Starting phenix.real_space_refine on Wed Jul 30 13:53:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kch_22808/07_2025/7kch_22808.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kch_22808/07_2025/7kch_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_22808/07_2025/7kch_22808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kch_22808/07_2025/7kch_22808.map" model { file = "/net/cci-nas-00/data/ceres_data/7kch_22808/07_2025/7kch_22808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kch_22808/07_2025/7kch_22808.cif" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 34, 'HIS:plan': 19, 'TYR:plan': 20, 'ASN:plan1': 34, 'TRP:plan': 4, 'ASP:plan': 36, 'PHE:plan': 39, 'GLU:plan': 52, 'ARG:plan': 33} 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: 10.72, per 1000 atoms: 0.88 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: 3.18 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.67 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: 4.29 Time building geometry restraints manager: 3.76 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: 9.890 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.860 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5244 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.004 TRP G 79 HIS 0.016 0.004 HIS C 275 PHE 0.029 0.003 PHE B 255 TYR 0.008 0.002 TYR B 279 ARG 0.005 0.001 ARG B 196 Details of bonding type rmsd hydrogen bonds : bond 0.20495 ( 617) hydrogen bonds : angle 8.36831 ( 1701) covalent geometry : bond 0.01142 (12431) covalent geometry : angle 1.07387 (16978) *********************** 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 : 1.485 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: symmetry clash REVERT: G 41 GLN cc_start: 0.6624 (tt0) cc_final: 0.5894 (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: 0.6909 (tp30) REVERT: G 179 ASP cc_start: 0.6417 (m-30) cc_final: 0.6031 (p0) REVERT: B 176 MET cc_start: 0.4989 (mmm) cc_final: 0.4678 (tpp) REVERT: C 10 CYS cc_start: 0.6038 (p) cc_final: 0.5737 (p) REVERT: C 81 ASP cc_start: 0.7331 (m-30) cc_final: 0.6862 (m-30) REVERT: C 121 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7903 (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: 0.2228 time to fit residues: 122.7178 Evaluate side-chains 233 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 220 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 46 optimal weight: 40.0000 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 54 optimal weight: 40.0000 chunk 85 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 49 GLN G 73 HIS G 173 HIS ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN B 101 HIS B 280 ASN C 49 GLN C 73 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.069018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.054386 restraints weight = 65216.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.055740 restraints weight = 38824.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056673 restraints weight = 26135.410| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.8896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 12431 Z= 0.349 Angle : 1.007 16.726 16978 Z= 0.519 Chirality : 0.054 0.278 2010 Planarity : 0.007 0.070 2252 Dihedral : 13.061 178.412 1931 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.42 % Allowed : 6.50 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.18), residues: 1781 helix: -0.61 (0.17), residues: 754 sheet: -1.76 (0.29), residues: 283 loop : -2.43 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP B 79 HIS 0.011 0.003 HIS G 161 PHE 0.027 0.004 PHE B 31 TYR 0.042 0.003 TYR B 198 ARG 0.026 0.002 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.04874 ( 617) hydrogen bonds : angle 5.87305 ( 1701) covalent geometry : bond 0.00729 (12431) covalent geometry : angle 1.00651 (16978) *********************** 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 216 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 212 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.7269 (tt0) cc_final: 0.6579 (pt0) REVERT: G 87 HIS cc_start: 0.8926 (t-90) cc_final: 0.8712 (t70) REVERT: G 111 ASN cc_start: 0.8894 (m110) cc_final: 0.8600 (m110) REVERT: G 179 ASP cc_start: 0.8164 (m-30) cc_final: 0.7256 (p0) REVERT: G 187 ASP cc_start: 0.9001 (m-30) cc_final: 0.8515 (t0) REVERT: G 260 THR cc_start: 0.8168 (m) cc_final: 0.7574 (p) REVERT: G 299 MET cc_start: 0.8955 (mpp) cc_final: 0.8147 (mpp) REVERT: B 81 ASP cc_start: 0.7821 (m-30) cc_final: 0.7169 (p0) REVERT: B 82 MET cc_start: 0.6882 (ppp) cc_final: 0.6591 (ppp) REVERT: B 107 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: B 269 MET cc_start: 0.8471 (tpp) cc_final: 0.8245 (tpp) REVERT: B 278 THR cc_start: 0.9160 (m) cc_final: 0.8800 (p) REVERT: C 47 MET cc_start: 0.5240 (mpp) cc_final: 0.4623 (tmm) REVERT: C 111 ASN cc_start: 0.8773 (m110) cc_final: 0.8458 (m-40) outliers start: 4 outliers final: 1 residues processed: 216 average time/residue: 0.2100 time to fit residues: 68.0983 Evaluate side-chains 147 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 60 optimal weight: 30.0000 chunk 154 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 96 optimal weight: 50.0000 chunk 110 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 40 HIS G 73 HIS G 280 ASN G 353 GLN G 371 HIS B 87 HIS B 161 HIS C 41 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.068870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.053873 restraints weight = 64970.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055224 restraints weight = 38978.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.056213 restraints weight = 26532.294| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.9773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12431 Z= 0.135 Angle : 0.638 10.685 16978 Z= 0.317 Chirality : 0.045 0.138 2010 Planarity : 0.005 0.060 2252 Dihedral : 12.278 177.636 1931 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1781 helix: 0.36 (0.19), residues: 784 sheet: -1.18 (0.32), residues: 245 loop : -2.07 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 340 HIS 0.005 0.001 HIS B 87 PHE 0.015 0.002 PHE B 352 TYR 0.017 0.002 TYR G 188 ARG 0.003 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 617) hydrogen bonds : angle 4.73789 ( 1701) covalent geometry : bond 0.00300 (12431) covalent geometry : angle 0.63800 (16978) *********************** 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 179 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.7148 (tt0) cc_final: 0.6574 (pt0) REVERT: G 179 ASP cc_start: 0.8209 (m-30) cc_final: 0.7746 (p0) REVERT: G 187 ASP cc_start: 0.8984 (m-30) cc_final: 0.8454 (t0) REVERT: G 227 MET cc_start: 0.8440 (mmt) cc_final: 0.8098 (mmm) REVERT: G 259 GLU cc_start: 0.7378 (tt0) cc_final: 0.7103 (tt0) REVERT: G 260 THR cc_start: 0.8114 (m) cc_final: 0.7556 (p) REVERT: G 299 MET cc_start: 0.8780 (mpp) cc_final: 0.7917 (mpp) REVERT: G 313 MET cc_start: 0.7726 (tpt) cc_final: 0.7494 (tpp) REVERT: B 82 MET cc_start: 0.6787 (ppp) cc_final: 0.6576 (ppp) REVERT: B 189 LEU cc_start: 0.9203 (tp) cc_final: 0.8739 (mt) REVERT: B 269 MET cc_start: 0.8566 (tpp) cc_final: 0.8285 (tpp) REVERT: B 278 THR cc_start: 0.9174 (m) cc_final: 0.8821 (p) REVERT: C 47 MET cc_start: 0.5493 (mpp) cc_final: 0.4859 (tmm) REVERT: C 191 LYS cc_start: 0.8787 (ptmt) cc_final: 0.8022 (tptt) REVERT: C 227 MET cc_start: 0.7826 (mmm) cc_final: 0.7427 (tpt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2087 time to fit residues: 57.1345 Evaluate side-chains 130 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 164 optimal weight: 0.4980 chunk 135 optimal weight: 3.9990 chunk 106 optimal weight: 0.0270 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 ASN G 111 ASN G 371 HIS B 87 HIS B 101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.067067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.052458 restraints weight = 62303.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.053803 restraints weight = 37447.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.054739 restraints weight = 25514.872| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 1.0353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12431 Z= 0.108 Angle : 0.582 7.593 16978 Z= 0.290 Chirality : 0.044 0.151 2010 Planarity : 0.004 0.052 2252 Dihedral : 11.761 179.767 1931 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1781 helix: 0.84 (0.19), residues: 792 sheet: -1.07 (0.31), residues: 257 loop : -1.77 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 340 HIS 0.005 0.001 HIS B 87 PHE 0.014 0.001 PHE C 223 TYR 0.024 0.001 TYR B 279 ARG 0.004 0.000 ARG G 254 Details of bonding type rmsd hydrogen bonds : bond 0.02782 ( 617) hydrogen bonds : angle 4.44178 ( 1701) covalent geometry : bond 0.00236 (12431) covalent geometry : angle 0.58177 (16978) *********************** 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 165 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 44 MET cc_start: 0.8168 (tpp) cc_final: 0.7767 (tpt) REVERT: G 72 GLU cc_start: 0.7281 (tt0) cc_final: 0.6677 (pt0) REVERT: G 179 ASP cc_start: 0.8266 (m-30) cc_final: 0.7398 (p0) REVERT: G 187 ASP cc_start: 0.8957 (m-30) cc_final: 0.8590 (t0) REVERT: G 227 MET cc_start: 0.8477 (mmt) cc_final: 0.8140 (mmm) REVERT: G 299 MET cc_start: 0.8582 (mpp) cc_final: 0.7809 (mpp) REVERT: B 81 ASP cc_start: 0.8145 (m-30) cc_final: 0.7770 (m-30) REVERT: B 123 MET cc_start: 0.8470 (ppp) cc_final: 0.8250 (ppp) REVERT: B 189 LEU cc_start: 0.9311 (tp) cc_final: 0.9094 (tp) REVERT: C 47 MET cc_start: 0.5492 (mpp) cc_final: 0.4968 (tmm) REVERT: C 191 LYS cc_start: 0.8925 (ptmt) cc_final: 0.8712 (ttpp) REVERT: C 227 MET cc_start: 0.7793 (mmm) cc_final: 0.7394 (tpt) REVERT: C 303 THR cc_start: 0.8545 (p) cc_final: 0.8331 (t) REVERT: C 305 MET cc_start: 0.8432 (mmt) cc_final: 0.8229 (mmt) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1892 time to fit residues: 48.7146 Evaluate side-chains 121 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 152 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 38 optimal weight: 50.0000 chunk 122 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 114 optimal weight: 0.1980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 ASN G 371 HIS ** C 161 HIS ** 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 = 0.3324 r_free = 0.3324 target = 0.067140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.051831 restraints weight = 65628.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.053129 restraints weight = 39758.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.054041 restraints weight = 27410.697| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 1.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12431 Z= 0.149 Angle : 0.615 11.171 16978 Z= 0.305 Chirality : 0.045 0.141 2010 Planarity : 0.004 0.053 2252 Dihedral : 11.504 178.462 1931 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1781 helix: 1.22 (0.20), residues: 783 sheet: -0.87 (0.32), residues: 257 loop : -1.60 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.006 0.001 HIS C 275 PHE 0.014 0.002 PHE C 223 TYR 0.039 0.002 TYR B 279 ARG 0.010 0.001 ARG G 335 Details of bonding type rmsd hydrogen bonds : bond 0.02835 ( 617) hydrogen bonds : angle 4.34663 ( 1701) covalent geometry : bond 0.00325 (12431) covalent geometry : angle 0.61480 (16978) *********************** 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 150 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.7674 (tt0) cc_final: 0.6989 (pt0) REVERT: G 179 ASP cc_start: 0.8522 (m-30) cc_final: 0.7812 (p0) REVERT: G 227 MET cc_start: 0.8753 (mmt) cc_final: 0.8304 (mmm) REVERT: G 260 THR cc_start: 0.8433 (m) cc_final: 0.8099 (p) REVERT: B 81 ASP cc_start: 0.8379 (m-30) cc_final: 0.8126 (p0) REVERT: C 43 VAL cc_start: 0.8777 (m) cc_final: 0.8508 (p) REVERT: C 47 MET cc_start: 0.5895 (mpp) cc_final: 0.5209 (tmm) REVERT: C 227 MET cc_start: 0.8160 (mmm) cc_final: 0.7693 (tpt) REVERT: C 305 MET cc_start: 0.8538 (mmt) cc_final: 0.8094 (mmt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1753 time to fit residues: 42.8665 Evaluate side-chains 108 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 175 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 ASN G 49 GLN G 73 HIS ** C 161 HIS ** 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 = 0.3285 r_free = 0.3285 target = 0.065571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.050210 restraints weight = 66806.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051440 restraints weight = 40309.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.052321 restraints weight = 27926.600| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 1.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12431 Z= 0.171 Angle : 0.647 11.581 16978 Z= 0.318 Chirality : 0.046 0.144 2010 Planarity : 0.004 0.044 2252 Dihedral : 11.470 179.057 1931 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1781 helix: 1.20 (0.20), residues: 786 sheet: -0.76 (0.32), residues: 260 loop : -1.52 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 340 HIS 0.007 0.001 HIS B 87 PHE 0.015 0.002 PHE B 223 TYR 0.024 0.002 TYR B 198 ARG 0.004 0.001 ARG G 256 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 617) hydrogen bonds : angle 4.41438 ( 1701) covalent geometry : bond 0.00380 (12431) covalent geometry : angle 0.64660 (16978) *********************** 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 126 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: G 179 ASP cc_start: 0.8746 (m-30) cc_final: 0.8021 (p0) REVERT: G 227 MET cc_start: 0.8987 (mmt) cc_final: 0.8681 (mmm) REVERT: G 299 MET cc_start: 0.9292 (mmp) cc_final: 0.9065 (mmm) REVERT: B 123 MET cc_start: 0.8707 (ppp) cc_final: 0.8412 (ppp) REVERT: B 167 GLU cc_start: 0.8177 (pt0) cc_final: 0.7803 (tm-30) REVERT: B 189 LEU cc_start: 0.9457 (tp) cc_final: 0.9171 (tt) REVERT: B 224 GLU cc_start: 0.8449 (mp0) cc_final: 0.8086 (mm-30) REVERT: B 283 MET cc_start: 0.9309 (mmt) cc_final: 0.9027 (tpp) REVERT: C 43 VAL cc_start: 0.9034 (m) cc_final: 0.8761 (p) REVERT: C 47 MET cc_start: 0.5835 (mpp) cc_final: 0.5522 (tmm) REVERT: C 299 MET cc_start: 0.8227 (ppp) cc_final: 0.7842 (ppp) REVERT: C 305 MET cc_start: 0.8694 (mmt) cc_final: 0.8178 (mmt) REVERT: C 353 GLN cc_start: 0.8055 (mp-120) cc_final: 0.7765 (mp10) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1725 time to fit residues: 35.5280 Evaluate side-chains 101 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 41 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 160 optimal weight: 4.9990 chunk 104 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 82 optimal weight: 50.0000 chunk 15 optimal weight: 8.9990 chunk 44 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 121 GLN ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 92 ASN B 296 ASN B 314 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS ** C 354 GLN ** 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 = 0.3141 r_free = 0.3141 target = 0.059274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.044569 restraints weight = 64622.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.045646 restraints weight = 39623.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.046426 restraints weight = 27872.477| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 1.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.146 12431 Z= 0.449 Angle : 0.985 21.721 16978 Z= 0.486 Chirality : 0.054 0.266 2010 Planarity : 0.005 0.050 2252 Dihedral : 12.322 179.049 1931 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1781 helix: 0.82 (0.20), residues: 768 sheet: -1.09 (0.32), residues: 266 loop : -1.79 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 79 HIS 0.014 0.003 HIS C 275 PHE 0.022 0.003 PHE C 223 TYR 0.035 0.003 TYR C 294 ARG 0.007 0.001 ARG G 183 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 617) hydrogen bonds : angle 5.29126 ( 1701) covalent geometry : bond 0.00986 (12431) covalent geometry : angle 0.98541 (16978) *********************** 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 107 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: G 227 MET cc_start: 0.9219 (mmt) cc_final: 0.8798 (mmm) REVERT: B 132 MET cc_start: 0.9209 (ppp) cc_final: 0.8803 (ppp) REVERT: B 189 LEU cc_start: 0.9521 (tp) cc_final: 0.9317 (tt) REVERT: B 374 CYS cc_start: 0.8798 (m) cc_final: 0.8555 (m) REVERT: C 44 MET cc_start: 0.5069 (pmm) cc_final: 0.3917 (ptt) REVERT: C 47 MET cc_start: 0.5849 (mpp) cc_final: 0.5613 (tmm) REVERT: C 305 MET cc_start: 0.8812 (mmt) cc_final: 0.8430 (mmm) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.1833 time to fit residues: 32.8438 Evaluate side-chains 88 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 158 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 50.0000 chunk 139 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** 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 = 0.3255 r_free = 0.3255 target = 0.064504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.048856 restraints weight = 66504.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.050079 restraints weight = 39992.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050913 restraints weight = 27494.859| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 1.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12431 Z= 0.131 Angle : 0.645 11.325 16978 Z= 0.312 Chirality : 0.045 0.142 2010 Planarity : 0.003 0.041 2252 Dihedral : 11.404 171.574 1931 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1781 helix: 1.21 (0.20), residues: 773 sheet: -0.85 (0.32), residues: 275 loop : -1.54 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 340 HIS 0.005 0.001 HIS C 275 PHE 0.019 0.002 PHE B 352 TYR 0.017 0.002 TYR B 198 ARG 0.007 0.001 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 617) hydrogen bonds : angle 4.46235 ( 1701) covalent geometry : bond 0.00290 (12431) covalent geometry : angle 0.64461 (16978) *********************** 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 123 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.8656 (tp30) cc_final: 0.8043 (tp30) REVERT: G 227 MET cc_start: 0.9208 (mmt) cc_final: 0.8755 (mmm) REVERT: G 305 MET cc_start: 0.8574 (mmp) cc_final: 0.8362 (mmp) REVERT: B 132 MET cc_start: 0.9184 (ppp) cc_final: 0.8706 (ppp) REVERT: B 152 VAL cc_start: 0.9628 (t) cc_final: 0.9423 (p) REVERT: C 43 VAL cc_start: 0.9137 (m) cc_final: 0.8583 (p) REVERT: C 44 MET cc_start: 0.5015 (pmm) cc_final: 0.4137 (ptt) REVERT: C 82 MET cc_start: 0.8300 (mmp) cc_final: 0.7976 (mmp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2616 time to fit residues: 52.5383 Evaluate side-chains 90 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 135 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 159 optimal weight: 0.0670 chunk 125 optimal weight: 0.0570 chunk 106 optimal weight: 0.0770 chunk 85 optimal weight: 9.9990 chunk 32 optimal weight: 0.4980 chunk 102 optimal weight: 50.0000 chunk 78 optimal weight: 40.0000 chunk 94 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** 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 = 0.3263 r_free = 0.3263 target = 0.064089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.049300 restraints weight = 60847.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.050613 restraints weight = 35987.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.051513 restraints weight = 24228.118| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 1.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12431 Z= 0.100 Angle : 0.602 10.559 16978 Z= 0.288 Chirality : 0.044 0.158 2010 Planarity : 0.003 0.047 2252 Dihedral : 10.785 173.978 1931 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.21), residues: 1781 helix: 1.49 (0.20), residues: 770 sheet: -0.67 (0.32), residues: 275 loop : -1.34 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 340 HIS 0.003 0.001 HIS C 161 PHE 0.019 0.001 PHE B 124 TYR 0.014 0.001 TYR B 53 ARG 0.005 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.02567 ( 617) hydrogen bonds : angle 4.22273 ( 1701) covalent geometry : bond 0.00218 (12431) covalent geometry : angle 0.60238 (16978) *********************** 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 118 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.8632 (tp30) cc_final: 0.8029 (tp30) REVERT: G 227 MET cc_start: 0.9200 (mmt) cc_final: 0.8807 (mmm) REVERT: G 305 MET cc_start: 0.8676 (mmp) cc_final: 0.8273 (mmp) REVERT: G 313 MET cc_start: 0.8950 (mmm) cc_final: 0.8705 (tpt) REVERT: B 82 MET cc_start: 0.8933 (mmm) cc_final: 0.7965 (mmm) REVERT: B 132 MET cc_start: 0.9285 (ppp) cc_final: 0.8521 (ppp) REVERT: B 152 VAL cc_start: 0.9606 (t) cc_final: 0.9364 (p) REVERT: C 43 VAL cc_start: 0.9106 (m) cc_final: 0.8835 (p) REVERT: C 82 MET cc_start: 0.8093 (mmp) cc_final: 0.7771 (mmp) REVERT: C 176 MET cc_start: 0.8517 (mtp) cc_final: 0.8186 (mtp) REVERT: C 305 MET cc_start: 0.8602 (mmt) cc_final: 0.8275 (mmm) REVERT: C 353 GLN cc_start: 0.8126 (mp10) cc_final: 0.7836 (mp10) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1742 time to fit residues: 34.0149 Evaluate side-chains 95 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 136 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 77 optimal weight: 50.0000 chunk 22 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 63 optimal weight: 50.0000 chunk 113 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** 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 = 0.3261 r_free = 0.3261 target = 0.063915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.049057 restraints weight = 61151.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.050368 restraints weight = 36415.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.051258 restraints weight = 24708.534| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 1.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12431 Z= 0.106 Angle : 0.603 10.178 16978 Z= 0.290 Chirality : 0.044 0.168 2010 Planarity : 0.003 0.048 2252 Dihedral : 10.558 177.394 1931 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1781 helix: 1.50 (0.20), residues: 778 sheet: -0.59 (0.33), residues: 257 loop : -1.21 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.003 0.001 HIS C 161 PHE 0.017 0.001 PHE G 223 TYR 0.011 0.001 TYR C 279 ARG 0.008 0.001 ARG C 312 Details of bonding type rmsd hydrogen bonds : bond 0.02550 ( 617) hydrogen bonds : angle 4.20366 ( 1701) covalent geometry : bond 0.00239 (12431) covalent geometry : angle 0.60303 (16978) ********************** 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 121 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.8665 (tp30) cc_final: 0.8184 (tp30) REVERT: G 227 MET cc_start: 0.9276 (mmt) cc_final: 0.8821 (mmm) REVERT: G 305 MET cc_start: 0.8694 (mmp) cc_final: 0.8301 (mmp) REVERT: G 313 MET cc_start: 0.9010 (mmm) cc_final: 0.8764 (tpt) REVERT: B 152 VAL cc_start: 0.9604 (t) cc_final: 0.9387 (p) REVERT: B 299 MET cc_start: 0.8765 (mmm) cc_final: 0.8546 (mmm) REVERT: B 305 MET cc_start: 0.8286 (mmp) cc_final: 0.7909 (mmm) REVERT: C 43 VAL cc_start: 0.9113 (m) cc_final: 0.8862 (p) REVERT: C 82 MET cc_start: 0.8096 (mmp) cc_final: 0.7781 (mmp) REVERT: C 176 MET cc_start: 0.8595 (mtp) cc_final: 0.8265 (mtp) REVERT: C 305 MET cc_start: 0.8655 (mmt) cc_final: 0.8311 (mmm) REVERT: C 353 GLN cc_start: 0.8036 (mp10) cc_final: 0.7749 (mp10) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1927 time to fit residues: 37.9954 Evaluate side-chains 95 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 101 optimal weight: 50.0000 chunk 107 optimal weight: 0.0870 chunk 154 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 41 optimal weight: 30.0000 chunk 131 optimal weight: 0.0570 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3292 r_free = 0.3292 target = 0.065935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.050399 restraints weight = 66594.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.051638 restraints weight = 40266.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.052495 restraints weight = 27756.842| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 1.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12431 Z= 0.111 Angle : 0.607 10.099 16978 Z= 0.291 Chirality : 0.044 0.162 2010 Planarity : 0.003 0.049 2252 Dihedral : 10.369 176.274 1931 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1781 helix: 1.67 (0.20), residues: 760 sheet: -0.46 (0.34), residues: 252 loop : -1.12 (0.24), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.029 0.001 PHE G 223 TYR 0.012 0.001 TYR C 279 ARG 0.008 0.001 ARG G 312 Details of bonding type rmsd hydrogen bonds : bond 0.02537 ( 617) hydrogen bonds : angle 4.18222 ( 1701) covalent geometry : bond 0.00252 (12431) covalent geometry : angle 0.60654 (16978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4016.84 seconds wall clock time: 71 minutes 38.58 seconds (4298.58 seconds total)