Starting phenix.real_space_refine on Sat Sep 12 00:04:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kch_22808/09_2026/7kch_22808.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kch_22808/09_2026/7kch_22808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kch_22808/09_2026/7kch_22808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kch_22808/09_2026/7kch_22808.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kch_22808/09_2026/7kch_22808.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kch_22808/09_2026/7kch_22808.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kch_22808/09_2026/7kch_22808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kch_22808/09_2026/7kch_22808.cif" } resolution = 4.33 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 6 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 7597 2.51 5 N 2174 2.21 5 O 2405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s 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: 12248 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 3365 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 592} Link IDs: {'PTRANS': 21, 'TRANS': 658} Chain breaks: 8 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 2164 Unresolved non-hydrogen angles: 2757 Unresolved non-hydrogen dihedrals: 1796 Unresolved non-hydrogen chiralities: 187 Planarities with less than four sites: {'TRP:plan': 4, 'GLU:plan': 52, 'ASP:plan': 36, 'ARG:plan': 33, 'ASN:plan1': 34, 'TYR:plan': 20, 'HIS:plan': 19, 'PHE:plan': 39, 'GLN:plan1': 34} Unresolved non-hydrogen planarities: 1224 Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, G Time building chain proxies: 3.52, per 1000 atoms: 0.29 Number of scatterers: 12248 At special positions: 0 Unit cell: (123.848, 144.672, 140.288, 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 63 16.00 P 6 15.00 Mg 3 11.99 O 2405 8.00 N 2174 7.00 C 7597 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: 1.12 Conformation dependent library (CDL) restraints added in 664.3 milliseconds 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 22 sheets defined 48.2% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.537A pdb=" N MET G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.793A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 128 removed outlier: 3.700A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET G 123 " --> pdb=" O MET G 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE G 124 " --> pdb=" O THR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 removed outlier: 4.023A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 197 removed outlier: 3.638A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY G 197 " --> pdb=" O LEU G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 205 through 216 Processing helix chain 'G' and resid 224 through 230 Processing helix chain 'G' and resid 233 through 237 removed outlier: 4.607A pdb=" N LEU G 236 " --> pdb=" O SER G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 255 removed outlier: 3.814A pdb=" N ARG G 254 " --> pdb=" O GLY G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 removed outlier: 3.541A pdb=" N LEU G 261 " --> pdb=" O PRO G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 284 removed outlier: 3.551A pdb=" N LYS G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 296 removed outlier: 3.754A pdb=" N ALA G 295 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 removed outlier: 3.858A pdb=" N MET G 305 " --> pdb=" O GLY G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 removed outlier: 3.830A pdb=" N ALA G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.735A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 191 through 207 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.875A pdb=" N THR A 248 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.586A pdb=" N GLU A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 316 through 335 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.615A pdb=" N GLU A 347 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 393 through 425 removed outlier: 3.597A pdb=" N ASP A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.717A pdb=" N LEU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.588A pdb=" N GLN A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 593 Processing helix chain 'A' and resid 615 through 632 Processing helix chain 'A' and resid 654 through 665 Processing helix chain 'A' and resid 666 through 677 removed outlier: 3.668A pdb=" N GLY A 677 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 695 Processing helix chain 'A' and resid 710 through 718 Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.537A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.793A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 128 removed outlier: 3.700A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 4.023A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.637A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 233 through 237 removed outlier: 4.608A pdb=" N LEU B 236 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.814A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.541A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.551A pdb=" N LYS B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.754A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.858A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.829A pdb=" N ALA B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.735A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.537A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.792A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 128 removed outlier: 3.701A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 146 removed outlier: 4.023A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.638A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 233 through 237 removed outlier: 4.607A pdb=" N LEU C 236 " --> pdb=" O SER C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.814A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.541A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.551A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.755A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.858A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.829A pdb=" N ALA C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.736A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.952A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.603A pdb=" N ARG G 37 " --> pdb=" O THR G 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.533A pdb=" N ASP G 154 " --> pdb=" O HIS G 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL G 163 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET G 299 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 238 through 241 removed outlier: 3.693A pdb=" N LYS G 238 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 103 through 106 removed outlier: 7.033A pdb=" N LEU A 103 " --> pdb=" O ARG A 640 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL A 642 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA A 105 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN A 154 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LEU A 437 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE A 156 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 432 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU A 224 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA A 235 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN A 226 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.665A pdb=" N LYS A 381 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 680 through 683 Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.953A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.603A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.533A pdb=" N ASP B 154 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 299 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.692A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.952A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.603A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.532A pdb=" N ASP C 154 " --> pdb=" O HIS C 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET C 299 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.693A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3964 1.33 - 1.45: 1731 1.45 - 1.57: 6616 1.57 - 1.68: 9 1.68 - 1.80: 111 Bond restraints: 12431 Sorted by residual: bond pdb=" C GLY C 150 " pdb=" N ILE C 151 " ideal model delta sigma weight residual 1.333 1.292 0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" C GLY G 150 " pdb=" N ILE G 151 " ideal model delta sigma weight residual 1.333 1.293 0.040 1.20e-02 6.94e+03 1.12e+01 bond pdb=" C GLY B 150 " pdb=" N ILE B 151 " ideal model delta sigma weight residual 1.333 1.293 0.039 1.20e-02 6.94e+03 1.08e+01 bond pdb=" C VAL B 163 " pdb=" N PRO B 164 " ideal model delta sigma weight residual 1.331 1.293 0.038 1.28e-02 6.10e+03 9.01e+00 bond pdb=" C VAL G 163 " pdb=" N PRO G 164 " ideal model delta sigma weight residual 1.331 1.293 0.038 1.28e-02 6.10e+03 8.80e+00 ... (remaining 12426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 16259 2.42 - 4.85: 652 4.85 - 7.27: 55 7.27 - 9.70: 9 9.70 - 12.12: 3 Bond angle restraints: 16978 Sorted by residual: angle pdb=" C LEU C 94 " pdb=" N ARG C 95 " pdb=" CA ARG C 95 " ideal model delta sigma weight residual 121.54 129.47 -7.93 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C LEU B 94 " pdb=" N ARG B 95 " pdb=" CA ARG B 95 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C LEU G 94 " pdb=" N ARG G 95 " pdb=" CA ARG G 95 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ASN C 162 " pdb=" N VAL C 163 " pdb=" CA VAL C 163 " ideal model delta sigma weight residual 123.33 119.79 3.54 8.70e-01 1.32e+00 1.65e+01 angle pdb=" C ASN B 162 " pdb=" N VAL B 163 " pdb=" CA VAL B 163 " ideal model delta sigma weight residual 123.33 119.82 3.51 8.70e-01 1.32e+00 1.63e+01 ... (remaining 16973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 7241 34.14 - 68.29: 168 68.29 - 102.43: 3 102.43 - 136.57: 9 136.57 - 170.72: 6 Dihedral angle restraints: 7427 sinusoidal: 2214 harmonic: 5213 Sorted by residual: dihedral pdb=" C2' ADP C 401 " pdb=" C1' ADP C 401 " pdb=" N9 ADP C 401 " pdb=" C4 ADP C 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.73 -170.72 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2' ADP G 401 " pdb=" C1' ADP G 401 " pdb=" N9 ADP G 401 " pdb=" C4 ADP G 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.75 -170.70 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2' ADP B 401 " pdb=" C1' ADP B 401 " pdb=" N9 ADP B 401 " pdb=" C4 ADP B 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.79 -170.66 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 7424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1243 0.048 - 0.095: 571 0.095 - 0.143: 161 0.143 - 0.191: 26 0.191 - 0.238: 9 Chirality restraints: 2010 Sorted by residual: chirality pdb=" CB ILE B 34 " pdb=" CA ILE B 34 " pdb=" CG1 ILE B 34 " pdb=" CG2 ILE B 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE G 34 " pdb=" CA ILE G 34 " pdb=" CG1 ILE G 34 " pdb=" CG2 ILE G 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE C 34 " pdb=" CA ILE C 34 " pdb=" CG1 ILE C 34 " pdb=" CG2 ILE C 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2007 not shown) Planarity restraints: 2252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 257 " -0.053 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO B 258 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS G 257 " 0.053 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO G 258 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO G 258 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 258 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 257 " 0.053 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO C 258 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 258 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 258 " 0.045 5.00e-02 4.00e+02 ... (remaining 2249 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1318 2.72 - 3.26: 12209 3.26 - 3.81: 20335 3.81 - 4.35: 21634 4.35 - 4.90: 36872 Nonbonded interactions: 92368 Sorted by model distance: nonbonded pdb=" O ASN B 297 " pdb=" OD1 ASN B 297 " model vdw 2.175 3.040 nonbonded pdb=" O ASN G 297 " pdb=" OD1 ASN G 297 " model vdw 2.176 3.040 nonbonded pdb=" O ASN C 297 " pdb=" OD1 ASN C 297 " model vdw 2.176 3.040 nonbonded pdb=" CB MET G 47 " pdb=" NH2 ARG C 147 " model vdw 2.215 3.520 nonbonded pdb=" O SER C 155 " pdb=" OG1 THR C 303 " model vdw 2.241 3.040 ... (remaining 92363 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' selection = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.550 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5178 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 : 0.011 0.063 12431 Z= 0.554 Angle : 1.074 12.124 16978 Z= 0.619 Chirality : 0.057 0.238 2010 Planarity : 0.008 0.079 2252 Dihedral : 16.548 170.718 4055 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 4.72 % Allowed : 16.35 % Favored : 78.93 % 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: -4.19 (0.16), residues: 1781 helix: -2.75 (0.12), residues: 761 sheet: -1.81 (0.31), residues: 257 loop : -3.06 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 196 TYR 0.008 0.002 TYR B 279 PHE 0.029 0.003 PHE B 255 TRP 0.020 0.004 TRP G 79 HIS 0.016 0.004 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.01142 / 0.55 (12431) covalent geometry : angle 1.07387 / 0.62 (16978) hydrogen bonds : bond 0.20495 / 13.21 ( 617) hydrogen bonds : angle 8.36831 / 6.28 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 351 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 41 GLN cc_start: 0.6624 (tt0) cc_final: 0.5892 (pm20) REVERT: G 122 ILE cc_start: 0.7662 (mt) cc_final: 0.7175 (mt) REVERT: G 167 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.6905 (tp30) REVERT: G 179 ASP cc_start: 0.6416 (m-30) cc_final: 0.6035 (p0) REVERT: B 176 MET cc_start: 0.4988 (mmm) cc_final: 0.4674 (tpp) REVERT: C 10 CYS cc_start: 0.6037 (p) cc_final: 0.5741 (p) REVERT: C 81 ASP cc_start: 0.7331 (m-30) cc_final: 0.6863 (m-30) REVERT: C 121 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7901 (tm-30) REVERT: C 140 LEU cc_start: 0.7725 (mp) cc_final: 0.7410 (mp) outliers start: 45 outliers final: 12 residues processed: 380 average time/residue: 0.1008 time to fit residues: 56.5231 Evaluate side-chains 231 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 49 GLN G 101 HIS ** G 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 HIS G 353 GLN B 78 ASN B 101 HIS B 280 ASN B 353 GLN C 49 GLN C 101 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS C 246 GLN C 353 GLN C 371 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.070938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.056314 restraints weight = 63004.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.057679 restraints weight = 37387.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058654 restraints weight = 25146.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059349 restraints weight = 18546.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.059754 restraints weight = 14540.846| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 12431 Z= 0.222 Angle : 0.804 14.599 16978 Z= 0.409 Chirality : 0.050 0.228 2010 Planarity : 0.006 0.083 2252 Dihedral : 12.847 175.157 1931 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.31 % Allowed : 4.19 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.18), residues: 1781 helix: -0.41 (0.17), residues: 767 sheet: -1.68 (0.31), residues: 262 loop : -2.31 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG G 210 TYR 0.030 0.003 TYR B 198 PHE 0.022 0.003 PHE G 255 TRP 0.027 0.003 TRP B 79 HIS 0.011 0.002 HIS G 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (12431) covalent geometry : angle 0.80409 / 0.41 (16978) hydrogen bonds : bond 0.04018 / 2.62 ( 617) hydrogen bonds : angle 5.32846 / 3.98 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 243 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 179 ASP cc_start: 0.7038 (m-30) cc_final: 0.6704 (p0) REVERT: G 305 MET cc_start: 0.6495 (mmp) cc_final: 0.6211 (mmm) REVERT: G 352 PHE cc_start: 0.7417 (m-80) cc_final: 0.7041 (m-80) REVERT: B 82 MET cc_start: 0.6217 (ppp) cc_final: 0.5815 (ppp) REVERT: B 123 MET cc_start: 0.8538 (pmm) cc_final: 0.7081 (mmt) REVERT: B 267 ILE cc_start: 0.5821 (tp) cc_final: 0.5061 (tp) REVERT: B 341 ILE cc_start: 0.8673 (mt) cc_final: 0.8386 (mm) REVERT: C 107 GLU cc_start: 0.3628 (mt-10) cc_final: 0.3221 (mt-10) REVERT: C 118 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8584 (mtmt) REVERT: C 325 MET cc_start: 0.6378 (mmm) cc_final: 0.6126 (mmm) REVERT: C 359 LYS cc_start: 0.8645 (tptm) cc_final: 0.8435 (tptt) outliers start: 3 outliers final: 1 residues processed: 245 average time/residue: 0.0981 time to fit residues: 36.3136 Evaluate side-chains 184 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 152 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 167 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 65.7881 > 50:) chunk 156 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 40 HIS G 101 HIS B 73 HIS B 101 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN C 73 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.068355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053398 restraints weight = 65687.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.054729 restraints weight = 39971.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.055648 restraints weight = 27284.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.056310 restraints weight = 20298.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056744 restraints weight = 16105.232| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.9949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 12431 Z= 0.274 Angle : 0.860 20.785 16978 Z= 0.438 Chirality : 0.049 0.179 2010 Planarity : 0.006 0.078 2252 Dihedral : 12.011 178.475 1931 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % 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: -1.22 (0.20), residues: 1781 helix: 0.50 (0.19), residues: 776 sheet: -1.32 (0.30), residues: 289 loop : -2.03 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 312 TYR 0.023 0.003 TYR B 279 PHE 0.032 0.003 PHE G 124 TRP 0.019 0.003 TRP B 79 HIS 0.008 0.002 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.27 (12431) covalent geometry : angle 0.85981 / 0.44 (16978) hydrogen bonds : bond 0.04600 / 2.90 ( 617) hydrogen bonds : angle 4.96508 / 3.65 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.7511 (tt0) cc_final: 0.6904 (pt0) REVERT: G 176 MET cc_start: 0.8192 (mpp) cc_final: 0.7545 (mtp) REVERT: G 179 ASP cc_start: 0.8167 (m-30) cc_final: 0.7193 (p0) REVERT: G 184 ASP cc_start: 0.7993 (m-30) cc_final: 0.7727 (m-30) REVERT: G 187 ASP cc_start: 0.8960 (m-30) cc_final: 0.8446 (t0) REVERT: G 227 MET cc_start: 0.8220 (mmt) cc_final: 0.7739 (mmt) REVERT: G 260 THR cc_start: 0.8318 (m) cc_final: 0.7902 (p) REVERT: G 280 ASN cc_start: 0.8448 (t0) cc_final: 0.8170 (t0) REVERT: B 81 ASP cc_start: 0.7830 (m-30) cc_final: 0.7481 (p0) REVERT: B 269 MET cc_start: 0.8536 (tpp) cc_final: 0.8290 (tpp) REVERT: C 47 MET cc_start: 0.5145 (mpp) cc_final: 0.4377 (tmm) REVERT: C 227 MET cc_start: 0.7551 (mmm) cc_final: 0.7316 (tpt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0902 time to fit residues: 25.6061 Evaluate side-chains 120 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 2.9990 chunk 47 optimal weight: 40.0000 chunk 130 optimal weight: 0.6980 chunk 119 optimal weight: 0.0010 chunk 118 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 142 optimal weight: 10.0000 chunk 26 optimal weight: 0.0670 chunk 105 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 HIS C 111 ASN C 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.070409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.055455 restraints weight = 64013.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.056853 restraints weight = 37873.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.057821 restraints weight = 25497.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058509 restraints weight = 18758.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.058921 restraints weight = 14801.271| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 1.0330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12431 Z= 0.105 Angle : 0.599 8.256 16978 Z= 0.297 Chirality : 0.045 0.166 2010 Planarity : 0.004 0.056 2252 Dihedral : 11.470 176.265 1931 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: -0.62 (0.21), residues: 1781 helix: 0.98 (0.19), residues: 777 sheet: -0.97 (0.33), residues: 257 loop : -1.71 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 177 TYR 0.019 0.001 TYR B 198 PHE 0.020 0.002 PHE C 223 TRP 0.015 0.002 TRP B 356 HIS 0.006 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (12431) covalent geometry : angle 0.59941 / 0.30 (16978) hydrogen bonds : bond 0.02793 / 1.78 ( 617) hydrogen bonds : angle 4.46738 / 3.30 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.7080 (tt0) cc_final: 0.6515 (pt0) REVERT: G 122 ILE cc_start: 0.7131 (mt) cc_final: 0.6835 (mt) REVERT: G 132 MET cc_start: 0.8605 (tmm) cc_final: 0.8352 (tmm) REVERT: G 179 ASP cc_start: 0.8237 (m-30) cc_final: 0.7320 (p0) REVERT: G 187 ASP cc_start: 0.8953 (m-30) cc_final: 0.8511 (t0) REVERT: G 227 MET cc_start: 0.8153 (mmt) cc_final: 0.7433 (mmm) REVERT: G 280 ASN cc_start: 0.8396 (t0) cc_final: 0.7957 (t0) REVERT: G 283 MET cc_start: 0.7704 (mmp) cc_final: 0.7419 (mmm) REVERT: G 299 MET cc_start: 0.8425 (mpp) cc_final: 0.7656 (mpp) REVERT: G 303 THR cc_start: 0.9107 (p) cc_final: 0.8807 (t) REVERT: G 305 MET cc_start: 0.8594 (mmp) cc_final: 0.7900 (mmp) REVERT: B 81 ASP cc_start: 0.8047 (m-30) cc_final: 0.7513 (p0) REVERT: C 47 MET cc_start: 0.5303 (mpp) cc_final: 0.4833 (tmm) REVERT: C 227 MET cc_start: 0.7602 (mmm) cc_final: 0.7204 (tpt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0867 time to fit residues: 22.9839 Evaluate side-chains 122 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 178 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 40.0000 chunk 122 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 104 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 146 optimal weight: 0.3980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 12 ASN G 111 ASN B 92 ASN C 162 ASN C 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.065753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051036 restraints weight = 62615.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.052288 restraints weight = 38434.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.053182 restraints weight = 26541.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.053805 restraints weight = 20081.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.054251 restraints weight = 16242.711| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 1.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12431 Z= 0.145 Angle : 0.636 10.711 16978 Z= 0.315 Chirality : 0.045 0.179 2010 Planarity : 0.004 0.044 2252 Dihedral : 10.998 178.106 1931 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: -0.31 (0.21), residues: 1781 helix: 1.19 (0.20), residues: 804 sheet: -0.74 (0.33), residues: 258 loop : -1.63 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 183 TYR 0.020 0.002 TYR B 279 PHE 0.023 0.002 PHE C 223 TRP 0.011 0.002 TRP B 79 HIS 0.006 0.001 HIS G 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (12431) covalent geometry : angle 0.63560 / 0.32 (16978) hydrogen bonds : bond 0.03010 / 1.86 ( 617) hydrogen bonds : angle 4.41607 / 3.27 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.7725 (tt0) cc_final: 0.7046 (pt0) REVERT: G 179 ASP cc_start: 0.8392 (m-30) cc_final: 0.7962 (p0) REVERT: G 187 ASP cc_start: 0.9002 (m-30) cc_final: 0.8486 (t70) REVERT: G 227 MET cc_start: 0.8597 (mmt) cc_final: 0.8149 (mmm) REVERT: G 259 GLU cc_start: 0.7603 (tt0) cc_final: 0.7380 (tt0) REVERT: G 283 MET cc_start: 0.8202 (mmp) cc_final: 0.7776 (mmm) REVERT: G 305 MET cc_start: 0.8779 (mmp) cc_final: 0.8563 (mmm) REVERT: B 81 ASP cc_start: 0.8074 (m-30) cc_final: 0.7715 (p0) REVERT: C 47 MET cc_start: 0.5574 (mpp) cc_final: 0.4965 (tmm) REVERT: C 176 MET cc_start: 0.7934 (mtp) cc_final: 0.7621 (mtp) REVERT: C 223 PHE cc_start: 0.7666 (m-80) cc_final: 0.7356 (m-80) REVERT: C 227 MET cc_start: 0.7999 (mmm) cc_final: 0.7647 (tpt) REVERT: C 269 MET cc_start: 0.7374 (ttp) cc_final: 0.7053 (ttp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0808 time to fit residues: 19.4726 Evaluate side-chains 114 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 136 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 104 optimal weight: 50.0000 chunk 92 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 49 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 314 GLN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.047131 restraints weight = 67832.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.048295 restraints weight = 41450.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.049117 restraints weight = 28662.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.049697 restraints weight = 21768.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.050075 restraints weight = 17690.140| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 1.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 12431 Z= 0.371 Angle : 0.888 20.052 16978 Z= 0.441 Chirality : 0.051 0.260 2010 Planarity : 0.005 0.053 2252 Dihedral : 11.449 178.081 1931 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.44 % 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: -0.65 (0.21), residues: 1781 helix: 0.95 (0.20), residues: 785 sheet: -0.94 (0.32), residues: 260 loop : -1.76 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 196 TYR 0.019 0.003 TYR B 198 PHE 0.034 0.003 PHE C 223 TRP 0.011 0.002 TRP G 86 HIS 0.016 0.002 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00811 / 0.37 (12431) covalent geometry : angle 0.88798 / 0.44 (16978) hydrogen bonds : bond 0.03753 / 2.40 ( 617) hydrogen bonds : angle 5.05762 / 3.74 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: G 187 ASP cc_start: 0.9200 (m-30) cc_final: 0.8742 (t70) REVERT: G 227 MET cc_start: 0.8927 (mmt) cc_final: 0.8623 (mmm) REVERT: G 374 CYS cc_start: 0.7726 (m) cc_final: 0.7513 (m) REVERT: B 85 ILE cc_start: 0.9397 (pt) cc_final: 0.9114 (mt) REVERT: B 328 LYS cc_start: 0.7905 (tttt) cc_final: 0.7632 (ptmt) REVERT: C 43 VAL cc_start: 0.9181 (m) cc_final: 0.8564 (p) REVERT: C 44 MET cc_start: 0.5839 (pmm) cc_final: 0.4328 (ptt) REVERT: C 47 MET cc_start: 0.5249 (mpp) cc_final: 0.4971 (tmm) REVERT: C 176 MET cc_start: 0.8457 (mtp) cc_final: 0.8150 (mtp) REVERT: C 269 MET cc_start: 0.8486 (ttp) cc_final: 0.8213 (ttp) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.0835 time to fit residues: 15.9860 Evaluate side-chains 94 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 93 optimal weight: 5.9990 chunk 45 optimal weight: 50.0000 chunk 171 optimal weight: 1.9990 chunk 48 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 113 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.047253 restraints weight = 61835.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.048500 restraints weight = 37235.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.049381 restraints weight = 25510.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.050020 restraints weight = 19147.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.050464 restraints weight = 15349.704| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 1.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12431 Z= 0.203 Angle : 0.686 14.371 16978 Z= 0.336 Chirality : 0.047 0.252 2010 Planarity : 0.004 0.044 2252 Dihedral : 11.062 179.476 1931 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.21), residues: 1781 helix: 1.01 (0.20), residues: 806 sheet: -0.84 (0.33), residues: 254 loop : -1.76 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 335 TYR 0.023 0.002 TYR B 198 PHE 0.020 0.002 PHE G 223 TRP 0.015 0.002 TRP B 79 HIS 0.010 0.002 HIS C 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (12431) covalent geometry : angle 0.68561 / 0.34 (16978) hydrogen bonds : bond 0.03026 / 1.90 ( 617) hydrogen bonds : angle 4.58420 / 3.41 ( 1701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 179 ASP cc_start: 0.8687 (m-30) cc_final: 0.8410 (m-30) REVERT: G 227 MET cc_start: 0.8989 (mmt) cc_final: 0.8516 (mmm) REVERT: G 283 MET cc_start: 0.8799 (mmp) cc_final: 0.8540 (mmp) REVERT: B 132 MET cc_start: 0.9323 (ppp) cc_final: 0.8808 (ppp) REVERT: C 305 MET cc_start: 0.8591 (mmt) cc_final: 0.8390 (mmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0794 time to fit residues: 15.6356 Evaluate side-chains 93 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 77 optimal weight: 50.0000 chunk 40 optimal weight: 30.0000 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 40.0000 chunk 165 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.064931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.049254 restraints weight = 65982.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.050499 restraints weight = 39846.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.051356 restraints weight = 27314.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.051998 restraints weight = 20530.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.052418 restraints weight = 16452.011| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 1.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12431 Z= 0.165 Angle : 0.648 11.838 16978 Z= 0.315 Chirality : 0.045 0.237 2010 Planarity : 0.004 0.033 2252 Dihedral : 10.835 175.883 1931 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -0.28 (0.21), residues: 1781 helix: 1.23 (0.20), residues: 796 sheet: -0.78 (0.33), residues: 254 loop : -1.57 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 335 TYR 0.020 0.001 TYR B 198 PHE 0.022 0.002 PHE B 352 TRP 0.015 0.002 TRP C 340 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (12431) covalent geometry : angle 0.64829 / 0.31 (16978) hydrogen bonds : bond 0.02804 / 1.78 ( 617) hydrogen bonds : angle 4.39042 / 3.26 ( 1701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: G 65 LEU cc_start: 0.8835 (mt) cc_final: 0.8610 (mm) REVERT: G 179 ASP cc_start: 0.8634 (m-30) cc_final: 0.7928 (p0) REVERT: G 227 MET cc_start: 0.9032 (mmt) cc_final: 0.8525 (mmm) REVERT: G 283 MET cc_start: 0.8693 (mmp) cc_final: 0.8412 (mmp) REVERT: B 132 MET cc_start: 0.9438 (ppp) cc_final: 0.8911 (ppp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0739 time to fit residues: 14.5271 Evaluate side-chains 92 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 120 optimal weight: 4.9990 chunk 70 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 chunk 50 optimal weight: 40.0000 chunk 36 optimal weight: 0.0030 chunk 84 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 121 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.048690 restraints weight = 65771.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.049968 restraints weight = 39475.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050864 restraints weight = 26835.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051491 restraints weight = 20108.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.051862 restraints weight = 16131.490| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 1.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12431 Z= 0.169 Angle : 0.658 12.470 16978 Z= 0.317 Chirality : 0.046 0.240 2010 Planarity : 0.004 0.033 2252 Dihedral : 10.801 176.983 1931 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.10 % Allowed : 0.63 % Favored : 99.27 % 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: -0.12 (0.21), residues: 1781 helix: 1.37 (0.20), residues: 793 sheet: -0.67 (0.33), residues: 254 loop : -1.50 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 290 TYR 0.016 0.001 TYR B 198 PHE 0.021 0.002 PHE C 262 TRP 0.011 0.002 TRP B 79 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (12431) covalent geometry : angle 0.65756 / 0.32 (16978) hydrogen bonds : bond 0.02796 / 1.78 ( 617) hydrogen bonds : angle 4.34097 / 3.22 ( 1701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.465 Fit side-chains REVERT: G 179 ASP cc_start: 0.8681 (m-30) cc_final: 0.8003 (p0) REVERT: G 227 MET cc_start: 0.9162 (mmt) cc_final: 0.8647 (mmm) REVERT: G 283 MET cc_start: 0.8734 (mmp) cc_final: 0.8470 (mmp) REVERT: B 132 MET cc_start: 0.9470 (ppp) cc_final: 0.8850 (ppp) REVERT: B 305 MET cc_start: 0.8732 (mmm) cc_final: 0.8504 (mmm) REVERT: C 313 MET cc_start: 0.8875 (tpp) cc_final: 0.8658 (tpp) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.0764 time to fit residues: 14.2584 Evaluate side-chains 93 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 2 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.049250 restraints weight = 62411.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.050509 restraints weight = 38015.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.051390 restraints weight = 26174.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.051954 restraints weight = 19714.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.052414 restraints weight = 16057.715| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 1.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12431 Z= 0.105 Angle : 0.601 12.285 16978 Z= 0.288 Chirality : 0.045 0.234 2010 Planarity : 0.003 0.035 2252 Dihedral : 10.514 175.563 1931 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.13 (0.21), residues: 1781 helix: 1.59 (0.20), residues: 784 sheet: -0.59 (0.34), residues: 254 loop : -1.31 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 372 TYR 0.015 0.001 TYR B 198 PHE 0.015 0.001 PHE C 262 TRP 0.013 0.002 TRP G 340 HIS 0.004 0.001 HIS G 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (12431) covalent geometry : angle 0.60074 / 0.29 (16978) hydrogen bonds : bond 0.02488 / 1.60 ( 617) hydrogen bonds : angle 4.13581 / 3.07 ( 1701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 179 ASP cc_start: 0.8599 (m-30) cc_final: 0.7919 (p0) REVERT: G 227 MET cc_start: 0.9126 (mmt) cc_final: 0.8551 (mmm) REVERT: G 283 MET cc_start: 0.8766 (mmp) cc_final: 0.8507 (mmp) REVERT: G 305 MET cc_start: 0.8742 (mmp) cc_final: 0.8451 (mmp) REVERT: B 299 MET cc_start: 0.8909 (mmm) cc_final: 0.8665 (mmm) REVERT: B 305 MET cc_start: 0.8580 (mmm) cc_final: 0.8328 (mmm) REVERT: C 44 MET cc_start: 0.4686 (pmm) cc_final: 0.3968 (ptt) REVERT: C 353 GLN cc_start: 0.8044 (mp10) cc_final: 0.7778 (mp10) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0784 time to fit residues: 15.1111 Evaluate side-chains 93 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 92 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 77 optimal weight: 50.0000 chunk 45 optimal weight: 50.0000 chunk 69 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 296 ASN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.061828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.046727 restraints weight = 62588.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.047935 restraints weight = 38415.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.048804 restraints weight = 26704.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049393 restraints weight = 20198.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.049771 restraints weight = 16367.976| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 1.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12431 Z= 0.203 Angle : 0.686 12.758 16978 Z= 0.332 Chirality : 0.047 0.241 2010 Planarity : 0.004 0.033 2252 Dihedral : 10.725 179.117 1931 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.05 (0.22), residues: 1781 helix: 1.51 (0.20), residues: 792 sheet: -0.53 (0.34), residues: 258 loop : -1.44 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 37 TYR 0.020 0.002 TYR B 198 PHE 0.017 0.002 PHE B 262 TRP 0.010 0.002 TRP C 79 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (12431) covalent geometry : angle 0.68591 / 0.33 (16978) hydrogen bonds : bond 0.02892 / 1.85 ( 617) hydrogen bonds : angle 4.32011 / 3.21 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2027.92 seconds wall clock time: 35 minutes 53.53 seconds (2153.53 seconds total)