Starting phenix.real_space_refine on Thu Mar 5 10:16:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mcs_23757/03_2026/7mcs_23757.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mcs_23757/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mcs_23757/03_2026/7mcs_23757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mcs_23757/03_2026/7mcs_23757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mcs_23757/03_2026/7mcs_23757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mcs_23757/03_2026/7mcs_23757.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.95, per 1000 atoms: 0.23 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: 1.61 Conformation dependent library (CDL) restraints added in 969.6 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: 2.10 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: 2.97 Time building geometry restraints manager: 2.15 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: 11688 18.08 - 36.16: 1192 36.16 - 54.24: 304 54.24 - 72.32: 97 72.32 - 90.40: 47 Dihedral angle restraints: 13328 sinusoidal: 5762 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 13325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3092 0.084 - 0.167: 278 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: 1.860 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.760 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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= 0.268 Angle : 0.863 18.953 29998 Z= 0.418 Chirality : 0.048 0.418 3389 Planarity : 0.005 0.110 3747 Dihedral : 16.997 90.397 8456 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 covalent geometry : bond 0.00559 (22051) covalent geometry : angle 0.86347 (29998) hydrogen bonds : bond 0.20474 ( 862) hydrogen bonds : angle 6.78066 ( 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 : 0.800 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: 0.2034 time to fit residues: 142.6003 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 : 0.734 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 107 ASN 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 = 0.147415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119109 restraints weight = 32759.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118487 restraints weight = 32667.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119181 restraints weight = 34922.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119746 restraints weight = 27230.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119893 restraints weight = 24218.342| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22051 Z= 0.143 Angle : 0.616 8.757 29998 Z= 0.314 Chirality : 0.042 0.357 3389 Planarity : 0.005 0.052 3747 Dihedral : 13.362 59.294 3397 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 2.22 % Allowed : 9.16 % Favored : 88.62 % 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: -0.92 (0.16), residues: 2597 helix: -0.08 (0.15), residues: 1211 sheet: 0.12 (0.39), residues: 187 loop : -1.23 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 390 TYR 0.016 0.001 TYR G 375 PHE 0.022 0.001 PHE G 351 TRP 0.021 0.001 TRP G 316 HIS 0.018 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00322 (22051) covalent geometry : angle 0.61583 (29998) hydrogen bonds : bond 0.04347 ( 862) hydrogen bonds : angle 4.88216 ( 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 321 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 0.857 Fit side-chains REVERT: A 101 LEU cc_start: 0.7321 (mt) cc_final: 0.6975 (mp) REVERT: B 182 GLU cc_start: 0.5574 (mm-30) cc_final: 0.5349 (mm-30) REVERT: B 220 ILE cc_start: 0.8762 (mp) cc_final: 0.8429 (mp) REVERT: B 330 ASP cc_start: 0.6870 (p0) cc_final: 0.6589 (p0) REVERT: D 102 GLN cc_start: 0.6548 (OUTLIER) cc_final: 0.6121 (mm-40) REVERT: D 327 LEU cc_start: 0.8950 (pp) cc_final: 0.8509 (mt) REVERT: D 361 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7974 (mp) REVERT: E 248 MET cc_start: 0.7323 (ttt) cc_final: 0.7005 (ttt) REVERT: F 345 ASP cc_start: 0.7765 (t0) cc_final: 0.7455 (t0) REVERT: G 130 GLN cc_start: 0.1626 (mt0) cc_final: 0.0347 (mp10) REVERT: G 146 LEU cc_start: 0.8680 (tt) cc_final: 0.8390 (tt) REVERT: G 171 LYS cc_start: 0.7501 (pptt) cc_final: 0.6179 (mmmm) REVERT: G 181 LYS cc_start: 0.7065 (mptt) cc_final: 0.6830 (mptt) REVERT: G 248 MET cc_start: 0.7462 (tpt) cc_final: 0.7027 (tpt) REVERT: G 272 ARG cc_start: 0.6367 (mtm110) cc_final: 0.5665 (ptm160) outliers start: 50 outliers final: 29 residues processed: 306 average time/residue: 0.1624 time to fit residues: 75.1426 Evaluate side-chains 253 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 176 HIS Chi-restraints excluded: chain B residue 234 ILE 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 232 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 25 GLU 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 195 LEU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 184 CYS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 245 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 235 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 113 optimal weight: 0.0010 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS 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 E 297 GLN F 257 ASN F 355 GLN 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 = 0.3885 r_free = 0.3885 target = 0.146168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118001 restraints weight = 33040.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117227 restraints weight = 34422.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118159 restraints weight = 34738.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118467 restraints weight = 27069.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118612 restraints weight = 25402.556| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22051 Z= 0.135 Angle : 0.576 12.041 29998 Z= 0.291 Chirality : 0.041 0.288 3389 Planarity : 0.004 0.049 3747 Dihedral : 12.283 59.988 3397 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 2.31 % Allowed : 12.36 % Favored : 85.33 % 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: -0.71 (0.16), residues: 2597 helix: 0.15 (0.15), residues: 1217 sheet: -0.06 (0.38), residues: 197 loop : -1.15 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 390 TYR 0.017 0.001 TYR G 400 PHE 0.020 0.001 PHE G 351 TRP 0.013 0.001 TRP G 316 HIS 0.010 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00316 (22051) covalent geometry : angle 0.57552 (29998) hydrogen bonds : bond 0.03899 ( 862) hydrogen bonds : angle 4.56725 ( 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 289 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 0.780 Fit side-chains REVERT: A 101 LEU cc_start: 0.7318 (mt) cc_final: 0.6993 (mp) REVERT: B 220 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 330 ASP cc_start: 0.6947 (p0) cc_final: 0.6647 (p0) REVERT: C 164 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7811 (t) REVERT: D 327 LEU cc_start: 0.8911 (pp) cc_final: 0.8467 (mt) REVERT: F 213 MET cc_start: 0.7593 (mmt) cc_final: 0.7356 (mmt) REVERT: F 345 ASP cc_start: 0.7700 (t0) cc_final: 0.7475 (t0) REVERT: G 31 GLN cc_start: 0.4489 (pt0) cc_final: 0.4059 (mm-40) REVERT: G 130 GLN cc_start: 0.1983 (mt0) cc_final: 0.0490 (mp10) REVERT: G 146 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8102 (tt) REVERT: G 169 TYR cc_start: 0.8048 (p90) cc_final: 0.7688 (p90) REVERT: G 171 LYS cc_start: 0.7538 (pptt) cc_final: 0.6219 (mmmm) REVERT: G 248 MET cc_start: 0.7380 (tpt) cc_final: 0.7144 (tpt) outliers start: 52 outliers final: 35 residues processed: 268 average time/residue: 0.1695 time to fit residues: 68.2829 Evaluate side-chains 243 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 205 LEU 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 234 ILE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain D residue 68 ASP 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 273 GLU 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 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 F residue 334 ASP Chi-restraints excluded: chain G residue 12 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 99 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 236 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 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 = 0.3874 r_free = 0.3874 target = 0.145204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117173 restraints weight = 33001.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116443 restraints weight = 33609.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117308 restraints weight = 34630.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117610 restraints weight = 26178.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117685 restraints weight = 25335.202| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 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 = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22051 Z= 0.133 Angle : 0.548 9.937 29998 Z= 0.278 Chirality : 0.040 0.271 3389 Planarity : 0.004 0.048 3747 Dihedral : 11.758 59.509 3397 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 2.31 % Allowed : 14.36 % Favored : 83.33 % 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: 0.32 (0.15), residues: 1213 sheet: -0.01 (0.37), residues: 197 loop : -1.08 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 272 TYR 0.016 0.001 TYR D 400 PHE 0.017 0.001 PHE G 275 TRP 0.029 0.001 TRP F 308 HIS 0.010 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00314 (22051) covalent geometry : angle 0.54773 (29998) hydrogen bonds : bond 0.03621 ( 862) hydrogen bonds : angle 4.36839 ( 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 276 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 0.704 Fit side-chains REVERT: A 101 LEU cc_start: 0.7352 (mt) cc_final: 0.7072 (mp) REVERT: B 220 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8485 (mp) REVERT: B 330 ASP cc_start: 0.6827 (p0) cc_final: 0.6626 (p0) REVERT: C 164 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7850 (t) REVERT: D 327 LEU cc_start: 0.8948 (pp) cc_final: 0.8478 (mt) REVERT: D 361 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.7967 (mp) REVERT: F 210 ILE cc_start: 0.8174 (tt) cc_final: 0.7969 (tp) REVERT: F 241 ARG cc_start: 0.6615 (ptm-80) cc_final: 0.6405 (ptt90) REVERT: G 31 GLN cc_start: 0.4476 (pt0) cc_final: 0.3983 (mm-40) REVERT: G 51 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6176 (mp) REVERT: G 130 GLN cc_start: 0.2072 (mt0) cc_final: 0.0581 (mp10) REVERT: G 146 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8118 (mm) REVERT: G 169 TYR cc_start: 0.8060 (p90) cc_final: 0.7696 (p90) REVERT: G 171 LYS cc_start: 0.7555 (pptt) cc_final: 0.6255 (mmmm) REVERT: G 375 TYR cc_start: 0.8511 (t80) cc_final: 0.8060 (t80) outliers start: 52 outliers final: 35 residues processed: 261 average time/residue: 0.1568 time to fit residues: 62.3101 Evaluate side-chains 247 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 234 ILE Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL 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 382 VAL 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 222 ASN 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 12 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 128 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 238 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 257 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 176 HIS ** B 176 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 21 ASN ** 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 = 0.3842 r_free = 0.3842 target = 0.142650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114509 restraints weight = 33357.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112739 restraints weight = 40231.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113510 restraints weight = 37939.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114158 restraints weight = 29761.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114372 restraints weight = 26413.484| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22051 Z= 0.186 Angle : 0.611 10.971 29998 Z= 0.308 Chirality : 0.043 0.275 3389 Planarity : 0.004 0.049 3747 Dihedral : 11.703 59.050 3397 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 3.29 % Allowed : 15.11 % Favored : 81.60 % 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: -0.72 (0.16), residues: 2597 helix: 0.13 (0.15), residues: 1223 sheet: -0.07 (0.38), residues: 187 loop : -1.13 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 121 TYR 0.014 0.002 TYR E 153 PHE 0.018 0.002 PHE G 275 TRP 0.029 0.001 TRP G 316 HIS 0.011 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00451 (22051) covalent geometry : angle 0.61138 (29998) hydrogen bonds : bond 0.04205 ( 862) hydrogen bonds : angle 4.44502 ( 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 297 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 223 time to evaluate : 0.787 Fit side-chains REVERT: A 101 LEU cc_start: 0.7417 (mt) cc_final: 0.7117 (mp) REVERT: B 201 ARG cc_start: 0.7333 (mmp-170) cc_final: 0.6845 (mmp-170) REVERT: B 220 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8520 (mp) REVERT: C 164 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7715 (t) REVERT: D 327 LEU cc_start: 0.9009 (pp) cc_final: 0.8541 (mt) REVERT: F 241 ARG cc_start: 0.6731 (ptm-80) cc_final: 0.6518 (ptt90) REVERT: F 322 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: G 51 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6050 (mp) REVERT: G 146 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8189 (mm) REVERT: G 169 TYR cc_start: 0.8111 (p90) cc_final: 0.7710 (p90) REVERT: G 171 LYS cc_start: 0.7557 (pptt) cc_final: 0.6201 (mmmm) REVERT: G 356 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8181 (mt) outliers start: 74 outliers final: 49 residues processed: 274 average time/residue: 0.1636 time to fit residues: 67.1690 Evaluate side-chains 260 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 205 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 56 VAL 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 212 THR 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 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 332 VAL 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 36 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL 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 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 222 ASN Chi-restraints excluded: chain E residue 331 GLU 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 12 ASP 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 206 LYS Chi-restraints excluded: chain G residue 225 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 170 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 176 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 300 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN F 104 HIS ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116190 restraints weight = 33023.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115405 restraints weight = 34563.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116187 restraints weight = 35603.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116622 restraints weight = 26813.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116756 restraints weight = 24453.145| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 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 = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22051 Z= 0.123 Angle : 0.544 11.705 29998 Z= 0.276 Chirality : 0.040 0.257 3389 Planarity : 0.004 0.047 3747 Dihedral : 11.551 58.984 3397 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 2.71 % Allowed : 16.67 % Favored : 80.62 % 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: -0.50 (0.16), residues: 2597 helix: 0.31 (0.15), residues: 1235 sheet: 0.15 (0.39), residues: 181 loop : -1.05 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 272 TYR 0.014 0.001 TYR F 10 PHE 0.013 0.001 PHE G 275 TRP 0.036 0.001 TRP F 308 HIS 0.011 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00288 (22051) covalent geometry : angle 0.54350 (29998) hydrogen bonds : bond 0.03481 ( 862) hydrogen bonds : angle 4.26788 ( 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 277 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 0.815 Fit side-chains REVERT: A 101 LEU cc_start: 0.7406 (mt) cc_final: 0.7099 (mp) REVERT: A 199 TYR cc_start: 0.7108 (m-80) cc_final: 0.6899 (m-80) REVERT: B 201 ARG cc_start: 0.7223 (mmp-170) cc_final: 0.6807 (mmp-170) REVERT: B 220 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8496 (mp) REVERT: B 330 ASP cc_start: 0.6789 (p0) cc_final: 0.6363 (m-30) REVERT: B 336 TRP cc_start: 0.8726 (t60) cc_final: 0.8514 (t60) REVERT: C 164 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7731 (t) REVERT: D 327 LEU cc_start: 0.8979 (pp) cc_final: 0.8503 (mt) REVERT: E 211 GLU cc_start: 0.8127 (mp0) cc_final: 0.7861 (mp0) REVERT: G 51 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.5890 (mp) REVERT: G 86 MET cc_start: 0.7724 (mpp) cc_final: 0.7462 (mpp) REVERT: G 146 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8092 (mm) REVERT: G 169 TYR cc_start: 0.8092 (p90) cc_final: 0.7670 (p90) REVERT: G 171 LYS cc_start: 0.7587 (pptt) cc_final: 0.6235 (mmmm) REVERT: G 248 MET cc_start: 0.6976 (tpt) cc_final: 0.6572 (tpt) REVERT: G 375 TYR cc_start: 0.8535 (t80) cc_final: 0.8133 (t80) outliers start: 61 outliers final: 41 residues processed: 255 average time/residue: 0.1683 time to fit residues: 64.7976 Evaluate side-chains 245 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 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 234 ILE Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain C residue 288 PHE 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 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 256 VAL Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 133 LEU 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 G residue 12 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 1 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 254 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 107 optimal weight: 0.0370 chunk 215 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 overall best weight: 3.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN 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 = 0.3817 r_free = 0.3817 target = 0.141043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111273 restraints weight = 33282.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111348 restraints weight = 29854.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112061 restraints weight = 27716.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112456 restraints weight = 22249.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112577 restraints weight = 20821.661| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 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 = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22051 Z= 0.190 Angle : 0.627 12.392 29998 Z= 0.315 Chirality : 0.043 0.283 3389 Planarity : 0.005 0.047 3747 Dihedral : 11.586 59.761 3397 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 3.29 % Allowed : 16.84 % Favored : 79.87 % 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: -0.77 (0.16), residues: 2597 helix: 0.04 (0.15), residues: 1253 sheet: -0.04 (0.38), residues: 179 loop : -1.13 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 201 TYR 0.018 0.002 TYR F 10 PHE 0.020 0.002 PHE G 251 TRP 0.025 0.001 TRP F 308 HIS 0.010 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00458 (22051) covalent geometry : angle 0.62676 (29998) hydrogen bonds : bond 0.04298 ( 862) hydrogen bonds : angle 4.43507 ( 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 287 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 213 time to evaluate : 0.817 Fit side-chains REVERT: A 101 LEU cc_start: 0.7440 (mt) cc_final: 0.7229 (mp) REVERT: A 105 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7660 (mt) REVERT: B 201 ARG cc_start: 0.7186 (mmp-170) cc_final: 0.6786 (mmp-170) REVERT: B 220 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8480 (mp) REVERT: B 330 ASP cc_start: 0.6842 (p0) cc_final: 0.6324 (m-30) REVERT: D 327 LEU cc_start: 0.9004 (pp) cc_final: 0.8552 (mt) REVERT: D 361 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7870 (mp) REVERT: E 101 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6576 (pp) REVERT: F 322 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7896 (mm110) REVERT: G 51 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.5950 (mp) REVERT: G 86 MET cc_start: 0.7700 (mpp) cc_final: 0.7334 (mpp) REVERT: G 146 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8202 (mm) REVERT: G 169 TYR cc_start: 0.8193 (p90) cc_final: 0.7712 (p90) REVERT: G 171 LYS cc_start: 0.7650 (pptt) cc_final: 0.6209 (mmmm) REVERT: G 355 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.6892 (mp10) REVERT: G 400 TYR cc_start: 0.7172 (m-80) cc_final: 0.6797 (m-10) outliers start: 74 outliers final: 54 residues processed: 268 average time/residue: 0.1661 time to fit residues: 67.2351 Evaluate side-chains 260 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 208 HIS 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 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 157 ILE 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 C residue 405 VAL Chi-restraints excluded: chain D residue 36 SER 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 147 HIS Chi-restraints excluded: chain D residue 156 VAL 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 361 LEU 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 101 LEU 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 256 VAL Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 133 LEU 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 12 ASP 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 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 Chi-restraints excluded: chain G residue 355 GLN 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: 10.0000 chunk 44 optimal weight: 0.9980 chunk 236 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 160 optimal weight: 0.0040 chunk 258 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 176 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113127 restraints weight = 32930.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.113295 restraints weight = 30946.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114136 restraints weight = 27160.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114511 restraints weight = 22242.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114654 restraints weight = 20122.940| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22051 Z= 0.122 Angle : 0.551 12.926 29998 Z= 0.279 Chirality : 0.040 0.272 3389 Planarity : 0.004 0.053 3747 Dihedral : 11.435 59.784 3397 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 2.93 % Allowed : 17.87 % Favored : 79.20 % 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: -0.45 (0.16), residues: 2597 helix: 0.31 (0.15), residues: 1247 sheet: 0.06 (0.38), residues: 181 loop : -0.96 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 272 TYR 0.016 0.001 TYR F 10 PHE 0.016 0.001 PHE G 351 TRP 0.053 0.001 TRP F 308 HIS 0.011 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00288 (22051) covalent geometry : angle 0.55092 (29998) hydrogen bonds : bond 0.03425 ( 862) hydrogen bonds : angle 4.22754 ( 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 280 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7427 (mt) cc_final: 0.7080 (mp) REVERT: A 199 TYR cc_start: 0.7196 (m-80) cc_final: 0.6890 (m-80) REVERT: B 201 ARG cc_start: 0.7069 (mmp-170) cc_final: 0.6722 (mmp-170) REVERT: B 220 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8419 (mp) REVERT: B 330 ASP cc_start: 0.6796 (p0) cc_final: 0.6363 (m-30) REVERT: D 327 LEU cc_start: 0.8994 (pp) cc_final: 0.8514 (mt) REVERT: D 361 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7777 (mp) REVERT: G 86 MET cc_start: 0.7914 (mpp) cc_final: 0.7465 (mpp) REVERT: G 169 TYR cc_start: 0.8182 (p90) cc_final: 0.7624 (p90) REVERT: G 171 LYS cc_start: 0.7678 (pptt) cc_final: 0.6205 (mmmm) REVERT: G 272 ARG cc_start: 0.5944 (mtm180) cc_final: 0.5646 (mpp80) REVERT: G 351 PHE cc_start: 0.8431 (t80) cc_final: 0.8164 (t80) REVERT: G 400 TYR cc_start: 0.7179 (m-80) cc_final: 0.6811 (m-10) outliers start: 66 outliers final: 48 residues processed: 263 average time/residue: 0.1584 time to fit residues: 63.4357 Evaluate side-chains 248 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 332 VAL Chi-restraints excluded: chain C residue 344 MET 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 132 LEU Chi-restraints excluded: chain D residue 156 VAL 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 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 256 VAL Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain F residue 133 LEU 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 G residue 12 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 191 LEU 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 355 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 119 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 104 HIS G 166 GLN ** 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 = 0.3856 r_free = 0.3856 target = 0.144231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114660 restraints weight = 33021.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114753 restraints weight = 29153.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115445 restraints weight = 27059.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115920 restraints weight = 21839.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.116058 restraints weight = 20371.530| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 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 = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22051 Z= 0.110 Angle : 0.538 11.977 29998 Z= 0.272 Chirality : 0.040 0.233 3389 Planarity : 0.004 0.051 3747 Dihedral : 11.330 59.852 3397 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 2.58 % Allowed : 18.18 % 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: -0.32 (0.16), residues: 2597 helix: 0.46 (0.15), residues: 1247 sheet: 0.12 (0.38), residues: 181 loop : -0.95 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 272 TYR 0.015 0.001 TYR G 337 PHE 0.020 0.001 PHE G 251 TRP 0.045 0.001 TRP F 308 HIS 0.011 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00254 (22051) covalent geometry : angle 0.53794 (29998) hydrogen bonds : bond 0.03231 ( 862) hydrogen bonds : angle 4.12557 ( 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 271 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7340 (mt) cc_final: 0.7005 (mp) REVERT: A 199 TYR cc_start: 0.7229 (m-80) cc_final: 0.6971 (m-80) REVERT: B 201 ARG cc_start: 0.7151 (mmp-170) cc_final: 0.6798 (mmp-170) REVERT: B 220 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8447 (mp) REVERT: B 330 ASP cc_start: 0.6672 (p0) cc_final: 0.6427 (m-30) REVERT: D 62 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8160 (mt) REVERT: D 361 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7818 (mp) REVERT: G 53 LYS cc_start: 0.6306 (ttpp) cc_final: 0.5925 (ttpt) REVERT: G 86 MET cc_start: 0.7905 (mpp) cc_final: 0.7463 (mpp) REVERT: G 169 TYR cc_start: 0.8143 (p90) cc_final: 0.7636 (p90) REVERT: G 171 LYS cc_start: 0.7631 (pptt) cc_final: 0.6186 (mmmm) REVERT: G 272 ARG cc_start: 0.5803 (mtm180) cc_final: 0.5489 (mpp80) REVERT: G 375 TYR cc_start: 0.8411 (t80) cc_final: 0.7969 (t80) REVERT: G 400 TYR cc_start: 0.7167 (m-80) cc_final: 0.6749 (m-10) outliers start: 58 outliers final: 46 residues processed: 254 average time/residue: 0.1605 time to fit residues: 61.6316 Evaluate side-chains 255 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 332 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 62 ILE 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 156 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 361 LEU 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 256 VAL Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 157 ILE 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 12 ASP Chi-restraints excluded: chain G residue 191 LEU 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 355 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 55 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 63 optimal weight: 0.0770 chunk 19 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 overall best weight: 3.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 176 HIS B 113 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS G 166 GLN G 355 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110833 restraints weight = 32843.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111394 restraints weight = 28718.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111613 restraints weight = 26111.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112280 restraints weight = 21843.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112298 restraints weight = 20087.442| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 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 = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22051 Z= 0.187 Angle : 0.626 12.446 29998 Z= 0.315 Chirality : 0.043 0.284 3389 Planarity : 0.004 0.054 3747 Dihedral : 11.441 59.741 3397 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 2.62 % Allowed : 18.53 % Favored : 78.84 % 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: 0.16 (0.15), residues: 1260 sheet: 0.03 (0.38), residues: 181 loop : -1.03 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 272 TYR 0.017 0.002 TYR D 400 PHE 0.019 0.002 PHE G 351 TRP 0.054 0.002 TRP F 308 HIS 0.011 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00456 (22051) covalent geometry : angle 0.62559 (29998) hydrogen bonds : bond 0.04173 ( 862) hydrogen bonds : angle 4.35912 ( 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 268 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 209 time to evaluate : 0.683 Fit side-chains REVERT: A 101 LEU cc_start: 0.7393 (mt) cc_final: 0.7167 (mp) REVERT: A 105 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7591 (mt) REVERT: A 199 TYR cc_start: 0.7269 (m-80) cc_final: 0.7022 (m-80) REVERT: B 201 ARG cc_start: 0.7117 (mmp-170) cc_final: 0.6769 (mmp-170) REVERT: B 220 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8449 (mp) REVERT: F 255 MET cc_start: 0.8956 (ttm) cc_final: 0.8685 (ttm) REVERT: G 53 LYS cc_start: 0.6388 (ttpp) cc_final: 0.6073 (ttpt) REVERT: G 86 MET cc_start: 0.7945 (mpp) cc_final: 0.7508 (mpp) REVERT: G 171 LYS cc_start: 0.7630 (pptt) cc_final: 0.6204 (mmmm) REVERT: G 272 ARG cc_start: 0.5581 (mtm180) cc_final: 0.5200 (mpp80) REVERT: G 351 PHE cc_start: 0.8244 (t80) cc_final: 0.8021 (t80) REVERT: G 355 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: G 400 TYR cc_start: 0.7210 (m-80) cc_final: 0.6795 (m-10) outliers start: 59 outliers final: 47 residues processed: 251 average time/residue: 0.1705 time to fit residues: 63.8040 Evaluate side-chains 250 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 208 HIS 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 21 ASN 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 164 VAL 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 D residue 36 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 213 MET 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 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 256 VAL Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 157 ILE 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 12 ASP Chi-restraints excluded: chain G residue 85 VAL 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 265 LEU Chi-restraints excluded: chain G residue 355 GLN 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: 0.2980 chunk 108 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112044 restraints weight = 33268.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112379 restraints weight = 29997.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112630 restraints weight = 27653.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.113285 restraints weight = 23465.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.113301 restraints weight = 21848.698| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 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 = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22051 Z= 0.155 Angle : 0.594 12.888 29998 Z= 0.301 Chirality : 0.042 0.266 3389 Planarity : 0.004 0.050 3747 Dihedral : 11.410 59.630 3397 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 2.49 % Allowed : 18.89 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.16), residues: 2597 helix: 0.28 (0.15), residues: 1246 sheet: 0.04 (0.38), residues: 181 loop : -0.98 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 201 TYR 0.013 0.001 TYR D 400 PHE 0.024 0.002 PHE G 351 TRP 0.074 0.002 TRP F 308 HIS 0.011 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00374 (22051) covalent geometry : angle 0.59444 (29998) hydrogen bonds : bond 0.03820 ( 862) hydrogen bonds : angle 4.30798 ( 2418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2989.99 seconds wall clock time: 52 minutes 28.46 seconds (3148.46 seconds total)