Starting phenix.real_space_refine on Sun Sep 13 06:25:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mcs_23757/09_2026/7mcs_23757.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mcs_23757/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mcs_23757/09_2026/7mcs_23757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mcs_23757/09_2026/7mcs_23757.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mcs_23757/09_2026/7mcs_23757.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mcs_23757/09_2026/7mcs_23757.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mcs_23757/09_2026/7mcs_23757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mcs_23757/09_2026/7mcs_23757.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 6 5.21 5 S 81 5.16 5 C 13494 2.51 5 N 3913 2.21 5 O 4058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21600 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1967 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3196 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 386} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3208 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 388} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3201 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 388} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3196 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 387} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3183 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 386} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2842 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 342} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.11, per 1000 atoms: 0.19 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: 1.45 Conformation dependent library (CDL) restraints added in 788.3 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: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 76 through 93 removed outlier: 3.654A pdb=" N GLY A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.635A pdb=" N HIS A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 removed outlier: 3.518A pdb=" N SER A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 195 removed outlier: 4.407A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 211 through 224 removed outlier: 3.616A pdb=" N ALA A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.241A pdb=" N SER A 240 " --> pdb=" O HIS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.840A pdb=" N ARG A 272 " --> pdb=" O PRO A 269 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 273 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.599A pdb=" N GLN B 52 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 75 through 91 removed outlier: 3.604A pdb=" N GLU B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 143 through 151 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.908A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.716A pdb=" N ALA B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.851A pdb=" N HIS B 236 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 256 removed outlier: 3.505A pdb=" N GLU B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 4.173A pdb=" N GLU B 273 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 305 through 317 removed outlier: 3.581A pdb=" N ILE B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 317 " --> pdb=" O ASP B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.709A pdb=" N GLY B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 382 through 392 removed outlier: 3.615A pdb=" N LEU B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU B 389 " --> pdb=" O MET B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.654A pdb=" N LEU C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 52' Processing helix chain 'C' and resid 54 through 63 Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 75 through 91 removed outlier: 4.037A pdb=" N GLU C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR C 91 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.907A pdb=" N HIS C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 179 through 195 removed outlier: 3.968A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 210 through 224 removed outlier: 4.369A pdb=" N LEU C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 245 through 258 Processing helix chain 'C' and resid 268 through 272 removed outlier: 3.629A pdb=" N ARG C 272 " --> pdb=" O PRO C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 305 through 317 Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.837A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 362 removed outlier: 3.555A pdb=" N VAL C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 348 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.787A pdb=" N LEU C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP C 377 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C 379 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.900A pdb=" N LEU C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.544A pdb=" N SER D 39 " --> pdb=" O ASN D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.730A pdb=" N LEU D 51 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 63 Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 75 through 90 removed outlier: 4.170A pdb=" N LEU D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY D 90 " --> pdb=" O MET D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.962A pdb=" N ASN D 95 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.831A pdb=" N LEU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 150 Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 179 through 195 removed outlier: 3.766A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.687A pdb=" N ARG D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU D 205 " --> pdb=" O ARG D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.675A pdb=" N ALA D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 244 through 258 removed outlier: 3.687A pdb=" N MET D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 274 removed outlier: 3.966A pdb=" N GLU D 273 " --> pdb=" O LYS D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 286 removed outlier: 3.518A pdb=" N ALA D 282 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 removed outlier: 3.511A pdb=" N ILE D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.524A pdb=" N LEU D 339 " --> pdb=" O VAL D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 362 removed outlier: 3.812A pdb=" N VAL D 348 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 378 Processing helix chain 'D' and resid 382 through 392 removed outlier: 3.522A pdb=" N GLY D 392 " --> pdb=" O ALA D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 398 removed outlier: 3.596A pdb=" N ILE D 397 " --> pdb=" O ILE D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 26 removed outlier: 3.656A pdb=" N GLU E 25 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 21 through 26' Processing helix chain 'E' and resid 32 through 38 removed outlier: 4.009A pdb=" N ALA E 37 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 38 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' Processing helix chain 'E' and resid 47 through 52 removed outlier: 3.606A pdb=" N LEU E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 64 through 69 Processing helix chain 'E' and resid 75 through 90 removed outlier: 3.871A pdb=" N LEU E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 114 removed outlier: 3.555A pdb=" N LEU E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 151 Processing helix chain 'E' and resid 179 through 195 removed outlier: 4.113A pdb=" N ILE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'E' and resid 209 through 224 removed outlier: 4.091A pdb=" N ALA E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 239 removed outlier: 3.828A pdb=" N HIS E 236 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER E 238 " --> pdb=" O GLN E 235 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG E 239 " --> pdb=" O HIS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 258 removed outlier: 3.695A pdb=" N PHE E 251 " --> pdb=" O GLU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 removed outlier: 3.705A pdb=" N ARG E 272 " --> pdb=" O PRO E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 286 removed outlier: 3.602A pdb=" N ALA E 282 " --> pdb=" O ASP E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 317 removed outlier: 3.502A pdb=" N ILE E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN E 317 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 343 through 362 Processing helix chain 'E' and resid 367 through 379 removed outlier: 3.568A pdb=" N GLN E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 379 " --> pdb=" O TYR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 391 removed outlier: 3.645A pdb=" N LEU E 386 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER E 391 " --> pdb=" O GLU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 398 removed outlier: 3.602A pdb=" N ALA E 398 " --> pdb=" O PRO E 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 32 through 38 Processing helix chain 'F' and resid 47 through 52 removed outlier: 3.815A pdb=" N LEU F 51 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN F 52 " --> pdb=" O SER F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 52' Processing helix chain 'F' and resid 54 through 62 removed outlier: 3.793A pdb=" N ILE F 62 " --> pdb=" O ARG F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 75 through 91 removed outlier: 3.510A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY F 90 " --> pdb=" O MET F 86 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR F 91 " --> pdb=" O ILE F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 95 removed outlier: 3.666A pdb=" N ASN F 95 " --> pdb=" O VAL F 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 95' Processing helix chain 'F' and resid 100 through 114 removed outlier: 4.429A pdb=" N HIS F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN F 113 " --> pdb=" O TYR F 109 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'F' and resid 181 through 195 removed outlier: 3.793A pdb=" N PHE F 188 " --> pdb=" O CYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 224 removed outlier: 3.632A pdb=" N ALA F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER F 218 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 removed outlier: 3.563A pdb=" N LEU F 237 " --> pdb=" O ILE F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 258 Processing helix chain 'F' and resid 268 through 276 removed outlier: 4.097A pdb=" N GLU F 273 " --> pdb=" O LYS F 270 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE F 274 " --> pdb=" O ALA F 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 276 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 286 removed outlier: 3.878A pdb=" N ALA F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 318 removed outlier: 3.630A pdb=" N GLN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 341 removed outlier: 3.741A pdb=" N GLU F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 360 removed outlier: 3.557A pdb=" N VAL F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 379 removed outlier: 3.565A pdb=" N LEU F 379 " --> pdb=" O TYR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 392 removed outlier: 3.565A pdb=" N GLY F 392 " --> pdb=" O ALA F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 400 removed outlier: 4.493A pdb=" N TYR F 400 " --> pdb=" O ARG F 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 41 Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 54 through 64 removed outlier: 3.631A pdb=" N ARG G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 93 removed outlier: 3.846A pdb=" N LEU G 79 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG G 88 " --> pdb=" O SER G 84 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR G 91 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY G 93 " --> pdb=" O GLY G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 151 removed outlier: 3.917A pdb=" N LEU G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 195 removed outlier: 4.044A pdb=" N ILE G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE G 187 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE G 188 " --> pdb=" O CYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 203 removed outlier: 3.723A pdb=" N ARG G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 224 removed outlier: 3.582A pdb=" N HIS G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 259 removed outlier: 3.506A pdb=" N PHE G 251 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE G 252 " --> pdb=" O MET G 248 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE G 259 " --> pdb=" O MET G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 274 removed outlier: 4.243A pdb=" N GLU G 273 " --> pdb=" O LYS G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 317 removed outlier: 4.087A pdb=" N ILE G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 341 removed outlier: 3.710A pdb=" N TRP G 336 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR G 337 " --> pdb=" O ARG G 333 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU G 338 " --> pdb=" O ASP G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 362 removed outlier: 3.674A pdb=" N VAL G 347 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL G 348 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY G 362 " --> pdb=" O ALA G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 379 removed outlier: 3.535A pdb=" N LEU G 379 " --> pdb=" O TYR G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 392 removed outlier: 3.609A pdb=" N ALA G 388 " --> pdb=" O PRO G 384 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY G 392 " --> pdb=" O ALA G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 398 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 6.424A pdb=" N ILE A 6 " --> pdb=" O TYR A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173 removed outlier: 3.837A pdb=" N ASP A 232 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 229 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 266 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 231 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A 134 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 133 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.425A pdb=" N LEU B 229 " --> pdb=" O MET B 264 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE B 266 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 231 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 133 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TRP B 293 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 135 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.554A pdb=" N HIS B 159 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 164 " --> pdb=" O HIS B 159 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 225 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 167 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 167 through 173 removed outlier: 6.950A pdb=" N VAL C 168 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU C 132 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N GLY C 267 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU C 134 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ILE C 291 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU C 133 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N TRP C 293 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 135 " --> pdb=" O TRP C 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 170 through 173 Processing sheet with id=AA7, first strand: chain 'D' and resid 156 through 159 removed outlier: 3.846A pdb=" N VAL D 164 " --> pdb=" O HIS D 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 6 through 7 removed outlier: 6.335A pdb=" N ILE E 6 " --> pdb=" O TYR E 158 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 164 " --> pdb=" O HIS E 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 170 through 173 removed outlier: 6.715A pdb=" N LEU E 229 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE E 266 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE E 231 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ILE E 291 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU E 133 " --> pdb=" O ILE E 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 6 through 7 removed outlier: 6.644A pdb=" N ILE F 6 " --> pdb=" O TYR F 158 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL F 164 " --> pdb=" O HIS F 159 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N LEU F 226 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N GLN F 166 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N LEU F 228 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL F 168 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL F 230 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU F 170 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ASP F 232 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE F 172 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N MET F 264 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU F 229 " --> pdb=" O MET F 264 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE F 266 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE F 231 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ILE F 291 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU F 133 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 264 through 267 removed outlier: 7.327A pdb=" N LEU G 132 " --> pdb=" O LEU G 265 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY G 267 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU G 134 " --> pdb=" O GLY G 267 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N TRP G 293 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE G 135 " --> pdb=" O TRP G 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 170 through 173 removed outlier: 6.120A pdb=" N LEU G 170 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP G 232 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE G 172 " --> pdb=" O ASP G 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 817 hydrogen bonds defined for protein. 2328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3868 1.32 - 1.45: 5625 1.45 - 1.57: 12328 1.57 - 1.70: 95 1.70 - 1.82: 135 Bond restraints: 22051 Sorted by residual: bond pdb=" O3A ANP E 601 " pdb=" PB ANP E 601 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" O3A ANP F 601 " pdb=" PB ANP F 601 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" O3A ANP B 601 " pdb=" PB ANP B 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP D 601 " pdb=" PB ANP D 601 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" O3A ANP C 601 " pdb=" PB ANP C 601 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.08e+01 ... (remaining 22046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 29749 3.79 - 7.58: 205 7.58 - 11.37: 36 11.37 - 15.16: 2 15.16 - 18.95: 6 Bond angle restraints: 29998 Sorted by residual: angle pdb=" CA PRO G 22 " pdb=" N PRO G 22 " pdb=" CD PRO G 22 " ideal model delta sigma weight residual 112.00 99.75 12.25 1.40e+00 5.10e-01 7.65e+01 angle pdb=" PB ANP G 601 " pdb=" N3B ANP G 601 " pdb=" PG ANP G 601 " ideal model delta sigma weight residual 126.95 108.00 18.95 3.00e+00 1.11e-01 3.99e+01 angle pdb=" PB ANP E 601 " pdb=" N3B ANP E 601 " pdb=" PG ANP E 601 " ideal model delta sigma weight residual 126.95 108.21 18.74 3.00e+00 1.11e-01 3.90e+01 angle pdb=" PB ANP C 601 " pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 126.95 108.44 18.51 3.00e+00 1.11e-01 3.81e+01 angle pdb=" PB ANP D 601 " pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 126.95 108.49 18.46 3.00e+00 1.11e-01 3.79e+01 ... (remaining 29993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 11631 18.08 - 36.16: 1158 36.16 - 54.24: 283 54.24 - 72.32: 65 72.32 - 90.40: 23 Dihedral angle restraints: 13160 sinusoidal: 5594 harmonic: 7566 Sorted by residual: dihedral pdb=" CA HIS D 147 " pdb=" C HIS D 147 " pdb=" N ARG D 148 " pdb=" CA ARG D 148 " ideal model delta harmonic sigma weight residual 180.00 154.43 25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" C HIS C 224 " pdb=" N HIS C 224 " pdb=" CA HIS C 224 " pdb=" CB HIS C 224 " ideal model delta harmonic sigma weight residual -122.60 -109.95 -12.65 0 2.50e+00 1.60e-01 2.56e+01 dihedral pdb=" CA PRO C 269 " pdb=" C PRO C 269 " pdb=" N LYS C 270 " pdb=" CA LYS C 270 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 13157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3086 0.084 - 0.167: 284 0.167 - 0.251: 10 0.251 - 0.334: 8 0.334 - 0.418: 1 Chirality restraints: 3389 Sorted by residual: chirality pdb=" CA HIS C 224 " pdb=" N HIS C 224 " pdb=" C HIS C 224 " pdb=" CB HIS C 224 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C3' ANP C 601 " pdb=" C2' ANP C 601 " pdb=" C4' ANP C 601 " pdb=" O3' ANP C 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C3' ANP F 601 " pdb=" C2' ANP F 601 " pdb=" C4' ANP F 601 " pdb=" O3' ANP F 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 3386 not shown) Planarity restraints: 3747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 21 " 0.079 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO G 22 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO G 22 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO G 22 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 261 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO F 262 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO F 262 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 262 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 95 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO G 96 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 96 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 96 " -0.033 5.00e-02 4.00e+02 ... (remaining 3744 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 138 2.58 - 3.16: 16889 3.16 - 3.74: 32198 3.74 - 4.32: 44203 4.32 - 4.90: 73858 Nonbonded interactions: 167286 Sorted by model distance: nonbonded pdb=" OG1 THR D 143 " pdb="MG MG D 602 " model vdw 1.994 2.170 nonbonded pdb=" OG1 THR B 143 " pdb="MG MG B 602 " model vdw 2.031 2.170 nonbonded pdb=" OG1 THR G 143 " pdb="MG MG G 602 " model vdw 2.033 2.170 nonbonded pdb=" O1G ANP B 601 " pdb="MG MG B 602 " model vdw 2.061 2.170 nonbonded pdb=" O3G ANP D 601 " pdb="MG MG D 602 " model vdw 2.094 2.170 ... (remaining 167281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 405 or resid 601 through 602)) selection = (chain 'C' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 405 or resid 601 through 602)) selection = (chain 'D' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 602)) selection = (chain 'E' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 602)) selection = (chain 'F' and (resid 5 through 98 or resid 129 through 238 or resid 245 through \ 277 or resid 289 through 602)) selection = (chain 'G' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 405 or resid 601 through 602)) } ncs_group { reference = (chain 'H' and resid 1 through 14) selection = (chain 'I' and resid 2 through 15) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.61 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.950 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.150 22051 Z= 0.295 Angle : 0.870 18.953 29998 Z= 0.436 Chirality : 0.049 0.418 3389 Planarity : 0.005 0.110 3747 Dihedral : 15.873 90.397 8288 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.65 % Rotamer: Outliers : 0.04 % Allowed : 0.53 % Favored : 99.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 2597 helix: -0.58 (0.15), residues: 1180 sheet: 0.22 (0.40), residues: 184 loop : -1.37 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 111 TYR 0.015 0.001 TYR A 199 PHE 0.016 0.002 PHE D 288 TRP 0.020 0.001 TRP G 316 HIS 0.009 0.001 HIS G 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.30 (22051) covalent geometry : angle 0.87028 / 0.44 (29998) hydrogen bonds : bond 0.20474 / 13.90 ( 862) hydrogen bonds : angle 6.78066 / 4.76 ( 2418) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 501 time to evaluate : 0.804 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: 0.1948 time to fit residues: 137.6945 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 : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 258 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS B 60 HIS B 355 GLN ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119287 restraints weight = 32655.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118670 restraints weight = 33057.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119440 restraints weight = 34418.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119863 restraints weight = 26631.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120005 restraints weight = 23589.176| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 22051 Z= 0.149 Angle : 0.638 9.657 29998 Z= 0.327 Chirality : 0.043 0.357 3389 Planarity : 0.005 0.051 3747 Dihedral : 11.888 59.243 3229 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 2.09 % Allowed : 8.98 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2597 helix: -0.15 (0.15), residues: 1218 sheet: 0.14 (0.38), residues: 188 loop : -1.30 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 390 TYR 0.018 0.002 TYR G 375 PHE 0.020 0.002 PHE G 351 TRP 0.023 0.001 TRP G 316 HIS 0.022 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (22051) covalent geometry : angle 0.63757 / 0.33 (29998) hydrogen bonds : bond 0.04995 / 3.39 ( 862) hydrogen bonds : angle 5.05505 / 3.56 ( 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 317 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 270 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7297 (mt) cc_final: 0.7009 (mp) REVERT: B 220 ILE cc_start: 0.8747 (mp) cc_final: 0.8443 (mp) REVERT: B 330 ASP cc_start: 0.6780 (p0) cc_final: 0.6563 (p0) REVERT: D 327 LEU cc_start: 0.8934 (pp) cc_final: 0.8675 (mt) REVERT: D 361 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7928 (mp) REVERT: G 130 GLN cc_start: 0.1656 (mt0) cc_final: 0.0678 (mp10) REVERT: G 171 LYS cc_start: 0.7482 (pptt) cc_final: 0.6048 (mmmm) REVERT: G 248 MET cc_start: 0.7473 (tpt) cc_final: 0.7043 (tpt) outliers start: 47 outliers final: 29 residues processed: 300 average time/residue: 0.1540 time to fit residues: 70.1640 Evaluate side-chains 255 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 205 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 180 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 184 CYS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 206 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 235 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 85 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 249 optimal weight: 0.0770 chunk 156 optimal weight: 9.9990 chunk 113 optimal weight: 0.0070 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 HIS D 250 ASN E 35 ASN E 222 ASN F 257 ASN G 355 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.149495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121487 restraints weight = 32690.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120845 restraints weight = 33106.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121761 restraints weight = 34784.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122180 restraints weight = 25353.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.122308 restraints weight = 23735.157| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22051 Z= 0.108 Angle : 0.552 12.408 29998 Z= 0.284 Chirality : 0.040 0.306 3389 Planarity : 0.004 0.048 3747 Dihedral : 11.776 59.633 3229 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 2.04 % Allowed : 11.38 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2597 helix: 0.21 (0.15), residues: 1218 sheet: -0.05 (0.38), residues: 188 loop : -1.13 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 399 TYR 0.014 0.001 TYR G 400 PHE 0.025 0.001 PHE G 187 TRP 0.013 0.001 TRP G 316 HIS 0.011 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (22051) covalent geometry : angle 0.55165 / 0.28 (29998) hydrogen bonds : bond 0.03781 / 2.56 ( 862) hydrogen bonds : angle 4.62295 / 3.25 ( 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 294 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7323 (mt) cc_final: 0.7045 (mp) REVERT: B 220 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8444 (mp) REVERT: B 330 ASP cc_start: 0.6866 (p0) cc_final: 0.6600 (p0) REVERT: D 327 LEU cc_start: 0.8944 (pp) cc_final: 0.8558 (mt) REVERT: D 361 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7912 (mp) REVERT: G 31 GLN cc_start: 0.4397 (pt0) cc_final: 0.4045 (mm-40) REVERT: G 130 GLN cc_start: 0.1744 (mt0) cc_final: 0.0399 (mp10) REVERT: G 146 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8079 (tt) REVERT: G 169 TYR cc_start: 0.7987 (p90) cc_final: 0.7594 (p90) REVERT: G 171 LYS cc_start: 0.7511 (pptt) cc_final: 0.6171 (mmmm) REVERT: G 180 LEU cc_start: 0.7050 (mm) cc_final: 0.6203 (tp) outliers start: 46 outliers final: 28 residues processed: 274 average time/residue: 0.1580 time to fit residues: 65.4550 Evaluate side-chains 239 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 334 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 99 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 252 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 236 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 GLN F 198 ASN G 21 ASN G 355 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115505 restraints weight = 33148.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114605 restraints weight = 35508.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115540 restraints weight = 36055.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115923 restraints weight = 27129.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115984 restraints weight = 24952.088| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 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 = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22051 Z= 0.184 Angle : 0.631 9.214 29998 Z= 0.318 Chirality : 0.044 0.309 3389 Planarity : 0.005 0.048 3747 Dihedral : 11.827 59.620 3229 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 2.31 % Allowed : 14.80 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.16), residues: 2597 helix: 0.12 (0.15), residues: 1218 sheet: -0.18 (0.38), residues: 188 loop : -1.15 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 82 TYR 0.015 0.002 TYR E 153 PHE 0.019 0.002 PHE G 351 TRP 0.033 0.002 TRP F 308 HIS 0.009 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (22051) covalent geometry : angle 0.63118 / 0.32 (29998) hydrogen bonds : bond 0.04457 / 3.01 ( 862) hydrogen bonds : angle 4.59973 / 3.23 ( 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 : 0.776 Fit side-chains REVERT: A 101 LEU cc_start: 0.7327 (mt) cc_final: 0.7012 (mp) REVERT: B 220 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8476 (mp) REVERT: B 330 ASP cc_start: 0.7021 (p0) cc_final: 0.6731 (p0) REVERT: D 182 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6811 (tp30) REVERT: D 327 LEU cc_start: 0.8956 (pp) cc_final: 0.8503 (mt) REVERT: F 241 ARG cc_start: 0.6550 (ptm-80) cc_final: 0.6329 (ptt90) REVERT: G 130 GLN cc_start: 0.2119 (mt0) cc_final: 0.0574 (mp10) REVERT: G 146 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8160 (mm) REVERT: G 169 TYR cc_start: 0.8066 (p90) cc_final: 0.7638 (p90) REVERT: G 171 LYS cc_start: 0.7608 (pptt) cc_final: 0.6253 (mmmm) REVERT: G 272 ARG cc_start: 0.6155 (mtm110) cc_final: 0.5510 (ttm110) outliers start: 52 outliers final: 37 residues processed: 257 average time/residue: 0.1545 time to fit residues: 60.1690 Evaluate side-chains 236 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 195 LEU 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 191 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 230 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 128 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 238 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 248 optimal weight: 0.0570 chunk 172 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 159 HIS A 176 HIS ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115901 restraints weight = 33281.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114935 restraints weight = 36070.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115521 restraints weight = 37136.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116176 restraints weight = 29235.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116345 restraints weight = 26040.033| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 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 = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22051 Z= 0.165 Angle : 0.591 11.310 29998 Z= 0.299 Chirality : 0.042 0.313 3389 Planarity : 0.004 0.047 3747 Dihedral : 11.779 62.111 3229 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 2.62 % Allowed : 16.44 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.16), residues: 2597 helix: 0.16 (0.15), residues: 1230 sheet: -0.12 (0.37), residues: 197 loop : -1.19 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 82 TYR 0.019 0.002 TYR F 10 PHE 0.020 0.002 PHE G 187 TRP 0.012 0.001 TRP G 316 HIS 0.014 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (22051) covalent geometry : angle 0.59103 / 0.30 (29998) hydrogen bonds : bond 0.03990 / 2.70 ( 862) hydrogen bonds : angle 4.49915 / 3.16 ( 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 271 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7334 (mt) cc_final: 0.7032 (mp) REVERT: B 201 ARG cc_start: 0.7329 (mmp-170) cc_final: 0.6850 (mmp-170) REVERT: B 220 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8511 (mp) REVERT: B 330 ASP cc_start: 0.6874 (p0) cc_final: 0.6658 (p0) REVERT: C 164 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7803 (t) REVERT: D 182 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6792 (tp30) REVERT: D 327 LEU cc_start: 0.8968 (pp) cc_final: 0.8493 (mt) REVERT: E 211 GLU cc_start: 0.8220 (mp0) cc_final: 0.7932 (mp0) REVERT: F 121 ARG cc_start: 0.7102 (mmm-85) cc_final: 0.6844 (mmm-85) REVERT: G 31 GLN cc_start: 0.4573 (pt0) cc_final: 0.4058 (mm-40) REVERT: G 146 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8100 (mm) REVERT: G 169 TYR cc_start: 0.8097 (p90) cc_final: 0.7666 (p90) REVERT: G 171 LYS cc_start: 0.7605 (pptt) cc_final: 0.6293 (mmmm) REVERT: G 255 MET cc_start: 0.3489 (ttt) cc_final: 0.3286 (ttt) outliers start: 59 outliers final: 42 residues processed: 253 average time/residue: 0.1570 time to fit residues: 60.5472 Evaluate side-chains 239 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 A residue 236 HIS Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 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 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 117 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 146 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 265 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 170 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 190 optimal weight: 0.0970 chunk 123 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 236 optimal weight: 0.0980 chunk 50 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 176 HIS ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN F 104 HIS ** 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 = 0.3887 r_free = 0.3887 target = 0.146365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118462 restraints weight = 32793.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117528 restraints weight = 38223.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118372 restraints weight = 35845.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118878 restraints weight = 27349.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118949 restraints weight = 24663.161| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 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 = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22051 Z= 0.099 Angle : 0.530 12.365 29998 Z= 0.269 Chirality : 0.040 0.293 3389 Planarity : 0.004 0.047 3747 Dihedral : 11.668 61.825 3229 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 2.36 % Allowed : 17.20 % Favored : 80.44 % 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: -0.40 (0.16), residues: 2597 helix: 0.41 (0.15), residues: 1232 sheet: 0.09 (0.38), residues: 191 loop : -1.00 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 55 TYR 0.018 0.001 TYR F 10 PHE 0.025 0.001 PHE G 187 TRP 0.030 0.001 TRP G 316 HIS 0.012 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (22051) covalent geometry : angle 0.53031 / 0.27 (29998) hydrogen bonds : bond 0.03210 / 2.16 ( 862) hydrogen bonds : angle 4.25115 / 2.99 ( 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 269 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7318 (mt) cc_final: 0.7011 (mp) REVERT: B 201 ARG cc_start: 0.7195 (mmp-170) cc_final: 0.6766 (mmp-170) REVERT: B 220 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8505 (mp) REVERT: C 164 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7827 (t) REVERT: C 213 MET cc_start: 0.6922 (ttp) cc_final: 0.6710 (ptm) REVERT: D 327 LEU cc_start: 0.8965 (pp) cc_final: 0.8502 (mt) REVERT: F 345 ASP cc_start: 0.7770 (t0) cc_final: 0.7570 (t0) REVERT: G 31 GLN cc_start: 0.4356 (pt0) cc_final: 0.3965 (mm-40) REVERT: G 51 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6211 (mp) REVERT: G 146 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7998 (mm) REVERT: G 169 TYR cc_start: 0.8034 (p90) cc_final: 0.7602 (p90) REVERT: G 171 LYS cc_start: 0.7557 (pptt) cc_final: 0.6207 (mmmm) REVERT: G 356 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8226 (mt) outliers start: 53 outliers final: 31 residues processed: 250 average time/residue: 0.1582 time to fit residues: 60.0651 Evaluate side-chains 233 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 27 LEU 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 226 LEU Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 1 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 254 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 65 optimal weight: 0.0770 chunk 133 optimal weight: 0.0970 chunk 25 optimal weight: 0.0060 overall best weight: 0.3752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 176 HIS C 21 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119587 restraints weight = 32849.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119092 restraints weight = 34664.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119969 restraints weight = 33487.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120382 restraints weight = 26251.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121144 restraints weight = 24854.874| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22051 Z= 0.093 Angle : 0.513 13.642 29998 Z= 0.260 Chirality : 0.039 0.243 3389 Planarity : 0.004 0.055 3747 Dihedral : 11.567 59.719 3229 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 2.27 % Allowed : 17.64 % Favored : 80.09 % 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: -0.18 (0.16), residues: 2597 helix: 0.62 (0.16), residues: 1226 sheet: 0.11 (0.38), residues: 191 loop : -0.89 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 121 TYR 0.018 0.001 TYR F 10 PHE 0.035 0.001 PHE G 351 TRP 0.018 0.001 TRP G 316 HIS 0.011 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (22051) covalent geometry : angle 0.51339 / 0.26 (29998) hydrogen bonds : bond 0.02936 / 1.98 ( 862) hydrogen bonds : angle 4.07710 / 2.86 ( 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 273 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7265 (mt) cc_final: 0.6958 (mp) REVERT: B 201 ARG cc_start: 0.7209 (mmp-170) cc_final: 0.6850 (mmp-170) REVERT: B 220 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8493 (mp) REVERT: D 327 LEU cc_start: 0.8935 (pp) cc_final: 0.8483 (mt) REVERT: G 31 GLN cc_start: 0.4330 (pt0) cc_final: 0.4046 (mm-40) REVERT: G 51 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6184 (mp) REVERT: G 169 TYR cc_start: 0.8005 (p90) cc_final: 0.7590 (p90) REVERT: G 171 LYS cc_start: 0.7532 (pptt) cc_final: 0.6129 (mmmm) REVERT: G 375 TYR cc_start: 0.8468 (t80) cc_final: 0.7921 (t80) outliers start: 51 outliers final: 33 residues processed: 257 average time/residue: 0.1543 time to fit residues: 60.3304 Evaluate side-chains 230 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 56 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 288 PHE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 265 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 169 optimal weight: 0.4980 chunk 19 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 176 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS G 383 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115867 restraints weight = 33090.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115020 restraints weight = 36238.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115853 restraints weight = 37284.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116273 restraints weight = 27701.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116373 restraints weight = 24992.953| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22051 Z= 0.165 Angle : 0.582 10.388 29998 Z= 0.293 Chirality : 0.042 0.262 3389 Planarity : 0.004 0.047 3747 Dihedral : 11.580 59.767 3229 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 2.62 % Allowed : 17.69 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2597 helix: 0.43 (0.15), residues: 1242 sheet: 0.08 (0.39), residues: 181 loop : -0.99 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 121 TYR 0.013 0.001 TYR E 153 PHE 0.023 0.002 PHE G 351 TRP 0.016 0.001 TRP G 316 HIS 0.020 0.001 HIS G 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (22051) covalent geometry : angle 0.58178 / 0.29 (29998) hydrogen bonds : bond 0.03713 / 2.50 ( 862) hydrogen bonds : angle 4.19835 / 2.94 ( 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 259 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 0.813 Fit side-chains REVERT: A 101 LEU cc_start: 0.7330 (mt) cc_final: 0.6987 (mp) REVERT: B 201 ARG cc_start: 0.7193 (mmp-170) cc_final: 0.6822 (mmp-170) REVERT: B 220 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8448 (mp) REVERT: D 327 LEU cc_start: 0.8993 (pp) cc_final: 0.8522 (mt) REVERT: F 322 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: G 31 GLN cc_start: 0.4531 (pt0) cc_final: 0.4228 (mm-40) REVERT: G 51 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6191 (mp) REVERT: G 169 TYR cc_start: 0.8000 (p90) cc_final: 0.7594 (p90) REVERT: G 171 LYS cc_start: 0.7578 (pptt) cc_final: 0.6151 (mmmm) REVERT: G 248 MET cc_start: 0.6796 (tpt) cc_final: 0.6389 (tpt) outliers start: 59 outliers final: 45 residues processed: 237 average time/residue: 0.1659 time to fit residues: 59.5932 Evaluate side-chains 241 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 161 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 THR 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 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 331 GLU 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 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 180 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 383 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 119 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 132 optimal weight: 0.0970 chunk 33 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 176 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS G 383 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.145435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117417 restraints weight = 33014.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116667 restraints weight = 34067.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117307 restraints weight = 36984.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117841 restraints weight = 27452.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117977 restraints weight = 24584.023| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 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 = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22051 Z= 0.109 Angle : 0.543 11.031 29998 Z= 0.272 Chirality : 0.040 0.246 3389 Planarity : 0.004 0.048 3747 Dihedral : 11.551 59.865 3229 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 2.27 % Allowed : 18.31 % Favored : 79.42 % 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: -0.27 (0.16), residues: 2597 helix: 0.54 (0.15), residues: 1242 sheet: 0.10 (0.39), residues: 181 loop : -0.96 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 121 TYR 0.010 0.001 TYR F 10 PHE 0.023 0.001 PHE G 351 TRP 0.015 0.001 TRP G 316 HIS 0.019 0.001 HIS G 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (22051) covalent geometry : angle 0.54263 / 0.27 (29998) hydrogen bonds : bond 0.03276 / 2.20 ( 862) hydrogen bonds : angle 4.13763 / 2.90 ( 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 251 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 0.845 Fit side-chains REVERT: A 101 LEU cc_start: 0.7275 (mt) cc_final: 0.6946 (mp) REVERT: B 201 ARG cc_start: 0.7194 (mmp-170) cc_final: 0.6837 (mmp-170) REVERT: B 220 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8521 (mp) REVERT: D 158 TYR cc_start: 0.7512 (t80) cc_final: 0.7312 (t80) REVERT: D 327 LEU cc_start: 0.8984 (pp) cc_final: 0.8525 (mt) REVERT: F 121 ARG cc_start: 0.7237 (mmm-85) cc_final: 0.7030 (mmm-85) REVERT: F 322 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: G 31 GLN cc_start: 0.4497 (pt0) cc_final: 0.4111 (mm-40) REVERT: G 51 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6175 (mp) REVERT: G 169 TYR cc_start: 0.7994 (p90) cc_final: 0.7591 (p90) REVERT: G 171 LYS cc_start: 0.7510 (pptt) cc_final: 0.6125 (mmmm) REVERT: G 375 TYR cc_start: 0.8321 (t80) cc_final: 0.7902 (t80) outliers start: 51 outliers final: 41 residues processed: 235 average time/residue: 0.1599 time to fit residues: 57.4440 Evaluate side-chains 239 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 9 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 382 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 55 optimal weight: 5.9990 chunk 150 optimal weight: 0.0980 chunk 76 optimal weight: 10.0000 chunk 172 optimal weight: 0.0030 chunk 10 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 19 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 176 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.145122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117339 restraints weight = 33020.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115952 restraints weight = 40004.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116978 restraints weight = 36270.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117466 restraints weight = 27883.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.117565 restraints weight = 25247.475| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 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 = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22051 Z= 0.119 Angle : 0.551 11.395 29998 Z= 0.276 Chirality : 0.040 0.239 3389 Planarity : 0.004 0.050 3747 Dihedral : 11.513 59.598 3229 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 2.18 % Allowed : 18.31 % Favored : 79.51 % 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: -0.27 (0.16), residues: 2597 helix: 0.55 (0.15), residues: 1251 sheet: 0.08 (0.39), residues: 181 loop : -0.98 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 201 TYR 0.008 0.001 TYR E 153 PHE 0.022 0.001 PHE G 351 TRP 0.016 0.001 TRP G 316 HIS 0.011 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (22051) covalent geometry : angle 0.55068 / 0.28 (29998) hydrogen bonds : bond 0.03315 / 2.22 ( 862) hydrogen bonds : angle 4.10976 / 2.89 ( 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 255 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.730 Fit side-chains REVERT: A 101 LEU cc_start: 0.7289 (mt) cc_final: 0.6953 (mp) REVERT: B 201 ARG cc_start: 0.7217 (mmp-170) cc_final: 0.6854 (mmp-170) REVERT: B 220 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8498 (mp) REVERT: D 158 TYR cc_start: 0.7515 (t80) cc_final: 0.7314 (t80) REVERT: D 327 LEU cc_start: 0.8983 (pp) cc_final: 0.8523 (mt) REVERT: F 121 ARG cc_start: 0.7240 (mmm-85) cc_final: 0.7033 (mmm-85) REVERT: F 322 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: G 31 GLN cc_start: 0.4542 (pt0) cc_final: 0.4025 (mm-40) REVERT: G 51 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6184 (mp) REVERT: G 169 TYR cc_start: 0.8017 (p90) cc_final: 0.7602 (p90) REVERT: G 171 LYS cc_start: 0.7514 (pptt) cc_final: 0.6141 (mmmm) REVERT: G 272 ARG cc_start: 0.6312 (mtm-85) cc_final: 0.5565 (mpp80) outliers start: 49 outliers final: 40 residues processed: 239 average time/residue: 0.1551 time to fit residues: 56.4679 Evaluate side-chains 243 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 162 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 331 GLU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 265 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 134 optimal weight: 0.0060 chunk 50 optimal weight: 0.2980 chunk 108 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 167 optimal weight: 0.0070 chunk 61 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 overall best weight: 1.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 176 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117231 restraints weight = 33110.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116585 restraints weight = 34925.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117422 restraints weight = 36583.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117801 restraints weight = 27758.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117884 restraints weight = 25203.081| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 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 = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22051 Z= 0.114 Angle : 0.551 15.530 29998 Z= 0.275 Chirality : 0.040 0.329 3389 Planarity : 0.004 0.048 3747 Dihedral : 11.479 59.836 3229 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 2.27 % Allowed : 18.27 % Favored : 79.47 % 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: -0.22 (0.16), residues: 2597 helix: 0.58 (0.15), residues: 1256 sheet: 0.12 (0.39), residues: 181 loop : -0.95 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 201 TYR 0.008 0.001 TYR A 199 PHE 0.028 0.001 PHE G 187 TRP 0.047 0.001 TRP G 316 HIS 0.011 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (22051) covalent geometry : angle 0.55081 / 0.27 (29998) hydrogen bonds : bond 0.03241 / 2.18 ( 862) hydrogen bonds : angle 4.07390 / 2.86 ( 2418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2915.04 seconds wall clock time: 51 minutes 20.99 seconds (3080.99 seconds total)