mmm) cc_final: 0.7654 (mmt) REVERT: F 40 TRP cc_start: 0.8443 (t60) cc_final: 0.8215 (t60) REVERT: F 62 ASP cc_start: 0.7720 (p0) cc_final: 0.7349 (p0) REVERT: F 70 LEU cc_start: 0.9297 (tp) cc_final: 0.8904 (tp) REVERT: F 71 GLU cc_start: 0.8954 (tt0) cc_final: 0.8629 (tt0) REVERT: F 95 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8205 (ttm110) REVERT: F 98 GLN cc_start: 0.8380 (mt0) cc_final: 0.7895 (pt0) REVERT: F 102 GLN cc_start: 0.9074 (mt0) cc_final: 0.8752 (mt0) REVERT: G 25 ARG cc_start: 0.8158 (tpp80) cc_final: 0.7896 (tpp80) REVERT: G 27 ASP cc_start: 0.8277 (m-30) cc_final: 0.7980 (m-30) REVERT: G 56 MET cc_start: 0.9023 (tpp) cc_final: 0.8743 (tpp) REVERT: G 62 ASP cc_start: 0.8470 (p0) cc_final: 0.8177 (p0) REVERT: G 71 GLU cc_start: 0.8730 (pt0) cc_final: 0.8152 (tt0) REVERT: G 81 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7142 (mm-30) REVERT: G 92 ASN cc_start: 0.8884 (m-40) cc_final: 0.8600 (m-40) REVERT: H 23 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7997 (tppt) REVERT: H 25 ARG cc_start: 0.7446 (tpp80) cc_final: 0.7197 (mmm-85) REVERT: H 28 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: H 31 ASP cc_start: 0.8429 (m-30) cc_final: 0.8040 (m-30) REVERT: H 103 ASN cc_start: 0.8338 (m-40) cc_final: 0.7919 (t0) REVERT: H 126 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7387 (pt) outliers start: 80 outliers final: 59 residues processed: 304 average time/residue: 0.3066 time to fit residues: 140.6528 Evaluate side-chains 297 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 230 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 177 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 210 optimal weight: 30.0000 chunk 204 optimal weight: 0.0270 chunk 128 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN G 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.071378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.056327 restraints weight = 45393.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.057780 restraints weight = 22149.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.058449 restraints weight = 14381.815| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17729 Z= 0.145 Angle : 0.581 8.551 24044 Z= 0.283 Chirality : 0.043 0.165 2691 Planarity : 0.003 0.051 3070 Dihedral : 7.217 72.533 2498 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.11 % Allowed : 18.32 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 2188 helix: 0.51 (0.18), residues: 945 sheet: -1.67 (0.28), residues: 320 loop : -0.95 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 40 HIS 0.008 0.001 HIS A 161 PHE 0.008 0.001 PHE D 255 TYR 0.010 0.001 TYR E 166 ARG 0.006 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 696) hydrogen bonds : angle 4.60750 ( 1896) covalent geometry : bond 0.00345 (17729) covalent geometry : angle 0.58056 (24044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 235 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9180 (pt) REVERT: A 132 MET cc_start: 0.8743 (tmm) cc_final: 0.8428 (tmm) REVERT: A 213 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9077 (tttt) REVERT: B 47 MET cc_start: 0.8797 (mmm) cc_final: 0.8482 (mmm) REVERT: C 14 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8931 (p) REVERT: C 132 MET cc_start: 0.8932 (ptm) cc_final: 0.8598 (ptm) REVERT: C 180 LEU cc_start: 0.8985 (tp) cc_final: 0.8774 (tp) REVERT: C 254 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7310 (mtm-85) REVERT: C 283 MET cc_start: 0.8626 (mmt) cc_final: 0.8334 (mmt) REVERT: D 167 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: D 192 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8852 (tp) REVERT: D 283 MET cc_start: 0.8638 (mmm) cc_final: 0.7597 (mmt) REVERT: F 70 LEU cc_start: 0.9298 (tp) cc_final: 0.8908 (tp) REVERT: F 71 GLU cc_start: 0.8956 (tt0) cc_final: 0.8627 (tt0) REVERT: F 95 ARG cc_start: 0.8439 (ttm110) cc_final: 0.8141 (ttm110) REVERT: F 98 GLN cc_start: 0.8394 (mt0) cc_final: 0.7853 (pt0) REVERT: F 102 GLN cc_start: 0.9064 (mt0) cc_final: 0.8682 (mt0) REVERT: F 103 ASN cc_start: 0.8464 (m-40) cc_final: 0.7735 (t0) REVERT: F 134 TRP cc_start: 0.8176 (m-90) cc_final: 0.7937 (m-90) REVERT: G 25 ARG cc_start: 0.8087 (tpp80) cc_final: 0.7798 (tpp80) REVERT: G 56 MET cc_start: 0.9055 (tpp) cc_final: 0.8622 (tpp) REVERT: G 62 ASP cc_start: 0.8447 (p0) cc_final: 0.8165 (p0) REVERT: G 71 GLU cc_start: 0.8731 (pt0) cc_final: 0.8156 (tt0) REVERT: G 81 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7141 (mm-30) REVERT: G 91 ASN cc_start: 0.8762 (m-40) cc_final: 0.8494 (m-40) REVERT: G 92 ASN cc_start: 0.8957 (m-40) cc_final: 0.8708 (m-40) REVERT: H 23 LYS cc_start: 0.8310 (mmmt) cc_final: 0.8043 (tppt) REVERT: H 31 ASP cc_start: 0.8439 (m-30) cc_final: 0.8048 (m-30) REVERT: H 103 ASN cc_start: 0.8343 (m-40) cc_final: 0.7923 (t0) REVERT: H 126 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7437 (pt) outliers start: 77 outliers final: 65 residues processed: 300 average time/residue: 0.4056 time to fit residues: 180.9015 Evaluate side-chains 302 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 230 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 134 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 208 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN B 59 GLN F 109 ASN G 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.071801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.057148 restraints weight = 44968.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.058454 restraints weight = 22722.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.059081 restraints weight = 15222.707| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17729 Z= 0.125 Angle : 0.581 12.983 24044 Z= 0.283 Chirality : 0.043 0.161 2691 Planarity : 0.003 0.053 3070 Dihedral : 7.036 68.681 2495 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.11 % Allowed : 18.32 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 2188 helix: 0.54 (0.18), residues: 948 sheet: -1.63 (0.29), residues: 320 loop : -0.93 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 40 HIS 0.007 0.001 HIS A 161 PHE 0.009 0.001 PHE B 31 TYR 0.014 0.001 TYR B 53 ARG 0.007 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 696) hydrogen bonds : angle 4.57658 ( 1896) covalent geometry : bond 0.00295 (17729) covalent geometry : angle 0.58086 (24044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 233 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9155 (pt) REVERT: A 132 MET cc_start: 0.8757 (tmm) cc_final: 0.8451 (tmm) REVERT: A 213 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9108 (tttt) REVERT: B 47 MET cc_start: 0.8666 (mmm) cc_final: 0.8397 (mmm) REVERT: C 14 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8937 (p) REVERT: C 132 MET cc_start: 0.8875 (ptm) cc_final: 0.8588 (ptm) REVERT: C 180 LEU cc_start: 0.8954 (tp) cc_final: 0.8735 (tp) REVERT: C 254 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.7297 (mtm-85) REVERT: C 283 MET cc_start: 0.8625 (mmt) cc_final: 0.8290 (mmt) REVERT: D 107 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: D 192 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8838 (tp) REVERT: D 283 MET cc_start: 0.8590 (mmm) cc_final: 0.7576 (mmt) REVERT: F 70 LEU cc_start: 0.9313 (tp) cc_final: 0.8893 (tp) REVERT: F 71 GLU cc_start: 0.8953 (tt0) cc_final: 0.8626 (tt0) REVERT: F 95 ARG cc_start: 0.8437 (ttm110) cc_final: 0.8148 (ttm110) REVERT: F 98 GLN cc_start: 0.8395 (mt0) cc_final: 0.7849 (pt0) REVERT: F 102 GLN cc_start: 0.9066 (mt0) cc_final: 0.8688 (mt0) REVERT: F 103 ASN cc_start: 0.8471 (m-40) cc_final: 0.7686 (t0) REVERT: G 25 ARG cc_start: 0.8084 (tpp80) cc_final: 0.7834 (tpp80) REVERT: G 56 MET cc_start: 0.9056 (tpp) cc_final: 0.8636 (tpp) REVERT: G 62 ASP cc_start: 0.8434 (p0) cc_final: 0.8158 (p0) REVERT: G 71 GLU cc_start: 0.8722 (pt0) cc_final: 0.8160 (tt0) REVERT: G 81 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7192 (mm-30) REVERT: G 91 ASN cc_start: 0.8731 (m-40) cc_final: 0.8485 (m-40) REVERT: G 92 ASN cc_start: 0.8929 (m-40) cc_final: 0.8680 (m-40) REVERT: G 95 ARG cc_start: 0.8698 (tpp80) cc_final: 0.8246 (ttm110) REVERT: H 23 LYS cc_start: 0.8310 (mmmt) cc_final: 0.8026 (tppt) REVERT: H 31 ASP cc_start: 0.8430 (m-30) cc_final: 0.8014 (m-30) REVERT: H 92 ASN cc_start: 0.8596 (m-40) cc_final: 0.8350 (m110) REVERT: H 103 ASN cc_start: 0.8271 (m-40) cc_final: 0.7985 (t0) REVERT: H 126 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7501 (pt) outliers start: 77 outliers final: 59 residues processed: 297 average time/residue: 0.3166 time to fit residues: 140.6050 Evaluate side-chains 297 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 231 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 31 optimal weight: 4.9990 chunk 201 optimal weight: 20.0000 chunk 76 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 205 optimal weight: 0.0370 chunk 199 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 29 HIS G 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.073634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.058735 restraints weight = 44383.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.060275 restraints weight = 21479.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.060950 restraints weight = 13607.097| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17729 Z= 0.089 Angle : 0.553 12.258 24044 Z= 0.268 Chirality : 0.042 0.160 2691 Planarity : 0.003 0.047 3070 Dihedral : 6.489 58.814 2489 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.10 % Allowed : 19.02 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 2188 helix: 0.76 (0.18), residues: 923 sheet: -1.48 (0.29), residues: 320 loop : -0.70 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 40 HIS 0.005 0.001 HIS E 161 PHE 0.010 0.001 PHE B 31 TYR 0.012 0.001 TYR B 53 ARG 0.009 0.000 ARG F 64 Details of bonding type rmsd hydrogen bonds : bond 0.02707 ( 696) hydrogen bonds : angle 4.44831 ( 1896) covalent geometry : bond 0.00199 (17729) covalent geometry : angle 0.55312 (24044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5178.34 seconds wall clock time: 92 minutes 38.35 seconds (5558.35 seconds total)