Starting phenix.real_space_refine on Mon Apr 6 06:59:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mm0_48383/04_2026/9mm0_48383.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mm0_48383/04_2026/9mm0_48383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mm0_48383/04_2026/9mm0_48383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mm0_48383/04_2026/9mm0_48383.map" model { file = "/net/cci-nas-00/data/ceres_data/9mm0_48383/04_2026/9mm0_48383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mm0_48383/04_2026/9mm0_48383.cif" } resolution = 2.19 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= 0.012 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 Mo 2 10.26 5 Fe 32 7.16 5 S 139 5.16 5 C 10170 2.51 5 N 2702 2.21 5 O 3820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16865 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3790 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 167 Classifications: {'water': 167} Link IDs: {None: 166} Chain: "B" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 260 Classifications: {'water': 260} Link IDs: {None: 259} Chain: "C" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 155 Classifications: {'water': 155} Link IDs: {None: 154} Chain: "D" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 256 Classifications: {'water': 256} Link IDs: {None: 255} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 26.523 37.542 35.727 1.00 30.08 S ATOM 4552 SG CYS B 95 31.339 54.567 51.213 1.00 19.87 S ATOM 1170 SG CYS A 154 27.410 56.846 48.028 1.00 26.58 S ATOM 465 SG CYS A 62 29.471 51.052 45.716 1.00 16.24 S ATOM 652 SG CYS A 88 33.510 56.735 45.605 1.00 25.85 S ATOM 652 SG CYS A 88 33.510 56.735 45.605 1.00 25.85 S ATOM 5005 SG CYS B 153 30.961 60.113 49.662 1.00 24.30 S ATOM 4372 SG CYS B 70 37.412 57.551 51.211 1.00 23.51 S ATOM 4552 SG CYS B 95 31.339 54.567 51.213 1.00 19.87 S ATOM 10056 SG CYS C 275 104.348 47.698 35.791 1.00 27.49 S ATOM 12516 SG CYS D 95 99.427 30.623 51.346 1.00 22.73 S ATOM 9134 SG CYS C 154 103.453 28.330 48.091 1.00 21.86 S ATOM 8429 SG CYS C 62 101.430 34.083 45.692 1.00 20.51 S ATOM 8616 SG CYS C 88 97.327 28.621 45.597 1.00 27.44 S ATOM 8616 SG CYS C 88 97.327 28.621 45.597 1.00 27.44 S ATOM 12969 SG CYS D 153 99.950 25.247 49.689 1.00 25.99 S ATOM 12336 SG CYS D 70 93.407 27.580 51.174 1.00 21.71 S ATOM 12516 SG CYS D 95 99.427 30.623 51.346 1.00 22.73 S Time building chain proxies: 5.47, per 1000 atoms: 0.32 Number of scatterers: 16865 At special positions: 0 Unit cell: (132.3, 85.995, 94.815, 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) Mo 2 41.97 Fe 32 26.01 S 139 16.00 O 3820 8.00 N 2702 7.00 C 10170 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 958.7 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 12 sheets defined 59.0% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.137A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.672A pdb=" N LYS A 44 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.792A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.897A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.779A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 3.505A pdb=" N MET A 279 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.574A pdb=" N LYS A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.011A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.748A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.690A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.549A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 47 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 81 removed outlier: 4.067A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.072A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.884A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.250A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.228A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.697A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.384A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.070A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.541A pdb=" N GLN C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.830A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 160 " --> pdb=" O ILE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.591A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.300A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.190A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 5.821A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.690A pdb=" N ILE C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY C 365 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA C 366 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.358A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.713A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.684A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.545A pdb=" N TRP C 472 " --> pdb=" O ASN C 469 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 473 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.638A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.044A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.058A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.879A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 309 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.355A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.879A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.406A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.563A pdb=" N LEU A 353 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR A 377 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.949A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.219A pdb=" N CYS A 249 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA A 224 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA A 251 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE A 226 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TRP A 253 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP A 222 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A 272 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA A 224 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 removed outlier: 8.515A pdb=" N VAL B 114 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.629A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.723A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 10.130A pdb=" N LEU C 399 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 375 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N TYR C 401 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 377 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU C 353 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR C 377 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.169A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 7.291A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.597A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.605A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) 788 hydrogen bonds defined for protein. 2265 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: 3.41 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.84: 16347 1.84 - 2.48: 102 2.48 - 3.12: 20 3.12 - 3.76: 10 3.76 - 4.40: 4 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.396 -2.196 2.00e-02 2.50e+03 1.21e+04 bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 4.387 -2.187 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.916 -1.716 2.00e-02 2.50e+03 7.37e+03 bond pdb="FE5 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.913 -1.713 2.00e-02 2.50e+03 7.34e+03 bond pdb=" S1 CLF B 602 " pdb="FE5 CLF B 602 " ideal model delta sigma weight residual 2.200 3.587 -1.387 2.00e-02 2.50e+03 4.81e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.89: 22235 6.89 - 13.78: 2 13.78 - 20.67: 2 20.67 - 27.56: 0 27.56 - 34.44: 4 Bond angle restraints: 22243 Sorted by residual: angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.59 34.41 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 60.71 29.29 3.00e+00 1.11e-01 9.53e+01 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 60.73 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" N LEU C 358 " pdb=" CA LEU C 358 " pdb=" C LEU C 358 " ideal model delta sigma weight residual 111.71 118.94 -7.23 1.15e+00 7.56e-01 3.95e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9299 17.99 - 35.98: 630 35.98 - 53.97: 104 53.97 - 71.96: 39 71.96 - 89.96: 29 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N ALA B 368 " pdb=" CA ALA B 368 " ideal model delta harmonic sigma weight residual 180.00 157.95 22.05 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA SER D 11 " pdb=" C SER D 11 " pdb=" N TYR D 12 " pdb=" CA TYR D 12 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA VAL A 206 " pdb=" C VAL A 206 " pdb=" N LEU A 207 " pdb=" CA LEU A 207 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1744 0.054 - 0.108: 465 0.108 - 0.162: 111 0.162 - 0.216: 10 0.216 - 0.270: 6 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA MET A 352 " pdb=" N MET A 352 " pdb=" C MET A 352 " pdb=" CB MET A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA TYR A 354 " pdb=" N TYR A 354 " pdb=" C TYR A 354 " pdb=" CB TYR A 354 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA PHE D 107 " pdb=" N PHE D 107 " pdb=" C PHE D 107 " pdb=" CB PHE D 107 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 357 " -0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C GLY C 357 " 0.085 2.00e-02 2.50e+03 pdb=" O GLY C 357 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU C 358 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 357 " -0.023 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C GLY A 357 " 0.080 2.00e-02 2.50e+03 pdb=" O GLY A 357 " -0.030 2.00e-02 2.50e+03 pdb=" N LEU A 358 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 446 " 0.040 2.00e-02 2.50e+03 2.94e-02 1.72e+01 pdb=" CG TYR C 446 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR C 446 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 446 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR C 446 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 446 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 446 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 446 " 0.008 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 183 2.53 - 3.13: 13455 3.13 - 3.72: 29929 3.72 - 4.31: 45374 4.31 - 4.90: 69197 Nonbonded interactions: 158138 Sorted by model distance: nonbonded pdb=" OE1 GLU D 109 " pdb="FE FE B 601 " model vdw 1.944 2.260 nonbonded pdb=" O ARG D 108 " pdb="FE FE B 601 " model vdw 2.047 2.260 nonbonded pdb=" O ARG B 108 " pdb="FE FE D 601 " model vdw 2.223 2.260 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 601 " model vdw 2.251 2.260 nonbonded pdb=" OH TYR A 450 " pdb=" OD2 ASP A 462 " model vdw 2.253 3.040 ... (remaining 158133 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 'A' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'C' and (resid 4 through 248 or resid 250 through 502)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.940 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.530 Find NCS groups from input model: 0.310 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 : 0.047 2.196 16499 Z= 2.391 Angle : 0.854 34.444 22243 Z= 0.476 Chirality : 0.052 0.270 2336 Planarity : 0.005 0.069 2858 Dihedral : 13.863 89.956 6433 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.99 % Allowed : 0.75 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.43 (0.18), residues: 1992 helix: 1.14 (0.17), residues: 976 sheet: -0.43 (0.38), residues: 174 loop : -0.50 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 277 TYR 0.071 0.003 TYR C 446 PHE 0.049 0.002 PHE A 118 TRP 0.016 0.002 TRP C 444 HIS 0.016 0.002 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.04710 (16483) covalent geometry : angle 0.85372 (22243) hydrogen bonds : bond 0.14870 ( 788) hydrogen bonds : angle 6.69060 ( 2265) Misc. bond : bond 0.13282 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 322 time to evaluate : 0.665 Fit side-chains REVERT: A 18 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7154 (mm-30) REVERT: A 26 LYS cc_start: 0.7977 (tttp) cc_final: 0.7605 (tttp) REVERT: A 173 GLU cc_start: 0.7746 (tt0) cc_final: 0.7483 (tt0) REVERT: A 209 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7817 (mtmt) REVERT: A 476 GLN cc_start: 0.7860 (tt0) cc_final: 0.7615 (tp40) REVERT: B 6 ASP cc_start: 0.7192 (m-30) cc_final: 0.6899 (p0) REVERT: B 7 LYS cc_start: 0.8012 (tttt) cc_final: 0.7688 (ttpt) REVERT: B 60 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 243 MET cc_start: 0.8643 (mtm) cc_final: 0.8252 (mtt) REVERT: B 503 GLU cc_start: 0.8504 (tt0) cc_final: 0.8054 (tm-30) REVERT: C 15 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6802 (mm-30) REVERT: D 6 ASP cc_start: 0.7107 (m-30) cc_final: 0.6766 (p0) REVERT: D 50 LYS cc_start: 0.8364 (mttp) cc_final: 0.8108 (mttm) REVERT: D 54 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8041 (mt-10) REVERT: D 312 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8038 (mp0) outliers start: 17 outliers final: 2 residues processed: 331 average time/residue: 0.9487 time to fit residues: 337.9167 Evaluate side-chains 218 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 380 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 252 GLN A 383 HIS B 104 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN C 98 ASN C 199 ASN C 274 HIS C 321 GLN C 469 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106374 restraints weight = 14458.650| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.98 r_work: 0.3175 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.470 16499 Z= 0.344 Angle : 0.815 31.350 22243 Z= 0.406 Chirality : 0.051 0.165 2336 Planarity : 0.006 0.091 2858 Dihedral : 5.345 58.038 2521 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.57 % Allowed : 6.91 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.48 (0.18), residues: 1992 helix: 1.15 (0.16), residues: 1000 sheet: -0.37 (0.35), residues: 194 loop : -0.47 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 277 TYR 0.021 0.003 TYR B 102 PHE 0.040 0.002 PHE C 118 TRP 0.017 0.002 TRP C 444 HIS 0.016 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00680 (16483) covalent geometry : angle 0.81469 (22243) hydrogen bonds : bond 0.07356 ( 788) hydrogen bonds : angle 5.79148 ( 2265) Misc. bond : bond 0.21733 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.607 Fit side-chains REVERT: A 4 MET cc_start: 0.1704 (ppp) cc_final: 0.1189 (ppp) REVERT: A 14 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7166 (mp-120) REVERT: A 173 GLU cc_start: 0.7798 (tt0) cc_final: 0.7552 (tt0) REVERT: A 209 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7869 (mtpm) REVERT: A 287 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: A 476 GLN cc_start: 0.8077 (tt0) cc_final: 0.7693 (tp40) REVERT: A 480 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6889 (mt-10) REVERT: B 6 ASP cc_start: 0.7479 (m-30) cc_final: 0.7251 (p0) REVERT: B 7 LYS cc_start: 0.8138 (tttt) cc_final: 0.7843 (ttpt) REVERT: B 50 LYS cc_start: 0.8509 (tptp) cc_final: 0.8080 (mttp) REVERT: B 60 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7958 (mt-10) REVERT: B 171 LYS cc_start: 0.8129 (ptmt) cc_final: 0.7806 (pttt) REVERT: C 15 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7420 (mt-10) REVERT: C 325 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8020 (mp0) REVERT: C 362 HIS cc_start: 0.8738 (OUTLIER) cc_final: 0.8395 (m170) REVERT: D 50 LYS cc_start: 0.8481 (mttp) cc_final: 0.8274 (mttm) outliers start: 27 outliers final: 8 residues processed: 233 average time/residue: 0.9334 time to fit residues: 234.5995 Evaluate side-chains 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 38 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 61 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 196 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 196 HIS A 383 HIS C 83 HIS C 196 HIS D 104 ASN ** D 128 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 = 0.3518 r_free = 0.3518 target = 0.127146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109015 restraints weight = 24325.188| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.35 r_work: 0.3202 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.335 16499 Z= 0.238 Angle : 0.697 30.753 22243 Z= 0.331 Chirality : 0.045 0.140 2336 Planarity : 0.004 0.052 2858 Dihedral : 4.879 58.769 2516 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.45 % Allowed : 8.07 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 1992 helix: 1.42 (0.17), residues: 1000 sheet: -0.33 (0.37), residues: 176 loop : -0.49 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.016 0.001 TYR B 102 PHE 0.019 0.001 PHE C 118 TRP 0.013 0.001 TRP A 253 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00452 (16483) covalent geometry : angle 0.69668 (22243) hydrogen bonds : bond 0.04982 ( 788) hydrogen bonds : angle 5.43901 ( 2265) Misc. bond : bond 0.14930 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.633 Fit side-chains REVERT: A 4 MET cc_start: 0.1770 (ppp) cc_final: 0.1148 (ppp) REVERT: A 14 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7162 (mp-120) REVERT: A 173 GLU cc_start: 0.7815 (tt0) cc_final: 0.7507 (tt0) REVERT: A 209 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7857 (mtpm) REVERT: A 476 GLN cc_start: 0.8125 (tt0) cc_final: 0.7726 (tp40) REVERT: A 480 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6851 (mt-10) REVERT: B 6 ASP cc_start: 0.7446 (m-30) cc_final: 0.7198 (p0) REVERT: B 7 LYS cc_start: 0.8110 (tttt) cc_final: 0.7781 (ttpt) REVERT: B 50 LYS cc_start: 0.8427 (tptp) cc_final: 0.8059 (mttp) REVERT: B 60 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7936 (mt-10) REVERT: B 171 LYS cc_start: 0.8197 (ptmt) cc_final: 0.7804 (pttt) REVERT: B 172 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: C 128 ASP cc_start: 0.7664 (m-30) cc_final: 0.7391 (m-30) REVERT: C 133 LYS cc_start: 0.8312 (tptm) cc_final: 0.8083 (tttm) REVERT: C 325 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7963 (mp0) REVERT: C 362 HIS cc_start: 0.8697 (OUTLIER) cc_final: 0.8145 (m170) REVERT: D 50 LYS cc_start: 0.8450 (mttp) cc_final: 0.8220 (mttm) REVERT: D 86 MET cc_start: 0.9043 (tpp) cc_final: 0.8715 (tpp) outliers start: 25 outliers final: 8 residues processed: 231 average time/residue: 0.9173 time to fit residues: 229.0001 Evaluate side-chains 211 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 38 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 22 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 383 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105293 restraints weight = 24147.590| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.34 r_work: 0.3152 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.367 16499 Z= 0.279 Angle : 0.741 30.761 22243 Z= 0.359 Chirality : 0.047 0.146 2336 Planarity : 0.005 0.072 2858 Dihedral : 4.947 47.925 2516 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.28 % Allowed : 8.88 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 1992 helix: 1.41 (0.17), residues: 1002 sheet: -0.25 (0.37), residues: 176 loop : -0.47 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.016 0.002 TYR B 102 PHE 0.015 0.002 PHE A 429 TRP 0.013 0.002 TRP C 444 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00545 (16483) covalent geometry : angle 0.74095 (22243) hydrogen bonds : bond 0.06019 ( 788) hydrogen bonds : angle 5.48990 ( 2265) Misc. bond : bond 0.17005 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.692 Fit side-chains REVERT: A 4 MET cc_start: 0.1621 (ppp) cc_final: 0.0947 (ppp) REVERT: A 14 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7192 (mp-120) REVERT: A 173 GLU cc_start: 0.7855 (tt0) cc_final: 0.7531 (tt0) REVERT: A 209 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7847 (mtpm) REVERT: A 287 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.6564 (tp30) REVERT: A 358 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8501 (tp) REVERT: A 476 GLN cc_start: 0.8136 (tt0) cc_final: 0.7716 (tp40) REVERT: A 480 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6985 (mt-10) REVERT: B 6 ASP cc_start: 0.7507 (m-30) cc_final: 0.7250 (p0) REVERT: B 7 LYS cc_start: 0.8196 (tttt) cc_final: 0.7821 (ttpt) REVERT: B 50 LYS cc_start: 0.8508 (tptp) cc_final: 0.8086 (mttp) REVERT: B 60 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7946 (mt-10) REVERT: B 172 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: C 133 LYS cc_start: 0.8391 (tptm) cc_final: 0.8173 (tttm) REVERT: C 325 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7991 (mp0) REVERT: C 362 HIS cc_start: 0.8786 (OUTLIER) cc_final: 0.8331 (m170) REVERT: D 50 LYS cc_start: 0.8469 (mttp) cc_final: 0.8232 (mttm) REVERT: D 379 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8589 (tt) outliers start: 22 outliers final: 9 residues processed: 216 average time/residue: 0.9065 time to fit residues: 211.9802 Evaluate side-chains 214 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 35 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 383 HIS A 432 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.109622 restraints weight = 18172.765| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.15 r_work: 0.3221 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.308 16499 Z= 0.233 Angle : 0.688 30.666 22243 Z= 0.326 Chirality : 0.044 0.142 2336 Planarity : 0.004 0.052 2858 Dihedral : 4.735 44.930 2516 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.22 % Allowed : 9.58 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.83 (0.19), residues: 1992 helix: 1.51 (0.17), residues: 1014 sheet: -0.28 (0.37), residues: 176 loop : -0.44 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.014 0.001 TYR D 88 PHE 0.012 0.001 PHE A 429 TRP 0.013 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00444 (16483) covalent geometry : angle 0.68830 (22243) hydrogen bonds : bond 0.04823 ( 788) hydrogen bonds : angle 5.32926 ( 2265) Misc. bond : bond 0.13957 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.674 Fit side-chains REVERT: A 4 MET cc_start: 0.1526 (ppp) cc_final: 0.0868 (pmt) REVERT: A 14 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7167 (mp-120) REVERT: A 173 GLU cc_start: 0.7829 (tt0) cc_final: 0.7540 (tt0) REVERT: A 287 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.6544 (tp30) REVERT: A 476 GLN cc_start: 0.8058 (tt0) cc_final: 0.7734 (tp40) REVERT: A 480 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6946 (mt-10) REVERT: B 6 ASP cc_start: 0.7392 (m-30) cc_final: 0.7177 (p0) REVERT: B 7 LYS cc_start: 0.8137 (tttt) cc_final: 0.7750 (ttpt) REVERT: B 50 LYS cc_start: 0.8427 (tptp) cc_final: 0.8075 (mttp) REVERT: B 60 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7910 (mt-10) REVERT: B 171 LYS cc_start: 0.8185 (ptmt) cc_final: 0.7915 (pttt) REVERT: C 133 LYS cc_start: 0.8261 (tptm) cc_final: 0.8028 (tttm) REVERT: C 325 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7911 (mp0) REVERT: C 362 HIS cc_start: 0.8748 (OUTLIER) cc_final: 0.8139 (m170) REVERT: D 50 LYS cc_start: 0.8488 (mttp) cc_final: 0.8252 (mttm) REVERT: D 86 MET cc_start: 0.9036 (tpp) cc_final: 0.8673 (tpp) outliers start: 21 outliers final: 8 residues processed: 219 average time/residue: 0.9038 time to fit residues: 214.1350 Evaluate side-chains 211 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 29 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 158 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 383 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105911 restraints weight = 23016.435| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.33 r_work: 0.3158 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.336 16499 Z= 0.261 Angle : 0.721 30.738 22243 Z= 0.346 Chirality : 0.046 0.146 2336 Planarity : 0.005 0.065 2858 Dihedral : 4.814 46.911 2516 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.68 % Allowed : 9.52 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.79 (0.19), residues: 1992 helix: 1.48 (0.17), residues: 1014 sheet: -0.27 (0.37), residues: 176 loop : -0.46 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.016 0.002 TYR D 88 PHE 0.014 0.002 PHE A 429 TRP 0.012 0.002 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00507 (16483) covalent geometry : angle 0.72086 (22243) hydrogen bonds : bond 0.05584 ( 788) hydrogen bonds : angle 5.38324 ( 2265) Misc. bond : bond 0.15660 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.714 Fit side-chains REVERT: A 4 MET cc_start: 0.1734 (ppp) cc_final: 0.0816 (pmm) REVERT: A 14 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7157 (mp-120) REVERT: A 173 GLU cc_start: 0.7877 (tt0) cc_final: 0.7565 (tt0) REVERT: A 476 GLN cc_start: 0.8083 (tt0) cc_final: 0.7725 (tp40) REVERT: A 480 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: B 6 ASP cc_start: 0.7445 (m-30) cc_final: 0.7178 (p0) REVERT: B 7 LYS cc_start: 0.8158 (tttt) cc_final: 0.7775 (ttpt) REVERT: B 60 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 128 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.6936 (tm-30) REVERT: B 171 LYS cc_start: 0.8177 (ptmt) cc_final: 0.7809 (pttt) REVERT: B 303 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8358 (mtmt) REVERT: B 507 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: C 133 LYS cc_start: 0.8314 (tptm) cc_final: 0.8079 (tttm) REVERT: C 325 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7934 (mp0) REVERT: C 362 HIS cc_start: 0.8773 (OUTLIER) cc_final: 0.8221 (m170) REVERT: D 50 LYS cc_start: 0.8485 (mttp) cc_final: 0.8217 (mttm) REVERT: D 86 MET cc_start: 0.9062 (tpp) cc_final: 0.8681 (tpp) REVERT: D 299 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: D 379 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8567 (tt) outliers start: 29 outliers final: 12 residues processed: 227 average time/residue: 0.9007 time to fit residues: 221.7197 Evaluate side-chains 223 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 111 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 chunk 185 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 383 HIS A 432 GLN C 53 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109729 restraints weight = 23100.744| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.32 r_work: 0.3218 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.289 16499 Z= 0.222 Angle : 0.677 30.635 22243 Z= 0.319 Chirality : 0.044 0.143 2336 Planarity : 0.004 0.048 2858 Dihedral : 4.606 43.971 2516 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.28 % Allowed : 10.27 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.86 (0.19), residues: 1992 helix: 1.57 (0.17), residues: 1016 sheet: -0.29 (0.37), residues: 176 loop : -0.46 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 108 TYR 0.012 0.001 TYR D 88 PHE 0.011 0.001 PHE A 429 TRP 0.014 0.001 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00424 (16483) covalent geometry : angle 0.67746 (22243) hydrogen bonds : bond 0.04536 ( 788) hydrogen bonds : angle 5.25351 ( 2265) Misc. bond : bond 0.12992 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.696 Fit side-chains REVERT: A 4 MET cc_start: 0.1653 (ppp) cc_final: 0.0697 (pmm) REVERT: A 11 SER cc_start: 0.8021 (m) cc_final: 0.7765 (p) REVERT: A 14 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7208 (mp-120) REVERT: A 173 GLU cc_start: 0.7823 (tt0) cc_final: 0.7529 (tt0) REVERT: A 358 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8428 (tp) REVERT: A 476 GLN cc_start: 0.8065 (tt0) cc_final: 0.7714 (tp40) REVERT: B 6 ASP cc_start: 0.7382 (m-30) cc_final: 0.7150 (p0) REVERT: B 7 LYS cc_start: 0.8097 (tttt) cc_final: 0.7712 (ttpt) REVERT: B 60 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7903 (mt-10) REVERT: B 171 LYS cc_start: 0.8164 (ptmt) cc_final: 0.7796 (pttt) REVERT: C 133 LYS cc_start: 0.8255 (tptm) cc_final: 0.8016 (tttm) REVERT: C 325 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7901 (mp0) REVERT: C 362 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.8063 (m170) REVERT: D 50 LYS cc_start: 0.8468 (mttp) cc_final: 0.8212 (mttm) REVERT: D 84 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8557 (mttp) REVERT: D 86 MET cc_start: 0.9008 (tpp) cc_final: 0.8658 (tpp) outliers start: 22 outliers final: 12 residues processed: 227 average time/residue: 0.8773 time to fit residues: 215.8752 Evaluate side-chains 214 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 187 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 383 HIS C 53 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110083 restraints weight = 17083.932| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.11 r_work: 0.3227 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.288 16499 Z= 0.230 Angle : 0.687 30.660 22243 Z= 0.324 Chirality : 0.044 0.144 2336 Planarity : 0.004 0.052 2858 Dihedral : 4.573 44.138 2516 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.28 % Allowed : 10.50 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.19), residues: 1992 helix: 1.61 (0.17), residues: 1016 sheet: -0.23 (0.37), residues: 176 loop : -0.44 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.014 0.001 TYR D 88 PHE 0.012 0.001 PHE A 429 TRP 0.012 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00442 (16483) covalent geometry : angle 0.68738 (22243) hydrogen bonds : bond 0.04786 ( 788) hydrogen bonds : angle 5.24895 ( 2265) Misc. bond : bond 0.13420 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.725 Fit side-chains REVERT: A 4 MET cc_start: 0.1549 (ppp) cc_final: 0.0697 (pmm) REVERT: A 11 SER cc_start: 0.8037 (m) cc_final: 0.7806 (p) REVERT: A 173 GLU cc_start: 0.7819 (tt0) cc_final: 0.7506 (tt0) REVERT: A 358 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8463 (tp) REVERT: A 476 GLN cc_start: 0.8056 (tt0) cc_final: 0.7730 (tp40) REVERT: B 7 LYS cc_start: 0.8117 (tttt) cc_final: 0.7749 (ttpt) REVERT: B 60 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7900 (mt-10) REVERT: B 171 LYS cc_start: 0.8132 (ptmt) cc_final: 0.7770 (pttt) REVERT: C 133 LYS cc_start: 0.8263 (tptm) cc_final: 0.8029 (tttm) REVERT: C 325 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7912 (mp0) REVERT: C 362 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.8187 (m170) REVERT: D 50 LYS cc_start: 0.8472 (mttp) cc_final: 0.8237 (mttm) REVERT: D 84 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8573 (mttp) REVERT: D 86 MET cc_start: 0.9029 (tpp) cc_final: 0.8677 (tpp) outliers start: 22 outliers final: 14 residues processed: 218 average time/residue: 0.8757 time to fit residues: 207.1953 Evaluate side-chains 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 113 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 383 HIS C 98 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.103896 restraints weight = 23424.419| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.33 r_work: 0.3135 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.382 16499 Z= 0.296 Angle : 0.765 30.686 22243 Z= 0.373 Chirality : 0.048 0.147 2336 Planarity : 0.005 0.076 2858 Dihedral : 4.925 49.906 2516 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.28 % Allowed : 10.97 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.18), residues: 1992 helix: 1.44 (0.17), residues: 1016 sheet: -0.22 (0.37), residues: 176 loop : -0.47 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 277 TYR 0.017 0.002 TYR D 88 PHE 0.015 0.002 PHE A 429 TRP 0.012 0.002 TRP C 444 HIS 0.011 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00588 (16483) covalent geometry : angle 0.76471 (22243) hydrogen bonds : bond 0.06364 ( 788) hydrogen bonds : angle 5.45971 ( 2265) Misc. bond : bond 0.17216 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.758 Fit side-chains REVERT: A 4 MET cc_start: 0.1697 (ppp) cc_final: 0.0774 (pmm) REVERT: A 173 GLU cc_start: 0.7882 (tt0) cc_final: 0.7588 (tt0) REVERT: A 476 GLN cc_start: 0.8109 (tt0) cc_final: 0.7711 (tp40) REVERT: B 7 LYS cc_start: 0.8145 (tttt) cc_final: 0.7773 (ttpt) REVERT: B 60 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7976 (mt-10) REVERT: B 128 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: B 171 LYS cc_start: 0.8169 (ptmt) cc_final: 0.7788 (pttt) REVERT: C 133 LYS cc_start: 0.8385 (tptm) cc_final: 0.8154 (tttm) REVERT: C 325 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7962 (mp0) REVERT: C 362 HIS cc_start: 0.8800 (OUTLIER) cc_final: 0.8359 (m170) REVERT: D 50 LYS cc_start: 0.8519 (mttp) cc_final: 0.8271 (mttm) REVERT: D 280 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8174 (mt-10) REVERT: D 379 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8569 (tt) outliers start: 22 outliers final: 11 residues processed: 220 average time/residue: 0.8852 time to fit residues: 211.2114 Evaluate side-chains 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 176 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 189 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 383 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.106593 restraints weight = 24098.887| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.35 r_work: 0.3173 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.314 16499 Z= 0.247 Angle : 0.709 30.693 22243 Z= 0.339 Chirality : 0.045 0.143 2336 Planarity : 0.004 0.058 2858 Dihedral : 4.768 46.994 2516 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.93 % Allowed : 11.26 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.82 (0.19), residues: 1992 helix: 1.52 (0.17), residues: 1016 sheet: -0.26 (0.37), residues: 176 loop : -0.48 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.014 0.002 TYR D 88 PHE 0.013 0.001 PHE A 429 TRP 0.012 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00476 (16483) covalent geometry : angle 0.70904 (22243) hydrogen bonds : bond 0.05209 ( 788) hydrogen bonds : angle 5.33707 ( 2265) Misc. bond : bond 0.14734 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.700 Fit side-chains REVERT: A 4 MET cc_start: 0.1617 (ppp) cc_final: 0.0559 (pmm) REVERT: A 11 SER cc_start: 0.8104 (m) cc_final: 0.7861 (p) REVERT: A 173 GLU cc_start: 0.7886 (tt0) cc_final: 0.7586 (tt0) REVERT: A 476 GLN cc_start: 0.8093 (tt0) cc_final: 0.7744 (tp40) REVERT: B 7 LYS cc_start: 0.8119 (tttt) cc_final: 0.7743 (ttpt) REVERT: B 60 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7956 (mt-10) REVERT: B 128 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: B 171 LYS cc_start: 0.8157 (ptmt) cc_final: 0.7775 (pttt) REVERT: C 133 LYS cc_start: 0.8330 (tptm) cc_final: 0.8095 (tttm) REVERT: C 325 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7943 (mp0) REVERT: C 362 HIS cc_start: 0.8790 (OUTLIER) cc_final: 0.8213 (m170) REVERT: D 50 LYS cc_start: 0.8498 (mttp) cc_final: 0.8245 (mttm) REVERT: D 84 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8579 (mttp) REVERT: D 86 MET cc_start: 0.9063 (tpp) cc_final: 0.8715 (tpp) outliers start: 16 outliers final: 9 residues processed: 212 average time/residue: 0.9114 time to fit residues: 209.1678 Evaluate side-chains 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 84 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 79 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 383 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.124890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106091 restraints weight = 25809.727| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.41 r_work: 0.3164 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.313 16499 Z= 0.251 Angle : 0.715 30.691 22243 Z= 0.342 Chirality : 0.045 0.145 2336 Planarity : 0.004 0.059 2858 Dihedral : 4.737 46.028 2516 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.99 % Allowed : 11.20 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.82 (0.19), residues: 1992 helix: 1.52 (0.17), residues: 1016 sheet: -0.25 (0.37), residues: 176 loop : -0.47 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.015 0.002 TYR D 88 PHE 0.013 0.001 PHE A 429 TRP 0.012 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00485 (16483) covalent geometry : angle 0.71466 (22243) hydrogen bonds : bond 0.05327 ( 788) hydrogen bonds : angle 5.33842 ( 2265) Misc. bond : bond 0.14843 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7579.74 seconds wall clock time: 129 minutes 43.91 seconds (7783.91 seconds total)