Starting phenix.real_space_refine on Wed Mar 4 23:56:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m5g_30085/03_2026/6m5g_30085.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m5g_30085/03_2026/6m5g_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 { model { file = "/net/cci-nas-00/data/ceres_data/6m5g_30085/03_2026/6m5g_30085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m5g_30085/03_2026/6m5g_30085.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m5g_30085/03_2026/6m5g_30085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m5g_30085/03_2026/6m5g_30085.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.98, per 1000 atoms: 0.23 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: 1.53 Conformation dependent library (CDL) restraints added in 734.2 milliseconds 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: 0.61 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: 2.86 Time building geometry restraints manager: 2.01 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 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 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 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 \ 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 \ 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: 1.150 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.800 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- 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 : 11.76 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.005 0.001 ARG B 254 TYR 0.012 0.002 TYR C 69 PHE 0.017 0.002 PHE B 262 TRP 0.020 0.002 TRP B 340 HIS 0.006 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.01038 (17729) covalent geometry : angle 0.82039 (24044) hydrogen bonds : bond 0.17912 ( 696) hydrogen bonds : angle 7.11317 ( 1896) *********************** 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 : 0.593 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: 0.1296 time to fit residues: 79.1495 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 : 0.714 ------------------------------------------------------------------------------- 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 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 C 111 ASN C 161 HIS C 162 ASN C 275 HIS D 40 HIS D 59 GLN D 88 HIS D 161 HIS D 296 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.070532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.055500 restraints weight = 45489.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.057384 restraints weight = 21617.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.057905 restraints weight = 13164.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.058115 restraints weight = 10357.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.058212 restraints weight = 10508.528| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17729 Z= 0.118 Angle : 0.627 8.668 24044 Z= 0.310 Chirality : 0.043 0.186 2691 Planarity : 0.004 0.061 3070 Dihedral : 10.645 105.270 2679 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 6.04 % Allowed : 13.35 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.17), residues: 2188 helix: -0.70 (0.16), residues: 973 sheet: -2.04 (0.31), residues: 260 loop : -2.12 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 95 TYR 0.008 0.001 TYR B 53 PHE 0.012 0.001 PHE E 352 TRP 0.014 0.001 TRP B 340 HIS 0.005 0.001 HIS G 133 Details of bonding type rmsd covalent geometry : bond 0.00262 (17729) covalent geometry : angle 0.62703 (24044) hydrogen bonds : bond 0.03795 ( 696) hydrogen bonds : angle 5.10422 ( 1896) *********************** 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 365 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 252 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9232 (pt) REVERT: A 44 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7921 (mtt) REVERT: A 162 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8102 (m-40) REVERT: A 213 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9053 (tttt) REVERT: B 305 MET cc_start: 0.8542 (mtp) cc_final: 0.8283 (mtp) REVERT: B 335 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8250 (ptt-90) REVERT: C 50 LYS cc_start: 0.7977 (tptt) cc_final: 0.7677 (tptp) REVERT: C 254 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7273 (mtm-85) REVERT: C 283 MET cc_start: 0.8690 (mmt) cc_final: 0.8403 (mmt) REVERT: D 192 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8828 (tp) REVERT: D 283 MET cc_start: 0.8786 (mmm) cc_final: 0.8437 (mmt) REVERT: D 355 MET cc_start: 0.8323 (mtt) cc_final: 0.8057 (mtm) REVERT: E 328 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7617 (ttpp) REVERT: F 23 LYS cc_start: 0.8244 (tppt) cc_final: 0.8030 (tppt) REVERT: F 34 LYS cc_start: 0.8940 (tttt) cc_final: 0.8736 (tttp) REVERT: F 56 MET cc_start: 0.8572 (tpp) cc_final: 0.8351 (tpp) REVERT: F 95 ARG cc_start: 0.8863 (tpp80) cc_final: 0.8298 (ttm110) REVERT: F 98 GLN cc_start: 0.8322 (mt0) cc_final: 0.7966 (pt0) REVERT: F 102 GLN cc_start: 0.9092 (mt0) cc_final: 0.8873 (mt0) REVERT: G 25 ARG cc_start: 0.8477 (tpp80) cc_final: 0.8148 (tpt170) REVERT: G 27 ASP cc_start: 0.7938 (m-30) cc_final: 0.7618 (m-30) REVERT: G 56 MET cc_start: 0.8986 (tpp) cc_final: 0.8728 (tpp) REVERT: G 71 GLU cc_start: 0.8766 (pt0) cc_final: 0.8315 (tt0) REVERT: G 81 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7530 (mm-30) REVERT: G 92 ASN cc_start: 0.8974 (m-40) cc_final: 0.8675 (m-40) REVERT: H 23 LYS cc_start: 0.8291 (mmmt) cc_final: 0.8034 (tppt) REVERT: H 24 SER cc_start: 0.9176 (m) cc_final: 0.8613 (p) REVERT: H 25 ARG cc_start: 0.7489 (tpp80) cc_final: 0.7017 (mmm-85) REVERT: H 31 ASP cc_start: 0.8529 (m-30) cc_final: 0.8121 (m-30) outliers start: 113 outliers final: 66 residues processed: 353 average time/residue: 0.1378 time to fit residues: 72.8960 Evaluate side-chains 309 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 235 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 59 GLN 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 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 122 ILE 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 29 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 157 optimal weight: 0.0670 chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 107 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.071502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.056445 restraints weight = 45507.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.058343 restraints weight = 21451.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.058864 restraints weight = 13174.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.058888 restraints weight = 10381.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.058998 restraints weight = 10750.306| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17729 Z= 0.104 Angle : 0.581 6.918 24044 Z= 0.285 Chirality : 0.043 0.303 2691 Planarity : 0.003 0.042 3070 Dihedral : 9.109 92.118 2559 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.70 % Allowed : 14.96 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.18), residues: 2188 helix: -0.19 (0.17), residues: 968 sheet: -2.12 (0.28), residues: 320 loop : -1.70 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 64 TYR 0.007 0.001 TYR C 166 PHE 0.017 0.001 PHE G 37 TRP 0.010 0.001 TRP B 340 HIS 0.006 0.001 HIS G 133 Details of bonding type rmsd covalent geometry : bond 0.00235 (17729) covalent geometry : angle 0.58143 (24044) hydrogen bonds : bond 0.03294 ( 696) hydrogen bonds : angle 4.84151 ( 1896) *********************** 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 339 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 251 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9207 (pt) REVERT: A 44 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8022 (mtt) REVERT: A 213 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9108 (tttt) REVERT: C 50 LYS cc_start: 0.7935 (tptt) cc_final: 0.7639 (tptp) REVERT: C 254 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.7195 (mtm-85) REVERT: C 283 MET cc_start: 0.8697 (mmt) cc_final: 0.8386 (mmt) REVERT: D 167 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: D 192 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8780 (tp) REVERT: D 283 MET cc_start: 0.8703 (mmm) cc_final: 0.7681 (mmt) REVERT: F 34 LYS cc_start: 0.8996 (tttt) cc_final: 0.8776 (tttp) REVERT: F 56 MET cc_start: 0.8743 (tpp) cc_final: 0.8506 (tpp) REVERT: F 62 ASP cc_start: 0.7976 (p0) cc_final: 0.7726 (p0) REVERT: F 98 GLN cc_start: 0.8312 (mt0) cc_final: 0.7925 (pt0) REVERT: F 102 GLN cc_start: 0.9057 (mt0) cc_final: 0.8760 (mt0) REVERT: G 25 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8129 (tpp80) REVERT: G 27 ASP cc_start: 0.7985 (m-30) cc_final: 0.7616 (m-30) REVERT: G 56 MET cc_start: 0.8983 (tpp) cc_final: 0.8598 (tpp) REVERT: G 71 GLU cc_start: 0.8745 (pt0) cc_final: 0.8275 (tt0) REVERT: G 81 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7516 (mm-30) REVERT: G 92 ASN cc_start: 0.9066 (m-40) cc_final: 0.8764 (m-40) REVERT: H 23 LYS cc_start: 0.8304 (mmmt) cc_final: 0.8057 (tppt) REVERT: H 24 SER cc_start: 0.9149 (m) cc_final: 0.8650 (p) REVERT: H 25 ARG cc_start: 0.7463 (tpp80) cc_final: 0.7218 (mmm-85) REVERT: H 31 ASP cc_start: 0.8481 (m-30) cc_final: 0.8088 (m-30) REVERT: H 71 GLU cc_start: 0.8458 (tt0) cc_final: 0.8248 (tt0) outliers start: 88 outliers final: 61 residues processed: 329 average time/residue: 0.1309 time to fit residues: 64.5143 Evaluate side-chains 306 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 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 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 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 10 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 123 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 201 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN 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 = 0.3021 r_free = 0.3021 target = 0.072501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.057615 restraints weight = 45216.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.059251 restraints weight = 21507.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.059856 restraints weight = 13776.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.059924 restraints weight = 10780.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.060069 restraints weight = 11173.811| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2192 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= 0.093 Angle : 0.555 6.809 24044 Z= 0.270 Chirality : 0.042 0.290 2691 Planarity : 0.003 0.040 3070 Dihedral : 8.201 78.502 2528 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.49 % Allowed : 15.87 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.18), residues: 2188 helix: 0.29 (0.18), residues: 938 sheet: -1.92 (0.28), residues: 320 loop : -1.33 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 64 TYR 0.007 0.001 TYR B 53 PHE 0.013 0.001 PHE G 37 TRP 0.009 0.001 TRP C 356 HIS 0.007 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00206 (17729) covalent geometry : angle 0.55531 (24044) hydrogen bonds : bond 0.02860 ( 696) hydrogen bonds : angle 4.63524 ( 1896) *********************** 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 336 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 252 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9158 (pt) REVERT: A 44 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8152 (mtt) REVERT: A 132 MET cc_start: 0.9194 (tmm) cc_final: 0.8950 (tmm) REVERT: A 213 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9136 (tttt) REVERT: A 313 MET cc_start: 0.8108 (tpp) cc_final: 0.7872 (ttt) REVERT: C 14 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8864 (p) REVERT: C 50 LYS cc_start: 0.7919 (tptt) cc_final: 0.7690 (tptp) REVERT: C 132 MET cc_start: 0.8831 (ptm) cc_final: 0.8483 (ptm) REVERT: C 254 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7183 (mtm-85) REVERT: C 283 MET cc_start: 0.8635 (mmt) cc_final: 0.8314 (mmt) REVERT: D 107 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: D 167 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: D 283 MET cc_start: 0.8604 (mmm) cc_final: 0.7616 (mmt) REVERT: F 23 LYS cc_start: 0.8601 (tppt) cc_final: 0.8331 (tppt) REVERT: F 34 LYS cc_start: 0.9002 (tttt) cc_final: 0.8719 (tttp) REVERT: F 56 MET cc_start: 0.8675 (tpp) cc_final: 0.7743 (tpp) REVERT: F 71 GLU cc_start: 0.8804 (tt0) cc_final: 0.8366 (tt0) REVERT: F 95 ARG cc_start: 0.8375 (ttm110) cc_final: 0.7969 (ttm110) REVERT: F 98 GLN cc_start: 0.8268 (mt0) cc_final: 0.7856 (pt0) REVERT: F 102 GLN cc_start: 0.9108 (mt0) cc_final: 0.8769 (mt0) REVERT: G 25 ARG cc_start: 0.8247 (tpp80) cc_final: 0.8001 (tpp80) REVERT: G 27 ASP cc_start: 0.8105 (m-30) cc_final: 0.7770 (m-30) REVERT: G 56 MET cc_start: 0.8984 (tpp) cc_final: 0.8604 (tpp) REVERT: G 71 GLU cc_start: 0.8735 (pt0) cc_final: 0.8151 (tt0) REVERT: H 23 LYS cc_start: 0.8280 (mmmt) cc_final: 0.8017 (tppt) REVERT: H 24 SER cc_start: 0.9135 (m) cc_final: 0.8583 (p) REVERT: H 25 ARG cc_start: 0.7395 (tpp80) cc_final: 0.7074 (mmm-85) REVERT: H 28 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7057 (pp20) REVERT: H 31 ASP cc_start: 0.8485 (m-30) cc_final: 0.8112 (m-30) REVERT: H 121 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7524 (tttp) outliers start: 84 outliers final: 55 residues processed: 324 average time/residue: 0.1358 time to fit residues: 66.0827 Evaluate side-chains 303 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 240 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 44 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 253 GLU 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 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 190 MET 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 134 VAL 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 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 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 70 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 143 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 217 optimal weight: 8.9990 chunk 157 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 HIS C 162 ASN G 42 ASN H 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.070981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.056241 restraints weight = 45290.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.057551 restraints weight = 22542.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.058123 restraints weight = 15695.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.058241 restraints weight = 12080.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.058323 restraints weight = 12296.883| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2121 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= 0.154 Angle : 0.579 6.821 24044 Z= 0.282 Chirality : 0.044 0.261 2691 Planarity : 0.003 0.040 3070 Dihedral : 7.864 80.821 2512 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.97 % Allowed : 16.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.18), residues: 2188 helix: 0.29 (0.18), residues: 943 sheet: -1.89 (0.28), residues: 320 loop : -1.24 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 64 TYR 0.006 0.001 TYR C 69 PHE 0.008 0.001 PHE D 255 TRP 0.010 0.001 TRP H 40 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00360 (17729) covalent geometry : angle 0.57903 (24044) hydrogen bonds : bond 0.03140 ( 696) hydrogen bonds : angle 4.66468 ( 1896) *********************** 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 336 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 243 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9197 (pt) REVERT: A 213 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9105 (tttt) REVERT: C 14 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8839 (p) REVERT: C 50 LYS cc_start: 0.7936 (tptt) cc_final: 0.7704 (tptp) REVERT: C 132 MET cc_start: 0.8906 (ptm) cc_final: 0.8574 (ptm) REVERT: C 283 MET cc_start: 0.8664 (mmt) cc_final: 0.8342 (mmt) REVERT: D 167 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7445 (mm-30) REVERT: D 283 MET cc_start: 0.8647 (mmm) cc_final: 0.7563 (mmt) REVERT: F 23 LYS cc_start: 0.8545 (tppt) cc_final: 0.8314 (tppt) REVERT: F 34 LYS cc_start: 0.9006 (tttt) cc_final: 0.8733 (tttp) REVERT: F 56 MET cc_start: 0.8760 (tpp) cc_final: 0.7818 (tpp) REVERT: F 71 GLU cc_start: 0.8961 (tt0) cc_final: 0.8525 (tt0) REVERT: F 95 ARG cc_start: 0.8393 (ttm110) cc_final: 0.8142 (ttm110) REVERT: F 98 GLN cc_start: 0.8365 (mt0) cc_final: 0.7904 (pt0) REVERT: F 102 GLN cc_start: 0.9096 (mt0) cc_final: 0.8763 (mt0) REVERT: G 25 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7984 (tpp80) REVERT: G 27 ASP cc_start: 0.8152 (m-30) cc_final: 0.7785 (m-30) REVERT: G 56 MET cc_start: 0.9012 (tpp) cc_final: 0.8620 (tpp) REVERT: G 71 GLU cc_start: 0.8743 (pt0) cc_final: 0.8215 (tt0) REVERT: G 81 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7512 (mm-30) REVERT: H 23 LYS cc_start: 0.8275 (mmmt) cc_final: 0.8038 (tppt) REVERT: H 24 SER cc_start: 0.9151 (m) cc_final: 0.8610 (p) REVERT: H 25 ARG cc_start: 0.7462 (tpp80) cc_final: 0.7093 (mmm-85) REVERT: H 28 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7048 (pp20) REVERT: H 31 ASP cc_start: 0.8456 (m-30) cc_final: 0.8135 (m-30) REVERT: H 98 GLN cc_start: 0.8439 (mt0) cc_final: 0.8208 (mt0) REVERT: H 103 ASN cc_start: 0.8352 (m-40) cc_final: 0.7776 (t0) outliers start: 93 outliers final: 67 residues processed: 319 average time/residue: 0.1233 time to fit residues: 60.2167 Evaluate side-chains 311 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 239 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 297 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 351 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 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 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 134 VAL 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 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 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 70 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 65 optimal weight: 0.0270 chunk 163 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 143 optimal weight: 0.0980 chunk 141 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS C 12 ASN G 42 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 = 0.3009 r_free = 0.3009 target = 0.071888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.056864 restraints weight = 44825.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.058350 restraints weight = 21719.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.058951 restraints weight = 13819.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.060221 restraints weight = 10896.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.059934 restraints weight = 10393.896| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17729 Z= 0.113 Angle : 0.558 6.642 24044 Z= 0.271 Chirality : 0.042 0.231 2691 Planarity : 0.003 0.051 3070 Dihedral : 7.519 74.546 2508 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.38 % Allowed : 16.88 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.18), residues: 2188 helix: 0.40 (0.18), residues: 948 sheet: -1.83 (0.28), residues: 320 loop : -1.16 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 95 TYR 0.008 0.001 TYR B 53 PHE 0.007 0.001 PHE D 255 TRP 0.009 0.001 TRP B 340 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00260 (17729) covalent geometry : angle 0.55830 (24044) hydrogen bonds : bond 0.02908 ( 696) hydrogen bonds : angle 4.56647 ( 1896) *********************** 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 325 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 243 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9120 (pt) REVERT: A 213 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9087 (tttt) REVERT: B 47 MET cc_start: 0.8764 (mmm) cc_final: 0.8493 (mmm) REVERT: C 14 SER cc_start: 0.9184 (OUTLIER) cc_final: 0.8883 (p) REVERT: C 50 LYS cc_start: 0.7939 (tptt) cc_final: 0.7695 (tptp) REVERT: C 132 MET cc_start: 0.8906 (ptm) cc_final: 0.8566 (ptm) REVERT: C 254 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.7165 (mtm-85) REVERT: C 283 MET cc_start: 0.8630 (mmt) cc_final: 0.8323 (mmt) REVERT: C 299 MET cc_start: 0.8478 (mtm) cc_final: 0.8277 (mtm) REVERT: D 167 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: D 283 MET cc_start: 0.8601 (mmm) cc_final: 0.7561 (mmt) REVERT: F 23 LYS cc_start: 0.8492 (tppt) cc_final: 0.8200 (tppt) REVERT: F 34 LYS cc_start: 0.9025 (tttt) cc_final: 0.8809 (tttp) REVERT: F 56 MET cc_start: 0.8678 (tpp) cc_final: 0.8186 (tpp) REVERT: F 70 LEU cc_start: 0.9315 (tp) cc_final: 0.8972 (tt) REVERT: F 71 GLU cc_start: 0.8956 (tt0) cc_final: 0.8660 (tt0) REVERT: F 95 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7939 (ttm110) REVERT: F 98 GLN cc_start: 0.8304 (mt0) cc_final: 0.7883 (pt0) REVERT: F 102 GLN cc_start: 0.9085 (mt0) cc_final: 0.8762 (mt0) REVERT: G 25 ARG cc_start: 0.8170 (tpp80) cc_final: 0.7901 (tpt170) REVERT: G 27 ASP cc_start: 0.8153 (m-30) cc_final: 0.7816 (m-30) REVERT: G 56 MET cc_start: 0.9044 (tpp) cc_final: 0.8659 (tpp) REVERT: G 71 GLU cc_start: 0.8754 (pt0) cc_final: 0.8154 (tt0) REVERT: H 23 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7927 (tppt) REVERT: H 24 SER cc_start: 0.9148 (m) cc_final: 0.8470 (p) REVERT: H 25 ARG cc_start: 0.7249 (tpp80) cc_final: 0.6926 (mmm-85) REVERT: H 28 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6926 (pp20) REVERT: H 31 ASP cc_start: 0.8431 (m-30) cc_final: 0.8082 (m-30) REVERT: H 98 GLN cc_start: 0.8554 (mt0) cc_final: 0.8312 (mt0) REVERT: H 103 ASN cc_start: 0.8389 (m-40) cc_final: 0.7869 (t0) outliers start: 82 outliers final: 63 residues processed: 314 average time/residue: 0.1323 time to fit residues: 62.5126 Evaluate side-chains 304 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 235 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 297 ASN Chi-restraints excluded: chain A residue 305 MET 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 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 134 VAL 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 114 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 0.1980 chunk 95 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 ASN G 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.073122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.058049 restraints weight = 44664.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.059574 restraints weight = 21613.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.060109 restraints weight = 13943.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.060727 restraints weight = 10979.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.060740 restraints weight = 10897.559| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17729 Z= 0.090 Angle : 0.548 8.906 24044 Z= 0.265 Chirality : 0.042 0.200 2691 Planarity : 0.003 0.046 3070 Dihedral : 6.987 63.639 2502 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.85 % Allowed : 17.47 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 2188 helix: 0.64 (0.18), residues: 923 sheet: -1.66 (0.28), residues: 320 loop : -0.92 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 95 TYR 0.015 0.001 TYR B 53 PHE 0.007 0.001 PHE B 31 TRP 0.009 0.001 TRP A 356 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00201 (17729) covalent geometry : angle 0.54819 (24044) hydrogen bonds : bond 0.02683 ( 696) hydrogen bonds : angle 4.46211 ( 1896) *********************** 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 319 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 247 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9099 (pt) REVERT: A 132 MET cc_start: 0.9007 (tmm) cc_final: 0.8673 (tmm) REVERT: B 47 MET cc_start: 0.8744 (mmm) cc_final: 0.8411 (mmm) REVERT: B 305 MET cc_start: 0.8128 (mtp) cc_final: 0.7914 (mmm) REVERT: C 14 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.8974 (p) REVERT: C 132 MET cc_start: 0.8837 (ptm) cc_final: 0.8510 (ptm) REVERT: C 180 LEU cc_start: 0.8867 (tp) cc_final: 0.8654 (tp) REVERT: C 254 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7279 (mtm-85) REVERT: C 283 MET cc_start: 0.8601 (mmt) cc_final: 0.8283 (mmt) REVERT: D 167 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: D 283 MET cc_start: 0.8602 (mmm) cc_final: 0.7657 (mmt) REVERT: F 56 MET cc_start: 0.8648 (tpp) cc_final: 0.8138 (tpp) REVERT: F 70 LEU cc_start: 0.9304 (tp) cc_final: 0.8833 (tp) REVERT: F 71 GLU cc_start: 0.8976 (tt0) cc_final: 0.8648 (tt0) REVERT: F 95 ARG cc_start: 0.8279 (ttm110) cc_final: 0.7925 (ttm110) REVERT: F 98 GLN cc_start: 0.8286 (mt0) cc_final: 0.7828 (pt0) REVERT: F 102 GLN cc_start: 0.9104 (mt0) cc_final: 0.8675 (mt0) REVERT: F 114 ASP cc_start: 0.8473 (m-30) cc_final: 0.8237 (m-30) REVERT: G 25 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7825 (tpp80) REVERT: G 71 GLU cc_start: 0.8751 (pt0) cc_final: 0.8148 (tt0) REVERT: G 81 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6632 (mm-30) REVERT: H 23 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7985 (tppt) REVERT: H 24 SER cc_start: 0.9129 (m) cc_final: 0.8665 (p) REVERT: H 25 ARG cc_start: 0.7343 (tpp80) cc_final: 0.6992 (mmm-85) REVERT: H 28 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: H 31 ASP cc_start: 0.8421 (m-30) cc_final: 0.8048 (m-30) REVERT: H 98 GLN cc_start: 0.8480 (mt0) cc_final: 0.8243 (mt0) REVERT: H 103 ASN cc_start: 0.8333 (m-40) cc_final: 0.7923 (t0) REVERT: H 126 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7147 (pt) outliers start: 72 outliers final: 52 residues processed: 307 average time/residue: 0.1363 time to fit residues: 62.2447 Evaluate side-chains 294 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 236 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 190 MET 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 344 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL 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 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 16 LEU 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 54 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 216 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.057878 restraints weight = 44661.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.059737 restraints weight = 20726.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.060207 restraints weight = 12962.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.060586 restraints weight = 10376.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.060652 restraints weight = 10753.328| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 17729 Z= 0.102 Angle : 0.553 12.643 24044 Z= 0.266 Chirality : 0.042 0.195 2691 Planarity : 0.003 0.048 3070 Dihedral : 6.689 59.715 2489 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.69 % Allowed : 17.68 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 2188 helix: 0.71 (0.18), residues: 920 sheet: -1.57 (0.29), residues: 320 loop : -0.80 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 95 TYR 0.011 0.001 TYR B 53 PHE 0.007 0.001 PHE D 255 TRP 0.013 0.001 TRP A 356 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00238 (17729) covalent geometry : angle 0.55296 (24044) hydrogen bonds : bond 0.02743 ( 696) hydrogen bonds : angle 4.46451 ( 1896) *********************** 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 308 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 239 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9071 (pt) REVERT: A 132 MET cc_start: 0.9058 (tmm) cc_final: 0.8649 (tmm) REVERT: B 47 MET cc_start: 0.8797 (mmm) cc_final: 0.8481 (mmm) REVERT: B 305 MET cc_start: 0.8159 (mtp) cc_final: 0.7938 (mmm) REVERT: C 14 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.8969 (p) REVERT: C 132 MET cc_start: 0.8868 (ptm) cc_final: 0.8522 (ptm) REVERT: C 254 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.7247 (mtm-85) REVERT: C 283 MET cc_start: 0.8600 (mmt) cc_final: 0.8241 (mmt) REVERT: D 107 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: D 283 MET cc_start: 0.8556 (mmm) cc_final: 0.7574 (mmt) REVERT: F 62 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7695 (p0) REVERT: F 70 LEU cc_start: 0.9306 (tp) cc_final: 0.8831 (tp) REVERT: F 71 GLU cc_start: 0.8985 (tt0) cc_final: 0.8655 (tt0) REVERT: F 95 ARG cc_start: 0.8280 (ttm110) cc_final: 0.7934 (ttm110) REVERT: F 98 GLN cc_start: 0.8302 (mt0) cc_final: 0.7875 (pt0) REVERT: F 102 GLN cc_start: 0.9107 (mt0) cc_final: 0.8791 (mt0) REVERT: F 114 ASP cc_start: 0.8490 (m-30) cc_final: 0.8250 (m-30) REVERT: G 25 ARG cc_start: 0.8060 (tpp80) cc_final: 0.7831 (tpp80) REVERT: G 37 PHE cc_start: 0.7880 (m-80) cc_final: 0.7625 (m-80) REVERT: G 71 GLU cc_start: 0.8742 (pt0) cc_final: 0.8167 (tt0) REVERT: G 81 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6566 (mm-30) REVERT: H 23 LYS cc_start: 0.8301 (mmmt) cc_final: 0.8014 (tppt) REVERT: H 24 SER cc_start: 0.9136 (m) cc_final: 0.8621 (p) REVERT: H 25 ARG cc_start: 0.7388 (tpp80) cc_final: 0.6993 (mmm-85) REVERT: H 31 ASP cc_start: 0.8358 (m-30) cc_final: 0.7980 (m-30) REVERT: H 103 ASN cc_start: 0.8267 (m-40) cc_final: 0.7959 (t0) REVERT: H 126 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7183 (pt) outliers start: 69 outliers final: 57 residues processed: 295 average time/residue: 0.1393 time to fit residues: 61.6757 Evaluate side-chains 300 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 237 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 190 MET 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 344 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL 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 159 VAL Chi-restraints excluded: chain B residue 190 MET 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 54 VAL Chi-restraints excluded: chain C residue 57 GLU 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 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 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 201 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 62 ASP 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 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 G residue 135 GLN Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 67 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 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 209 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 213 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 132 optimal weight: 0.0020 chunk 13 optimal weight: 0.7980 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS F 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.071819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.057157 restraints weight = 45010.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.058605 restraints weight = 22113.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.059198 restraints weight = 15116.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.059201 restraints weight = 11409.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.059669 restraints weight = 11517.204| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17729 Z= 0.143 Angle : 0.574 11.442 24044 Z= 0.278 Chirality : 0.043 0.217 2691 Planarity : 0.003 0.048 3070 Dihedral : 6.412 60.684 2479 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.11 % Allowed : 17.57 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 2188 helix: 0.55 (0.18), residues: 954 sheet: -1.58 (0.29), residues: 320 loop : -0.94 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 95 TYR 0.010 0.001 TYR B 53 PHE 0.007 0.001 PHE D 255 TRP 0.007 0.001 TRP B 340 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00338 (17729) covalent geometry : angle 0.57422 (24044) hydrogen bonds : bond 0.02971 ( 696) hydrogen bonds : angle 4.51971 ( 1896) *********************** 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 318 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 241 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9146 (pt) REVERT: B 47 MET cc_start: 0.8704 (mmm) cc_final: 0.8431 (mmm) REVERT: B 305 MET cc_start: 0.8184 (mtp) cc_final: 0.7973 (mmm) REVERT: C 14 SER cc_start: 0.9246 (OUTLIER) cc_final: 0.9009 (p) REVERT: C 132 MET cc_start: 0.8870 (ptm) cc_final: 0.8543 (ptm) REVERT: C 254 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.7200 (mtm-85) REVERT: C 283 MET cc_start: 0.8631 (mmt) cc_final: 0.8334 (mmt) REVERT: D 107 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: D 283 MET cc_start: 0.8609 (mmm) cc_final: 0.7603 (mmt) REVERT: F 62 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7612 (p0) REVERT: F 70 LEU cc_start: 0.9304 (tp) cc_final: 0.8833 (tp) REVERT: F 71 GLU cc_start: 0.8996 (tt0) cc_final: 0.8655 (tt0) REVERT: F 95 ARG cc_start: 0.8354 (ttm110) cc_final: 0.7931 (ttm110) REVERT: F 98 GLN cc_start: 0.8318 (mt0) cc_final: 0.7880 (pt0) REVERT: F 102 GLN cc_start: 0.9086 (mt0) cc_final: 0.8760 (mt0) REVERT: F 114 ASP cc_start: 0.8523 (m-30) cc_final: 0.8259 (m-30) REVERT: G 25 ARG cc_start: 0.8044 (tpp80) cc_final: 0.7827 (tpp80) REVERT: G 37 PHE cc_start: 0.7930 (m-80) cc_final: 0.7719 (m-80) REVERT: G 71 GLU cc_start: 0.8756 (pt0) cc_final: 0.8188 (tt0) REVERT: G 81 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6778 (mm-30) REVERT: H 23 LYS cc_start: 0.8306 (mmmt) cc_final: 0.8018 (tppt) REVERT: H 25 ARG cc_start: 0.7421 (tpp80) cc_final: 0.7154 (mmm-85) REVERT: H 31 ASP cc_start: 0.8360 (m-30) cc_final: 0.7961 (m-30) REVERT: H 103 ASN cc_start: 0.8274 (m-40) cc_final: 0.8006 (t0) REVERT: H 126 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7306 (pt) outliers start: 77 outliers final: 58 residues processed: 300 average time/residue: 0.1377 time to fit residues: 61.8200 Evaluate side-chains 303 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 239 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 190 MET 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 297 ASN Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET 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 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 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 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 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 62 ASP 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 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 G residue 135 GLN Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 67 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 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 205 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 29 HIS F 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.072802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.058058 restraints weight = 44681.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.059387 restraints weight = 21633.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.060081 restraints weight = 14967.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.060422 restraints weight = 11733.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.060493 restraints weight = 11740.181| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17729 Z= 0.105 Angle : 0.563 12.670 24044 Z= 0.271 Chirality : 0.042 0.202 2691 Planarity : 0.003 0.052 3070 Dihedral : 6.167 57.291 2475 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.31 % Allowed : 18.43 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.19), residues: 2188 helix: 0.63 (0.18), residues: 954 sheet: -1.52 (0.29), residues: 320 loop : -0.87 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 95 TYR 0.010 0.001 TYR B 53 PHE 0.008 0.001 PHE B 31 TRP 0.018 0.001 TRP G 40 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00245 (17729) covalent geometry : angle 0.56339 (24044) hydrogen bonds : bond 0.02781 ( 696) hydrogen bonds : angle 4.46071 ( 1896) ********************** 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 300 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 238 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9114 (pt) REVERT: A 132 MET cc_start: 0.8825 (tmm) cc_final: 0.8568 (tmm) REVERT: B 47 MET cc_start: 0.8682 (mmm) cc_final: 0.8439 (mmm) REVERT: C 14 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8986 (p) REVERT: C 50 LYS cc_start: 0.7943 (tptt) cc_final: 0.7729 (tptp) REVERT: C 132 MET cc_start: 0.8849 (ptm) cc_final: 0.8527 (ptm) REVERT: C 254 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.7279 (mtm-85) REVERT: C 283 MET cc_start: 0.8615 (mmt) cc_final: 0.8311 (mmt) REVERT: D 283 MET cc_start: 0.8556 (mmm) cc_final: 0.7565 (mmt) REVERT: E 47 MET cc_start: 0.7466 (mtt) cc_final: 0.7233 (ttp) REVERT: F 62 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7533 (p0) REVERT: F 70 LEU cc_start: 0.9321 (tp) cc_final: 0.8844 (tp) REVERT: F 71 GLU cc_start: 0.8978 (tt0) cc_final: 0.8641 (tt0) REVERT: F 95 ARG cc_start: 0.8283 (ttm110) cc_final: 0.7882 (ttm110) REVERT: F 98 GLN cc_start: 0.8313 (mt0) cc_final: 0.7867 (pt0) REVERT: F 102 GLN cc_start: 0.9097 (mt0) cc_final: 0.8741 (mt0) REVERT: F 103 ASN cc_start: 0.8432 (m-40) cc_final: 0.7772 (t0) REVERT: F 114 ASP cc_start: 0.8520 (m-30) cc_final: 0.8239 (m-30) REVERT: G 37 PHE cc_start: 0.7891 (m-80) cc_final: 0.7620 (m-80) REVERT: G 81 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7112 (mm-30) REVERT: H 23 LYS cc_start: 0.8320 (mmmt) cc_final: 0.8024 (tppt) REVERT: H 31 ASP cc_start: 0.8346 (m-30) cc_final: 0.7920 (m-30) REVERT: H 103 ASN cc_start: 0.8261 (m-40) cc_final: 0.8017 (t0) outliers start: 62 outliers final: 54 residues processed: 289 average time/residue: 0.1349 time to fit residues: 58.3905 Evaluate side-chains 295 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 237 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 190 MET 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 344 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET 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 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 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL 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 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 62 ASP 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 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 G residue 135 GLN Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 67 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 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 22 optimal weight: 0.0270 chunk 154 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.073065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.058562 restraints weight = 44905.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.060026 restraints weight = 21920.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.060611 restraints weight = 15207.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.061046 restraints weight = 11327.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.061075 restraints weight = 11411.773| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17729 Z= 0.112 Angle : 0.566 12.501 24044 Z= 0.272 Chirality : 0.042 0.204 2691 Planarity : 0.003 0.049 3070 Dihedral : 6.051 55.600 2472 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.26 % Allowed : 18.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.19), residues: 2188 helix: 0.61 (0.18), residues: 957 sheet: -1.46 (0.29), residues: 320 loop : -0.85 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 95 TYR 0.009 0.001 TYR B 53 PHE 0.007 0.001 PHE B 31 TRP 0.016 0.001 TRP G 40 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00261 (17729) covalent geometry : angle 0.56604 (24044) hydrogen bonds : bond 0.02826 ( 696) hydrogen bonds : angle 4.45816 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2446.10 seconds wall clock time: 43 minutes 11.45 seconds (2591.45 seconds total)