Starting phenix.real_space_refine on Sat Jul 4 14:24:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mcs_23757/07_2026/7mcs_23757.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mcs_23757/07_2026/7mcs_23757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mcs_23757/07_2026/7mcs_23757.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mcs_23757/07_2026/7mcs_23757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mcs_23757/07_2026/7mcs_23757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mcs_23757/07_2026/7mcs_23757.map" model { file = "/net/cci-nas-00/data/ceres_data/7mcs_23757/07_2026/7mcs_23757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mcs_23757/07_2026/7mcs_23757.cif" } resolution = 3.56 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= 0.003 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 48 5.49 5 Mg 6 5.21 5 S 81 5.16 5 C 13494 2.51 5 N 3913 2.21 5 O 4058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21600 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1967 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3196 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 386} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3208 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 388} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3201 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 388} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3196 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 387} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3183 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 386} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2842 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 342} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.38, per 1000 atoms: 0.20 Number of scatterers: 21600 At special positions: 0 Unit cell: (150.48, 153.9, 99.18, 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 81 16.00 P 48 15.00 Mg 6 11.99 O 4058 8.00 N 3913 7.00 C 13494 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: 1.62 Conformation dependent library (CDL) restraints added in 775.1 milliseconds 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4872 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 12 sheets defined 54.6% alpha, 5.7% beta 15 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 76 through 93 removed outlier: 3.654A pdb=" N GLY A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.635A pdb=" N HIS A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 removed outlier: 3.518A pdb=" N SER A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 195 removed outlier: 4.407A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 211 through 224 removed outlier: 3.616A pdb=" N ALA A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.241A pdb=" N SER A 240 " --> pdb=" O HIS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.840A pdb=" N ARG A 272 " --> pdb=" O PRO A 269 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 273 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.599A pdb=" N GLN B 52 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 75 through 91 removed outlier: 3.604A pdb=" N GLU B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 143 through 151 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.908A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.716A pdb=" N ALA B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.851A pdb=" N HIS B 236 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 256 removed outlier: 3.505A pdb=" N GLU B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 4.173A pdb=" N GLU B 273 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 305 through 317 removed outlier: 3.581A pdb=" N ILE B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 317 " --> pdb=" O ASP B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.709A pdb=" N GLY B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 382 through 392 removed outlier: 3.615A pdb=" N LEU B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU B 389 " --> pdb=" O MET B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.654A pdb=" N LEU C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 52' Processing helix chain 'C' and resid 54 through 63 Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 75 through 91 removed outlier: 4.037A pdb=" N GLU C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR C 91 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.907A pdb=" N HIS C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 179 through 195 removed outlier: 3.968A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 210 through 224 removed outlier: 4.369A pdb=" N LEU C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 245 through 258 Processing helix chain 'C' and resid 268 through 272 removed outlier: 3.629A pdb=" N ARG C 272 " --> pdb=" O PRO C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 305 through 317 Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.837A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 362 removed outlier: 3.555A pdb=" N VAL C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 348 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.787A pdb=" N LEU C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP C 377 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C 379 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.900A pdb=" N LEU C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.544A pdb=" N SER D 39 " --> pdb=" O ASN D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.730A pdb=" N LEU D 51 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 63 Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 75 through 90 removed outlier: 4.170A pdb=" N LEU D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY D 90 " --> pdb=" O MET D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.962A pdb=" N ASN D 95 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.831A pdb=" N LEU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 150 Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 179 through 195 removed outlier: 3.766A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.687A pdb=" N ARG D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU D 205 " --> pdb=" O ARG D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.675A pdb=" N ALA D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 244 through 258 removed outlier: 3.687A pdb=" N MET D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 274 removed outlier: 3.966A pdb=" N GLU D 273 " --> pdb=" O LYS D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 286 removed outlier: 3.518A pdb=" N ALA D 282 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 removed outlier: 3.511A pdb=" N ILE D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.524A pdb=" N LEU D 339 " --> pdb=" O VAL D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 362 removed outlier: 3.812A pdb=" N VAL D 348 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 378 Processing helix chain 'D' and resid 382 through 392 removed outlier: 3.522A pdb=" N GLY D 392 " --> pdb=" O ALA D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 398 removed outlier: 3.596A pdb=" N ILE D 397 " --> pdb=" O ILE D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 26 removed outlier: 3.656A pdb=" N GLU E 25 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 21 through 26' Processing helix chain 'E' and resid 32 through 38 removed outlier: 4.009A pdb=" N ALA E 37 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 38 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' Processing helix chain 'E' and resid 47 through 52 removed outlier: 3.606A pdb=" N LEU E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 64 through 69 Processing helix chain 'E' and resid 75 through 90 removed outlier: 3.871A pdb=" N LEU E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 114 removed outlier: 3.555A pdb=" N LEU E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 151 Processing helix chain 'E' and resid 179 through 195 removed outlier: 4.113A pdb=" N ILE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'E' and resid 209 through 224 removed outlier: 4.091A pdb=" N ALA E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 239 removed outlier: 3.828A pdb=" N HIS E 236 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER E 238 " --> pdb=" O GLN E 235 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG E 239 " --> pdb=" O HIS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 258 removed outlier: 3.695A pdb=" N PHE E 251 " --> pdb=" O GLU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 removed outlier: 3.705A pdb=" N ARG E 272 " --> pdb=" O PRO E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 286 removed outlier: 3.602A pdb=" N ALA E 282 " --> pdb=" O ASP E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 317 removed outlier: 3.502A pdb=" N ILE E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN E 317 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 343 through 362 Processing helix chain 'E' and resid 367 through 379 removed outlier: 3.568A pdb=" N GLN E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 379 " --> pdb=" O TYR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 391 removed outlier: 3.645A pdb=" N LEU E 386 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER E 391 " --> pdb=" O GLU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 398 removed outlier: 3.602A pdb=" N ALA E 398 " --> pdb=" O PRO E 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 32 through 38 Processing helix chain 'F' and resid 47 through 52 removed outlier: 3.815A pdb=" N LEU F 51 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN F 52 " --> pdb=" O SER F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 52' Processing helix chain 'F' and resid 54 through 62 removed outlier: 3.793A pdb=" N ILE F 62 " --> pdb=" O ARG F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 75 through 91 removed outlier: 3.510A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY F 90 " --> pdb=" O MET F 86 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR F 91 " --> pdb=" O ILE F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 95 removed outlier: 3.666A pdb=" N ASN F 95 " --> pdb=" O VAL F 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 95' Processing helix chain 'F' and resid 100 through 114 removed outlier: 4.429A pdb=" N HIS F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN F 113 " --> pdb=" O TYR F 109 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'F' and resid 181 through 195 removed outlier: 3.793A pdb=" N PHE F 188 " --> pdb=" O CYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 224 removed outlier: 3.632A pdb=" N ALA F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER F 218 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 removed outlier: 3.563A pdb=" N LEU F 237 " --> pdb=" O ILE F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 258 Processing helix chain 'F' and resid 268 through 276 removed outlier: 4.097A pdb=" N GLU F 273 " --> pdb=" O LYS F 270 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE F 274 " --> pdb=" O ALA F 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 276 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 286 removed outlier: 3.878A pdb=" N ALA F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 318 removed outlier: 3.630A pdb=" N GLN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 341 removed outlier: 3.741A pdb=" N GLU F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 360 removed outlier: 3.557A pdb=" N VAL F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 379 removed outlier: 3.565A pdb=" N LEU F 379 " --> pdb=" O TYR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 392 removed outlier: 3.565A pdb=" N GLY F 392 " --> pdb=" O ALA F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 400 removed outlier: 4.493A pdb=" N TYR F 400 " --> pdb=" O ARG F 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 41 Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 54 through 64 removed outlier: 3.631A pdb=" N ARG G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 93 removed outlier: 3.846A pdb=" N LEU G 79 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG G 88 " --> pdb=" O SER G 84 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR G 91 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY G 93 " --> pdb=" O GLY G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 151 removed outlier: 3.917A pdb=" N LEU G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 195 removed outlier: 4.044A pdb=" N ILE G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE G 187 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE G 188 " --> pdb=" O CYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 203 removed outlier: 3.723A pdb=" N ARG G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 224 removed outlier: 3.582A pdb=" N HIS G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 259 removed outlier: 3.506A pdb=" N PHE G 251 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE G 252 " --> pdb=" O MET G 248 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE G 259 " --> pdb=" O MET G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 274 removed outlier: 4.243A pdb=" N GLU G 273 " --> pdb=" O LYS G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 317 removed outlier: 4.087A pdb=" N ILE G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 341 removed outlier: 3.710A pdb=" N TRP G 336 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR G 337 " --> pdb=" O ARG G 333 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU G 338 " --> pdb=" O ASP G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 362 removed outlier: 3.674A pdb=" N VAL G 347 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL G 348 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY G 362 " --> pdb=" O ALA G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 379 removed outlier: 3.535A pdb=" N LEU G 379 " --> pdb=" O TYR G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 392 removed outlier: 3.609A pdb=" N ALA G 388 " --> pdb=" O PRO G 384 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY G 392 " --> pdb=" O ALA G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 398 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 6.424A pdb=" N ILE A 6 " --> pdb=" O TYR A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173 removed outlier: 3.837A pdb=" N ASP A 232 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 229 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 266 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 231 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A 134 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 133 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.425A pdb=" N LEU B 229 " --> pdb=" O MET B 264 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE B 266 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 231 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 133 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TRP B 293 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 135 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.554A pdb=" N HIS B 159 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 164 " --> pdb=" O HIS B 159 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 225 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 167 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 167 through 173 removed outlier: 6.950A pdb=" N VAL C 168 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU C 132 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N GLY C 267 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU C 134 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ILE C 291 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU C 133 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N TRP C 293 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 135 " --> pdb=" O TRP C 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 170 through 173 Processing sheet with id=AA7, first strand: chain 'D' and resid 156 through 159 removed outlier: 3.846A pdb=" N VAL D 164 " --> pdb=" O HIS D 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 6 through 7 removed outlier: 6.335A pdb=" N ILE E 6 " --> pdb=" O TYR E 158 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 164 " --> pdb=" O HIS E 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 170 through 173 removed outlier: 6.715A pdb=" N LEU E 229 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE E 266 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE E 231 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ILE E 291 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU E 133 " --> pdb=" O ILE E 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 6 through 7 removed outlier: 6.644A pdb=" N ILE F 6 " --> pdb=" O TYR F 158 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL F 164 " --> pdb=" O HIS F 159 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N LEU F 226 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N GLN F 166 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N LEU F 228 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL F 168 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL F 230 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU F 170 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ASP F 232 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE F 172 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N MET F 264 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU F 229 " --> pdb=" O MET F 264 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE F 266 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE F 231 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ILE F 291 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU F 133 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 264 through 267 removed outlier: 7.327A pdb=" N LEU G 132 " --> pdb=" O LEU G 265 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY G 267 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU G 134 " --> pdb=" O GLY G 267 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N TRP G 293 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE G 135 " --> pdb=" O TRP G 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 170 through 173 removed outlier: 6.120A pdb=" N LEU G 170 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP G 232 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE G 172 " --> pdb=" O ASP G 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 817 hydrogen bonds defined for protein. 2328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3868 1.32 - 1.45: 5625 1.45 - 1.57: 12328 1.57 - 1.70: 95 1.70 - 1.82: 135 Bond restraints: 22051 Sorted by residual: bond pdb=" O3A ANP E 601 " pdb=" PB ANP E 601 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" O3A ANP F 601 " pdb=" PB ANP F 601 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" O3A ANP B 601 " pdb=" PB ANP B 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP D 601 " pdb=" PB ANP D 601 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" O3A ANP C 601 " pdb=" PB ANP C 601 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.08e+01 ... (remaining 22046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 29749 3.79 - 7.58: 205 7.58 - 11.37: 36 11.37 - 15.16: 2 15.16 - 18.95: 6 Bond angle restraints: 29998 Sorted by residual: angle pdb=" CA PRO G 22 " pdb=" N PRO G 22 " pdb=" CD PRO G 22 " ideal model delta sigma weight residual 112.00 99.75 12.25 1.40e+00 5.10e-01 7.65e+01 angle pdb=" PB ANP G 601 " pdb=" N3B ANP G 601 " pdb=" PG ANP G 601 " ideal model delta sigma weight residual 126.95 108.00 18.95 3.00e+00 1.11e-01 3.99e+01 angle pdb=" PB ANP E 601 " pdb=" N3B ANP E 601 " pdb=" PG ANP E 601 " ideal model delta sigma weight residual 126.95 108.21 18.74 3.00e+00 1.11e-01 3.90e+01 angle pdb=" PB ANP C 601 " pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 126.95 108.44 18.51 3.00e+00 1.11e-01 3.81e+01 angle pdb=" PB ANP D 601 " pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 126.95 108.49 18.46 3.00e+00 1.11e-01 3.79e+01 ... (remaining 29993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 11631 18.08 - 36.16: 1158 36.16 - 54.24: 283 54.24 - 72.32: 65 72.32 - 90.40: 23 Dihedral angle restraints: 13160 sinusoidal: 5594 harmonic: 7566 Sorted by residual: dihedral pdb=" CA HIS D 147 " pdb=" C HIS D 147 " pdb=" N ARG D 148 " pdb=" CA ARG D 148 " ideal model delta harmonic sigma weight residual 180.00 154.43 25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" C HIS C 224 " pdb=" N HIS C 224 " pdb=" CA HIS C 224 " pdb=" CB HIS C 224 " ideal model delta harmonic sigma weight residual -122.60 -109.95 -12.65 0 2.50e+00 1.60e-01 2.56e+01 dihedral pdb=" CA PRO C 269 " pdb=" C PRO C 269 " pdb=" N LYS C 270 " pdb=" CA LYS C 270 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 13157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3086 0.084 - 0.167: 284 0.167 - 0.251: 10 0.251 - 0.334: 8 0.334 - 0.418: 1 Chirality restraints: 3389 Sorted by residual: chirality pdb=" CA HIS C 224 " pdb=" N HIS C 224 " pdb=" C HIS C 224 " pdb=" CB HIS C 224 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C3' ANP C 601 " pdb=" C2' ANP C 601 " pdb=" C4' ANP C 601 " pdb=" O3' ANP C 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C3' ANP F 601 " pdb=" C2' ANP F 601 " pdb=" C4' ANP F 601 " pdb=" O3' ANP F 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 3386 not shown) Planarity restraints: 3747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 21 " 0.079 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO G 22 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO G 22 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO G 22 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 261 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO F 262 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO F 262 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 262 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 95 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO G 96 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 96 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 96 " -0.033 5.00e-02 4.00e+02 ... (remaining 3744 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 138 2.58 - 3.16: 16889 3.16 - 3.74: 32198 3.74 - 4.32: 44203 4.32 - 4.90: 73858 Nonbonded interactions: 167286 Sorted by model distance: nonbonded pdb=" OG1 THR D 143 " pdb="MG MG D 602 " model vdw 1.994 2.170 nonbonded pdb=" OG1 THR B 143 " pdb="MG MG B 602 " model vdw 2.031 2.170 nonbonded pdb=" OG1 THR G 143 " pdb="MG MG G 602 " model vdw 2.033 2.170 nonbonded pdb=" O1G ANP B 601 " pdb="MG MG B 602 " model vdw 2.061 2.170 nonbonded pdb=" O3G ANP D 601 " pdb="MG MG D 602 " model vdw 2.094 2.170 ... (remaining 167281 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 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 405 or resid 601 through 602)) selection = (chain 'C' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 405 or resid 601 through 602)) selection = (chain 'D' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 602)) selection = (chain 'E' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 602)) selection = (chain 'F' and (resid 5 through 98 or resid 129 through 238 or resid 245 through \ 277 or resid 289 through 602)) selection = (chain 'G' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 405 or resid 601 through 602)) } ncs_group { reference = (chain 'H' and resid 1 through 14) selection = (chain 'I' and resid 2 through 15) } 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=0.61 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.280 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.006 0.150 22051 Z= 0.295 Angle : 0.870 18.953 29998 Z= 0.435 Chirality : 0.049 0.418 3389 Planarity : 0.005 0.110 3747 Dihedral : 15.873 90.397 8288 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.65 % Rotamer: Outliers : 0.04 % Allowed : 0.53 % Favored : 99.42 % Cbeta Deviations : 0.04 % 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: -1.38 (0.15), residues: 2597 helix: -0.58 (0.15), residues: 1180 sheet: 0.22 (0.40), residues: 184 loop : -1.37 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 111 TYR 0.015 0.001 TYR A 199 PHE 0.016 0.002 PHE D 288 TRP 0.020 0.001 TRP G 316 HIS 0.009 0.001 HIS G 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.30 (22051) covalent geometry : angle 0.86992 / 0.44 (29998) hydrogen bonds : bond 0.20474 / 13.90 ( 862) hydrogen bonds : angle 6.78066 / 4.76 ( 2418) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 501 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7066 (mt) cc_final: 0.6558 (mp) REVERT: B 330 ASP cc_start: 0.6698 (p0) cc_final: 0.6457 (p0) REVERT: D 327 LEU cc_start: 0.8863 (pp) cc_final: 0.8571 (mt) REVERT: F 248 MET cc_start: 0.8579 (ttm) cc_final: 0.8339 (ttt) REVERT: F 274 ILE cc_start: 0.8266 (pt) cc_final: 0.8049 (mt) REVERT: F 288 PHE cc_start: 0.7689 (t80) cc_final: 0.7138 (t80) REVERT: F 349 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8202 (ptpt) REVERT: G 130 GLN cc_start: 0.1692 (mt0) cc_final: 0.0493 (mp10) REVERT: G 171 LYS cc_start: 0.7259 (pptt) cc_final: 0.5970 (mmmm) REVERT: G 180 LEU cc_start: 0.6880 (mp) cc_final: 0.6500 (tp) REVERT: G 385 MET cc_start: 0.7676 (mmp) cc_final: 0.7367 (mmp) outliers start: 1 outliers final: 0 residues processed: 502 average time/residue: 0.1854 time to fit residues: 131.2568 Evaluate side-chains 241 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 258 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS B 60 HIS B 355 GLN ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN D 176 HIS ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN E 222 ASN F 35 ASN F 95 ASN F 355 GLN G 45 GLN G 355 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119273 restraints weight = 32684.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118644 restraints weight = 33159.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119389 restraints weight = 34573.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119850 restraints weight = 26667.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119982 restraints weight = 23637.612| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 22051 Z= 0.145 Angle : 0.636 9.672 29998 Z= 0.326 Chirality : 0.043 0.328 3389 Planarity : 0.005 0.051 3747 Dihedral : 11.900 59.742 3229 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 1.96 % Allowed : 8.89 % Favored : 89.16 % 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: -1.04 (0.16), residues: 2597 helix: -0.17 (0.15), residues: 1220 sheet: 0.15 (0.38), residues: 188 loop : -1.33 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 390 TYR 0.016 0.001 TYR G 375 PHE 0.020 0.002 PHE G 351 TRP 0.024 0.001 TRP G 316 HIS 0.019 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (22051) covalent geometry : angle 0.63563 / 0.33 (29998) hydrogen bonds : bond 0.05312 / 3.61 ( 862) hydrogen bonds : angle 5.08835 / 3.58 ( 2418) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7287 (mt) cc_final: 0.7004 (mp) REVERT: B 220 ILE cc_start: 0.8785 (mp) cc_final: 0.8481 (mp) REVERT: B 330 ASP cc_start: 0.6796 (p0) cc_final: 0.6581 (p0) REVERT: D 102 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.6156 (mm-40) REVERT: D 327 LEU cc_start: 0.8932 (pp) cc_final: 0.8674 (mt) REVERT: D 361 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7926 (mp) REVERT: G 130 GLN cc_start: 0.1566 (mt0) cc_final: 0.0605 (mp10) REVERT: G 171 LYS cc_start: 0.7483 (pptt) cc_final: 0.6051 (mmmm) REVERT: G 181 LYS cc_start: 0.7192 (mptt) cc_final: 0.6984 (mptt) REVERT: G 248 MET cc_start: 0.7482 (tpt) cc_final: 0.7054 (tpt) outliers start: 44 outliers final: 26 residues processed: 301 average time/residue: 0.1507 time to fit residues: 69.3633 Evaluate side-chains 257 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 184 CYS Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 235 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 249 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN E 222 ASN F 257 ASN G 355 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.120104 restraints weight = 32743.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118719 restraints weight = 38176.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119849 restraints weight = 35381.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120346 restraints weight = 25965.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120465 restraints weight = 23547.875| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22051 Z= 0.119 Angle : 0.568 11.606 29998 Z= 0.290 Chirality : 0.041 0.314 3389 Planarity : 0.004 0.047 3747 Dihedral : 11.823 59.844 3229 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 2.22 % Allowed : 11.29 % Favored : 86.49 % 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: -0.73 (0.16), residues: 2597 helix: 0.13 (0.15), residues: 1223 sheet: -0.08 (0.38), residues: 188 loop : -1.15 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 399 TYR 0.013 0.001 TYR G 400 PHE 0.023 0.001 PHE G 187 TRP 0.013 0.001 TRP G 316 HIS 0.011 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (22051) covalent geometry : angle 0.56795 / 0.29 (29998) hydrogen bonds : bond 0.04080 / 2.77 ( 862) hydrogen bonds : angle 4.70162 / 3.31 ( 2418) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7340 (mt) cc_final: 0.7053 (mp) REVERT: B 220 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8459 (mp) REVERT: B 330 ASP cc_start: 0.6851 (p0) cc_final: 0.6580 (p0) REVERT: D 327 LEU cc_start: 0.8955 (pp) cc_final: 0.8560 (mt) REVERT: D 361 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7934 (mp) REVERT: F 345 ASP cc_start: 0.7753 (t0) cc_final: 0.7530 (t0) REVERT: G 130 GLN cc_start: 0.1729 (mt0) cc_final: 0.0381 (mp10) REVERT: G 146 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8097 (tt) REVERT: G 171 LYS cc_start: 0.7568 (pptt) cc_final: 0.6184 (mmmm) REVERT: G 248 MET cc_start: 0.7191 (tpt) cc_final: 0.6957 (tpt) outliers start: 50 outliers final: 36 residues processed: 268 average time/residue: 0.1621 time to fit residues: 65.6958 Evaluate side-chains 249 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 334 ASP Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 184 CYS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 230 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 99 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 160 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 236 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 297 GLN F 198 ASN G 21 ASN G 355 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116296 restraints weight = 33117.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115367 restraints weight = 36420.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116362 restraints weight = 36579.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116721 restraints weight = 26714.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116868 restraints weight = 24587.727| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22051 Z= 0.181 Angle : 0.613 9.080 29998 Z= 0.312 Chirality : 0.043 0.315 3389 Planarity : 0.004 0.048 3747 Dihedral : 11.846 59.369 3229 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 2.49 % Allowed : 14.40 % Favored : 83.11 % 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: -0.76 (0.16), residues: 2597 helix: 0.13 (0.15), residues: 1222 sheet: -0.13 (0.37), residues: 197 loop : -1.20 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 323 TYR 0.014 0.002 TYR E 153 PHE 0.019 0.002 PHE G 351 TRP 0.012 0.001 TRP G 316 HIS 0.009 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (22051) covalent geometry : angle 0.61303 / 0.31 (29998) hydrogen bonds : bond 0.04266 / 2.88 ( 862) hydrogen bonds : angle 4.59936 / 3.24 ( 2418) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.793 Fit side-chains REVERT: A 101 LEU cc_start: 0.7308 (mt) cc_final: 0.7022 (mp) REVERT: B 220 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8507 (mp) REVERT: B 330 ASP cc_start: 0.6965 (p0) cc_final: 0.6699 (p0) REVERT: D 327 LEU cc_start: 0.8947 (pp) cc_final: 0.8513 (mt) REVERT: G 130 GLN cc_start: 0.2110 (mt0) cc_final: 0.0570 (mp10) REVERT: G 146 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8124 (mm) REVERT: G 169 TYR cc_start: 0.8045 (p90) cc_final: 0.7633 (p90) REVERT: G 171 LYS cc_start: 0.7583 (pptt) cc_final: 0.6242 (mmmm) REVERT: G 248 MET cc_start: 0.7330 (tpt) cc_final: 0.7061 (tpt) REVERT: G 272 ARG cc_start: 0.6104 (mtm110) cc_final: 0.5479 (ttm110) outliers start: 56 outliers final: 38 residues processed: 254 average time/residue: 0.1621 time to fit residues: 62.5458 Evaluate side-chains 237 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 184 CYS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 230 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 128 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 238 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 257 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115688 restraints weight = 33266.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114730 restraints weight = 37919.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115902 restraints weight = 35947.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116195 restraints weight = 27596.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116309 restraints weight = 24850.544| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22051 Z= 0.166 Angle : 0.591 10.639 29998 Z= 0.299 Chirality : 0.042 0.313 3389 Planarity : 0.004 0.048 3747 Dihedral : 11.826 60.778 3229 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 2.93 % Allowed : 15.42 % Favored : 81.64 % 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: -0.76 (0.16), residues: 2597 helix: 0.13 (0.15), residues: 1228 sheet: -0.14 (0.37), residues: 197 loop : -1.19 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 201 TYR 0.016 0.001 TYR G 400 PHE 0.020 0.002 PHE G 187 TRP 0.012 0.001 TRP G 316 HIS 0.010 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (22051) covalent geometry : angle 0.59116 / 0.30 (29998) hydrogen bonds : bond 0.04071 / 2.75 ( 862) hydrogen bonds : angle 4.52903 / 3.19 ( 2418) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7325 (mt) cc_final: 0.7018 (mp) REVERT: B 220 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8516 (mp) REVERT: D 327 LEU cc_start: 0.8959 (pp) cc_final: 0.8496 (mt) REVERT: F 121 ARG cc_start: 0.7077 (mmm-85) cc_final: 0.6805 (mmm-85) REVERT: F 210 ILE cc_start: 0.8202 (tt) cc_final: 0.7995 (tp) REVERT: G 31 GLN cc_start: 0.4551 (pt0) cc_final: 0.4053 (mm-40) REVERT: G 51 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6288 (mp) REVERT: G 146 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8131 (mm) REVERT: G 169 TYR cc_start: 0.8093 (p90) cc_final: 0.7662 (p90) REVERT: G 171 LYS cc_start: 0.7589 (pptt) cc_final: 0.6281 (mmmm) REVERT: G 255 MET cc_start: 0.3418 (ttt) cc_final: 0.3204 (ttt) outliers start: 66 outliers final: 45 residues processed: 250 average time/residue: 0.1448 time to fit residues: 56.1177 Evaluate side-chains 246 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 265 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 170 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 236 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117165 restraints weight = 32950.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115708 restraints weight = 40350.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116572 restraints weight = 35330.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117150 restraints weight = 27969.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117252 restraints weight = 25493.922| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22051 Z= 0.127 Angle : 0.553 11.822 29998 Z= 0.280 Chirality : 0.041 0.324 3389 Planarity : 0.004 0.047 3747 Dihedral : 11.748 62.459 3229 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 2.67 % Allowed : 16.36 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2597 helix: 0.28 (0.15), residues: 1231 sheet: 0.09 (0.39), residues: 181 loop : -1.13 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 201 TYR 0.018 0.001 TYR F 10 PHE 0.023 0.001 PHE G 187 TRP 0.032 0.001 TRP G 316 HIS 0.014 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (22051) covalent geometry : angle 0.55314 / 0.28 (29998) hydrogen bonds : bond 0.03572 / 2.41 ( 862) hydrogen bonds : angle 4.35085 / 3.06 ( 2418) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 212 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7322 (mt) cc_final: 0.7022 (mp) REVERT: B 201 ARG cc_start: 0.7280 (mmp-170) cc_final: 0.6815 (mmp-170) REVERT: B 220 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8507 (mp) REVERT: B 330 ASP cc_start: 0.6782 (p0) cc_final: 0.6435 (m-30) REVERT: C 164 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7790 (t) REVERT: D 327 LEU cc_start: 0.8968 (pp) cc_final: 0.8512 (mt) REVERT: F 322 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7286 (mp10) REVERT: G 31 GLN cc_start: 0.4468 (pt0) cc_final: 0.3981 (mm-40) REVERT: G 51 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6067 (mp) REVERT: G 146 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8088 (mm) REVERT: G 169 TYR cc_start: 0.8039 (p90) cc_final: 0.7612 (p90) REVERT: G 171 LYS cc_start: 0.7584 (pptt) cc_final: 0.6251 (mmmm) REVERT: G 356 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8200 (mt) outliers start: 60 outliers final: 41 residues processed: 253 average time/residue: 0.1607 time to fit residues: 61.6321 Evaluate side-chains 244 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 288 PHE Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 1 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN F 31 GLN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS F 176 HIS F 373 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108368 restraints weight = 32957.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108277 restraints weight = 28502.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108761 restraints weight = 27195.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109218 restraints weight = 23001.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109385 restraints weight = 20782.853| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 22051 Z= 0.305 Angle : 0.792 13.220 29998 Z= 0.395 Chirality : 0.049 0.361 3389 Planarity : 0.006 0.050 3747 Dihedral : 11.988 61.926 3229 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 3.24 % Allowed : 16.93 % Favored : 79.82 % 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: -1.34 (0.15), residues: 2597 helix: -0.43 (0.14), residues: 1246 sheet: -0.22 (0.38), residues: 179 loop : -1.43 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 283 TYR 0.028 0.003 TYR E 153 PHE 0.027 0.003 PHE D 288 TRP 0.045 0.002 TRP G 316 HIS 0.008 0.002 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.30 (22051) covalent geometry : angle 0.79194 / 0.39 (29998) hydrogen bonds : bond 0.05611 / 3.78 ( 862) hydrogen bonds : angle 4.83649 / 3.40 ( 2418) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 205 time to evaluate : 0.769 Fit side-chains REVERT: A 101 LEU cc_start: 0.7441 (mt) cc_final: 0.7080 (mp) REVERT: A 176 HIS cc_start: 0.3735 (OUTLIER) cc_final: 0.3351 (t-170) REVERT: B 201 ARG cc_start: 0.7233 (mmp-170) cc_final: 0.6810 (mmp-170) REVERT: B 220 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8397 (mp) REVERT: D 182 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7009 (tp30) REVERT: D 327 LEU cc_start: 0.9011 (pp) cc_final: 0.8543 (mt) REVERT: F 322 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7953 (mm110) REVERT: F 345 ASP cc_start: 0.7849 (t0) cc_final: 0.7627 (t0) REVERT: G 51 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6035 (mp) REVERT: G 146 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8209 (mm) REVERT: G 169 TYR cc_start: 0.8198 (p90) cc_final: 0.7748 (p90) REVERT: G 171 LYS cc_start: 0.7757 (pptt) cc_final: 0.6294 (mmmm) outliers start: 73 outliers final: 56 residues processed: 255 average time/residue: 0.1612 time to fit residues: 62.5251 Evaluate side-chains 250 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 265 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 169 optimal weight: 0.9990 chunk 19 optimal weight: 0.0060 chunk 44 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 258 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 300 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS F 373 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115655 restraints weight = 33024.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114116 restraints weight = 39864.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115238 restraints weight = 36897.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115693 restraints weight = 27719.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115747 restraints weight = 25815.940| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22051 Z= 0.111 Angle : 0.574 14.173 29998 Z= 0.291 Chirality : 0.041 0.378 3389 Planarity : 0.004 0.049 3747 Dihedral : 11.753 64.952 3229 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 2.44 % Allowed : 18.31 % Favored : 79.24 % 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: -0.67 (0.16), residues: 2597 helix: 0.19 (0.15), residues: 1239 sheet: -0.02 (0.38), residues: 181 loop : -1.14 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 272 TYR 0.011 0.001 TYR D 337 PHE 0.015 0.001 PHE C 251 TRP 0.026 0.001 TRP G 316 HIS 0.014 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (22051) covalent geometry : angle 0.57436 / 0.29 (29998) hydrogen bonds : bond 0.03508 / 2.36 ( 862) hydrogen bonds : angle 4.37967 / 3.09 ( 2418) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 216 time to evaluate : 0.677 Fit side-chains REVERT: A 101 LEU cc_start: 0.7399 (mt) cc_final: 0.7087 (mp) REVERT: B 201 ARG cc_start: 0.7169 (mmp-170) cc_final: 0.6732 (mmp-170) REVERT: B 220 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8526 (mp) REVERT: B 336 TRP cc_start: 0.8740 (t60) cc_final: 0.8517 (t60) REVERT: D 327 LEU cc_start: 0.9006 (pp) cc_final: 0.8568 (mt) REVERT: F 322 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7734 (mm110) REVERT: F 345 ASP cc_start: 0.7679 (t0) cc_final: 0.7464 (t0) REVERT: G 4 THR cc_start: 0.2994 (t) cc_final: 0.2793 (m) REVERT: G 31 GLN cc_start: 0.4662 (pt0) cc_final: 0.4196 (mm-40) REVERT: G 51 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6131 (mp) REVERT: G 146 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8181 (mm) REVERT: G 169 TYR cc_start: 0.8081 (p90) cc_final: 0.7628 (p90) REVERT: G 171 LYS cc_start: 0.7646 (pptt) cc_final: 0.6261 (mmmm) REVERT: G 375 TYR cc_start: 0.8468 (t80) cc_final: 0.8025 (t80) outliers start: 55 outliers final: 37 residues processed: 254 average time/residue: 0.1600 time to fit residues: 61.7464 Evaluate side-chains 237 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 288 PHE Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 265 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 119 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 176 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.143448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115309 restraints weight = 33190.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114601 restraints weight = 35202.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115000 restraints weight = 34573.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115715 restraints weight = 29177.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116538 restraints weight = 26589.366| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22051 Z= 0.118 Angle : 0.563 12.827 29998 Z= 0.283 Chirality : 0.041 0.330 3389 Planarity : 0.004 0.048 3747 Dihedral : 11.669 61.497 3229 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 2.18 % Allowed : 18.53 % Favored : 79.29 % 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 (0.16), residues: 2597 helix: 0.31 (0.15), residues: 1248 sheet: 0.07 (0.38), residues: 181 loop : -1.10 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 121 TYR 0.012 0.001 TYR F 10 PHE 0.033 0.001 PHE G 187 TRP 0.022 0.001 TRP G 316 HIS 0.010 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (22051) covalent geometry : angle 0.56317 / 0.28 (29998) hydrogen bonds : bond 0.03486 / 2.35 ( 862) hydrogen bonds : angle 4.25919 / 3.00 ( 2418) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7350 (mt) cc_final: 0.7032 (mp) REVERT: B 201 ARG cc_start: 0.7138 (mmp-170) cc_final: 0.6723 (mmp-170) REVERT: B 220 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8480 (mp) REVERT: B 336 TRP cc_start: 0.8728 (t60) cc_final: 0.8523 (t60) REVERT: D 327 LEU cc_start: 0.9008 (pp) cc_final: 0.8565 (mt) REVERT: F 322 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7754 (mm110) REVERT: F 345 ASP cc_start: 0.7776 (t0) cc_final: 0.7567 (t0) REVERT: G 4 THR cc_start: 0.3091 (t) cc_final: 0.2873 (m) REVERT: G 31 GLN cc_start: 0.4748 (pt0) cc_final: 0.4257 (mm-40) REVERT: G 51 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6124 (mp) REVERT: G 169 TYR cc_start: 0.8073 (p90) cc_final: 0.7639 (p90) REVERT: G 171 LYS cc_start: 0.7613 (pptt) cc_final: 0.6188 (mmmm) outliers start: 49 outliers final: 39 residues processed: 241 average time/residue: 0.1663 time to fit residues: 60.5156 Evaluate side-chains 241 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 265 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 55 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 0.0670 chunk 19 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** 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 = 0.3827 r_free = 0.3827 target = 0.141840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111993 restraints weight = 32635.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112465 restraints weight = 28182.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113039 restraints weight = 25213.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113421 restraints weight = 21633.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113582 restraints weight = 19293.386| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22051 Z= 0.158 Angle : 0.600 12.680 29998 Z= 0.301 Chirality : 0.042 0.327 3389 Planarity : 0.004 0.046 3747 Dihedral : 11.649 61.434 3229 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.80 % Rotamer: Outliers : 2.09 % Allowed : 18.67 % Favored : 79.24 % 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: -0.60 (0.16), residues: 2597 helix: 0.25 (0.15), residues: 1255 sheet: 0.04 (0.38), residues: 181 loop : -1.13 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 201 TYR 0.013 0.001 TYR D 400 PHE 0.015 0.002 PHE G 275 TRP 0.023 0.001 TRP G 316 HIS 0.010 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (22051) covalent geometry : angle 0.60044 / 0.30 (29998) hydrogen bonds : bond 0.03793 / 2.56 ( 862) hydrogen bonds : angle 4.32237 / 3.04 ( 2418) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.745 Fit side-chains REVERT: A 101 LEU cc_start: 0.7382 (mt) cc_final: 0.7016 (mp) REVERT: B 201 ARG cc_start: 0.7160 (mmp-170) cc_final: 0.6778 (mmp-170) REVERT: B 220 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8440 (mp) REVERT: B 336 TRP cc_start: 0.8754 (t60) cc_final: 0.8543 (t60) REVERT: D 327 LEU cc_start: 0.9002 (pp) cc_final: 0.8543 (mt) REVERT: F 322 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7848 (mm110) REVERT: G 4 THR cc_start: 0.3082 (t) cc_final: 0.2829 (m) REVERT: G 31 GLN cc_start: 0.4803 (pt0) cc_final: 0.4243 (mm-40) REVERT: G 86 MET cc_start: 0.7997 (mpp) cc_final: 0.7754 (mpp) REVERT: G 169 TYR cc_start: 0.8096 (p90) cc_final: 0.7650 (p90) REVERT: G 171 LYS cc_start: 0.7671 (pptt) cc_final: 0.6169 (mmmm) REVERT: G 272 ARG cc_start: 0.5550 (mtp180) cc_final: 0.5021 (mpp80) outliers start: 47 outliers final: 41 residues processed: 236 average time/residue: 0.1680 time to fit residues: 59.2622 Evaluate side-chains 240 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 265 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 134 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 0.0270 chunk 201 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** 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 = 0.3814 r_free = 0.3814 target = 0.140781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111016 restraints weight = 33303.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110984 restraints weight = 30027.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111562 restraints weight = 27931.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112044 restraints weight = 22884.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112221 restraints weight = 21092.429| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22051 Z= 0.184 Angle : 0.634 12.834 29998 Z= 0.318 Chirality : 0.043 0.342 3389 Planarity : 0.004 0.046 3747 Dihedral : 11.647 61.867 3229 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 2.53 % Allowed : 18.58 % Favored : 78.89 % 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: -0.69 (0.16), residues: 2597 helix: 0.17 (0.15), residues: 1254 sheet: 0.04 (0.39), residues: 179 loop : -1.18 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 201 TYR 0.015 0.002 TYR D 400 PHE 0.026 0.002 PHE G 187 TRP 0.023 0.001 TRP G 316 HIS 0.010 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (22051) covalent geometry : angle 0.63351 / 0.32 (29998) hydrogen bonds : bond 0.04093 / 2.76 ( 862) hydrogen bonds : angle 4.39784 / 3.10 ( 2418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3021.36 seconds wall clock time: 53 minutes 15.81 seconds (3195.81 seconds total)