Starting phenix.real_space_refine on Fri Oct 23 23:21:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pzn_72073/10_2026/9pzn_72073.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pzn_72073/10_2026/9pzn_72073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pzn_72073/10_2026/9pzn_72073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pzn_72073/10_2026/9pzn_72073.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pzn_72073/10_2026/9pzn_72073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pzn_72073/10_2026/9pzn_72073.map" } resolution = 2.86 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= -0.001 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 7175 2.51 5 N 1841 2.21 5 O 2153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11253 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3635 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 434} Chain breaks: 2 Chain: "C" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3589 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 427} Chain breaks: 2 Chain: "A" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3828 Classifications: {'peptide': 473} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 449} Chain breaks: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.78, per 1000 atoms: 0.25 Number of scatterers: 11253 At special positions: 0 Unit cell: (102.96, 104, 123.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2153 8.00 N 1841 7.00 C 7175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 241 " distance=2.04 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 480 " distance=2.03 Simple disulfide: pdb=" SG CYS B 408 " - pdb=" SG CYS B 476 " distance=2.03 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 444 " distance=2.04 Simple disulfide: pdb=" SG CYS B 423 " - pdb=" SG CYS B 437 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 255 " distance=2.03 Simple disulfide: pdb=" SG CYS C 195 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 241 " distance=2.04 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 480 " distance=2.04 Simple disulfide: pdb=" SG CYS C 408 " - pdb=" SG CYS C 476 " distance=2.04 Simple disulfide: pdb=" SG CYS C 412 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 444 " distance=2.04 Simple disulfide: pdb=" SG CYS C 423 " - pdb=" SG CYS C 437 " distance=2.03 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 253 " distance=2.04 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 341 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 489 " distance=2.04 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 422 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 447 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 701 " - " ASN A 294 " " NAG C 601 " - " ASN C 206 " " NAG D 1 " - " ASN B 415 " " NAG E 1 " - " ASN B 159 " " NAG F 1 " - " ASN C 159 " " NAG G 1 " - " ASN C 415 " " NAG H 1 " - " ASN A 425 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 471.2 milliseconds 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 39.2% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 100 through 124 Processing helix chain 'B' and resid 159 through 172 Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.597A pdb=" N ILE B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 244' Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 311 through 314 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 377 through 380 Processing helix chain 'B' and resid 404 through 422 Processing helix chain 'B' and resid 441 through 462 removed outlier: 3.524A pdb=" N GLN B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'B' and resid 541 through 557 Processing helix chain 'B' and resid 562 through 569 Processing helix chain 'C' and resid 98 through 124 removed outlier: 4.081A pdb=" N VAL C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 159 through 172 removed outlier: 3.709A pdb=" N ARG C 168 " --> pdb=" O TYR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 192 removed outlier: 3.504A pdb=" N ALA C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 377 through 380 Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 404 through 422 Processing helix chain 'C' and resid 441 through 461 removed outlier: 4.228A pdb=" N ASP C 450 " --> pdb=" O ASN C 446 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 453 " --> pdb=" O GLU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 557 Processing helix chain 'C' and resid 560 through 569 Processing helix chain 'A' and resid 95 through 119 Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.503A pdb=" N ARG A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.687A pdb=" N ILE A 392 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 414 through 432 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 451 through 473 removed outlier: 3.706A pdb=" N GLN A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 512 removed outlier: 3.663A pdb=" N THR A 508 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 561 Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.538A pdb=" N GLU A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 127 through 130 removed outlier: 7.125A pdb=" N SER B 534 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 372 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ARG B 536 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR B 374 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN B 362 " --> pdb=" O MET B 519 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY B 321 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR B 229 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 127 through 130 removed outlier: 7.125A pdb=" N SER B 534 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 372 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ARG B 536 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR B 374 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 486 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 135 through 136 Processing sheet with id=AA4, first strand: chain 'B' and resid 245 through 250 removed outlier: 7.442A pdb=" N VAL B 254 " --> pdb=" O PRO B 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.669A pdb=" N VAL B 436 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 126 through 130 removed outlier: 6.190A pdb=" N ILE C 372 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG C 536 " --> pdb=" O ILE C 372 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR C 374 " --> pdb=" O ARG C 536 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLU C 538 " --> pdb=" O THR C 374 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 135 through 136 Processing sheet with id=AA8, first strand: chain 'C' and resid 246 through 250 removed outlier: 7.387A pdb=" N VAL C 254 " --> pdb=" O PRO C 149 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS C 343 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.696A pdb=" N VAL C 436 " --> pdb=" O ARG C 209 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 237 through 239 removed outlier: 4.374A pdb=" N CYS C 232 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TYR C 229 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY C 321 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN C 362 " --> pdb=" O MET C 519 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 121 through 125 removed outlier: 6.817A pdb=" N ILE A 538 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR A 382 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ARG A 540 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 384 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ILE A 542 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP A 372 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE A 229 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 121 through 125 removed outlier: 6.817A pdb=" N ILE A 538 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR A 382 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ARG A 540 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 384 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ILE A 542 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 493 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB5, first strand: chain 'A' and resid 243 through 248 removed outlier: 6.960A pdb=" N ILE A 252 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 298 through 300 removed outlier: 3.558A pdb=" N SER A 300 " --> pdb=" O GLY A 304 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1410 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: 1.99 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3265 1.33 - 1.46: 2722 1.46 - 1.58: 5421 1.58 - 1.71: 0 1.71 - 1.83: 112 Bond restraints: 11520 Sorted by residual: bond pdb=" CG GLU A 404 " pdb=" CD GLU A 404 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.75e+00 bond pdb=" CB ASN A 257 " pdb=" CG ASN A 257 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.80e+00 bond pdb=" CB ASP B 439 " pdb=" CG ASP B 439 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.63e+00 bond pdb=" CB ARG A 235 " pdb=" CG ARG A 235 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CG GLN A 308 " pdb=" CD GLN A 308 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.53e+00 ... (remaining 11515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 14421 1.41 - 2.81: 1027 2.81 - 4.22: 135 4.22 - 5.63: 25 5.63 - 7.04: 6 Bond angle restraints: 15614 Sorted by residual: angle pdb=" CA TYR C 445 " pdb=" CB TYR C 445 " pdb=" CG TYR C 445 " ideal model delta sigma weight residual 113.90 120.94 -7.04 1.80e+00 3.09e-01 1.53e+01 angle pdb=" CA TYR B 445 " pdb=" CB TYR B 445 " pdb=" CG TYR B 445 " ideal model delta sigma weight residual 113.90 120.90 -7.00 1.80e+00 3.09e-01 1.51e+01 angle pdb=" CA TYR A 455 " pdb=" CB TYR A 455 " pdb=" CG TYR A 455 " ideal model delta sigma weight residual 113.90 120.23 -6.33 1.80e+00 3.09e-01 1.24e+01 angle pdb=" CB LYS B 420 " pdb=" CG LYS B 420 " pdb=" CD LYS B 420 " ideal model delta sigma weight residual 111.30 117.87 -6.57 2.30e+00 1.89e-01 8.17e+00 angle pdb=" CA TYR B 164 " pdb=" CB TYR B 164 " pdb=" CG TYR B 164 " ideal model delta sigma weight residual 113.90 119.00 -5.10 1.80e+00 3.09e-01 8.02e+00 ... (remaining 15609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6576 17.87 - 35.73: 414 35.73 - 53.60: 73 53.60 - 71.46: 37 71.46 - 89.33: 24 Dihedral angle restraints: 7124 sinusoidal: 3095 harmonic: 4029 Sorted by residual: dihedral pdb=" CA PRO A 138 " pdb=" C PRO A 138 " pdb=" N THR A 139 " pdb=" CA THR A 139 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA TYR A 237 " pdb=" C TYR A 237 " pdb=" N PHE A 238 " pdb=" CA PHE A 238 " ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ARG B 279 " pdb=" C ARG B 279 " pdb=" N GLU B 280 " pdb=" CA GLU B 280 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 7121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 993 0.035 - 0.070: 500 0.070 - 0.105: 194 0.105 - 0.140: 52 0.140 - 0.175: 13 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CA ILE C 127 " pdb=" N ILE C 127 " pdb=" C ILE C 127 " pdb=" CB ILE C 127 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA PRO B 345 " pdb=" N PRO B 345 " pdb=" C PRO B 345 " pdb=" CB PRO B 345 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA PRO C 345 " pdb=" N PRO C 345 " pdb=" C PRO C 345 " pdb=" CB PRO C 345 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 1749 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 387 " -0.220 9.50e-02 1.11e+02 9.88e-02 6.06e+00 pdb=" NE ARG B 387 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 387 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 387 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 387 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 387 " 0.204 9.50e-02 1.11e+02 9.17e-02 5.18e+00 pdb=" NE ARG C 387 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 387 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 387 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 387 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 279 " -0.198 9.50e-02 1.11e+02 8.88e-02 4.86e+00 pdb=" NE ARG C 279 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 279 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 279 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 279 " -0.008 2.00e-02 2.50e+03 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 6991 3.04 - 3.51: 10915 3.51 - 3.97: 18585 3.97 - 4.44: 22474 4.44 - 4.90: 34658 Nonbonded interactions: 93623 Sorted by model distance: nonbonded pdb=" OG1 THR B 375 " pdb=" O CYS B 480 " model vdw 2.581 3.040 nonbonded pdb=" OH TYR C 382 " pdb=" OE2 GLU C 538 " model vdw 2.585 3.040 nonbonded pdb=" N GLU A 493 " pdb=" O GLU A 493 " model vdw 2.601 2.496 nonbonded pdb=" OG SER A 385 " pdb=" O CYS A 489 " model vdw 2.605 3.040 nonbonded pdb=" N CYS B 255 " pdb=" O CYS B 255 " model vdw 2.606 2.496 ... (remaining 93618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 100 through 498 or resid 514 through 569)) selection = (chain 'C' and resid 100 through 569) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.330 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.330 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:8.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 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 : 0.007 0.054 11559 Z= 0.320 Angle : 0.829 8.330 15707 Z= 0.451 Chirality : 0.048 0.175 1752 Planarity : 0.007 0.099 1997 Dihedral : 14.063 89.327 4448 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.16 % Allowed : 1.61 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.20), residues: 1362 helix: -1.30 (0.19), residues: 471 sheet: -0.84 (0.33), residues: 231 loop : -0.64 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 540 TYR 0.034 0.003 TYR C 445 PHE 0.021 0.003 PHE A 198 TRP 0.019 0.003 TRP C 118 HIS 0.009 0.002 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.32 (11520) covalent geometry : angle 0.80231 / 0.45 (15614) SS BOND : bond 0.00482 / 0.30 ( 24) SS BOND : angle 1.59428 / 1.21 ( 48) hydrogen bonds : bond 0.12503 / 7.82 ( 506) hydrogen bonds : angle 7.31043 / 5.31 ( 1410) link_BETA1-4 : bond 0.01087 / 0.47 ( 8) link_BETA1-4 : angle 3.73983 / 2.31 ( 24) link_NAG-ASN : bond 0.00541 / 0.27 ( 7) link_NAG-ASN : angle 3.71729 / 2.37 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 THR cc_start: 0.7772 (m) cc_final: 0.7449 (t) REVERT: C 112 LYS cc_start: 0.8215 (tttt) cc_final: 0.7974 (tptp) REVERT: C 386 ARG cc_start: 0.8087 (tpt-90) cc_final: 0.7270 (ttt180) REVERT: C 514 ARG cc_start: 0.8114 (mmt90) cc_final: 0.7051 (pmt-80) REVERT: A 329 PHE cc_start: 0.8859 (t80) cc_final: 0.8560 (t80) outliers start: 2 outliers final: 3 residues processed: 242 average time/residue: 0.6818 time to fit residues: 175.9316 Evaluate side-chains 138 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 495 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 447 GLN C 123 ASN C 354 GLN C 392 GLN A 117 GLN A 204 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.106822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.089861 restraints weight = 19640.067| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.37 r_work: 0.3019 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11559 Z= 0.163 Angle : 0.626 7.857 15707 Z= 0.322 Chirality : 0.043 0.161 1752 Planarity : 0.005 0.054 1997 Dihedral : 9.078 120.576 1806 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.09 % Allowed : 9.32 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.22), residues: 1362 helix: 0.44 (0.22), residues: 487 sheet: -0.81 (0.33), residues: 238 loop : 0.15 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 313 TYR 0.028 0.002 TYR B 164 PHE 0.017 0.001 PHE B 457 TRP 0.015 0.001 TRP C 118 HIS 0.002 0.001 HIS B 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11520) covalent geometry : angle 0.61049 / 0.32 (15614) SS BOND : bond 0.00255 / 0.17 ( 24) SS BOND : angle 1.44644 / 1.35 ( 48) hydrogen bonds : bond 0.04300 / 2.78 ( 506) hydrogen bonds : angle 5.58467 / 4.03 ( 1410) link_BETA1-4 : bond 0.00331 / 0.17 ( 8) link_BETA1-4 : angle 2.42961 / 1.70 ( 24) link_NAG-ASN : bond 0.00346 / 0.16 ( 7) link_NAG-ASN : angle 2.09851 / 1.37 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 109 THR cc_start: 0.8283 (m) cc_final: 0.7808 (t) REVERT: B 196 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8778 (mm-30) REVERT: B 251 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8532 (mt-10) REVERT: B 447 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: B 513 LYS cc_start: 0.9254 (mtmm) cc_final: 0.8701 (mtmm) REVERT: C 112 LYS cc_start: 0.8219 (tttt) cc_final: 0.7663 (tptp) REVERT: C 119 ASP cc_start: 0.8279 (t0) cc_final: 0.7600 (m-30) REVERT: C 133 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8780 (mtmm) REVERT: C 204 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8434 (mt) REVERT: C 363 GLU cc_start: 0.8602 (tt0) cc_final: 0.8380 (tp30) REVERT: C 369 ARG cc_start: 0.8787 (mtp-110) cc_final: 0.8484 (mtp-110) REVERT: C 386 ARG cc_start: 0.8455 (tpt-90) cc_final: 0.7155 (ttt180) REVERT: C 495 ASP cc_start: 0.8076 (t0) cc_final: 0.7563 (t0) REVERT: C 514 ARG cc_start: 0.8163 (mmt90) cc_final: 0.6784 (pmt-80) REVERT: C 528 GLU cc_start: 0.9270 (mt-10) cc_final: 0.9042 (mt-10) REVERT: C 531 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8337 (p90) REVERT: A 329 PHE cc_start: 0.8988 (t80) cc_final: 0.8614 (t80) REVERT: A 497 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8816 (mt-10) outliers start: 26 outliers final: 5 residues processed: 173 average time/residue: 0.5858 time to fit residues: 108.9440 Evaluate side-chains 131 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 531 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain A residue 118 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [81, 46, 49, 63, 96, 27, 98, 76, 2, 77, 92] chunk 81 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 98 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 447 GLN A 117 GLN A 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.106911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089779 restraints weight = 19690.436| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.39 r_work: 0.3029 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11559 Z= 0.136 Angle : 0.568 9.639 15707 Z= 0.290 Chirality : 0.042 0.175 1752 Planarity : 0.004 0.047 1997 Dihedral : 6.466 55.153 1802 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.65 % Allowed : 10.61 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.22), residues: 1362 helix: 1.05 (0.23), residues: 490 sheet: -0.71 (0.33), residues: 236 loop : 0.50 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 313 TYR 0.023 0.002 TYR C 445 PHE 0.018 0.001 PHE B 170 TRP 0.012 0.001 TRP C 118 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (11520) covalent geometry : angle 0.55566 / 0.29 (15614) SS BOND : bond 0.00359 / 0.26 ( 24) SS BOND : angle 1.13741 / 1.00 ( 48) hydrogen bonds : bond 0.03797 / 2.48 ( 506) hydrogen bonds : angle 5.18943 / 3.74 ( 1410) link_BETA1-4 : bond 0.00436 / 0.20 ( 8) link_BETA1-4 : angle 2.10909 / 1.48 ( 24) link_NAG-ASN : bond 0.00243 / 0.10 ( 7) link_NAG-ASN : angle 1.92808 / 1.28 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 THR cc_start: 0.8344 (m) cc_final: 0.7896 (t) REVERT: B 447 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8748 (tm-30) REVERT: B 488 GLU cc_start: 0.8621 (mp0) cc_final: 0.8147 (mp0) REVERT: B 513 LYS cc_start: 0.9100 (mtmm) cc_final: 0.8645 (mtmm) REVERT: C 112 LYS cc_start: 0.8219 (tttt) cc_final: 0.7647 (tptp) REVERT: C 119 ASP cc_start: 0.8244 (t0) cc_final: 0.7534 (m-30) REVERT: C 133 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8781 (mtmm) REVERT: C 204 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8499 (mt) REVERT: C 363 GLU cc_start: 0.8631 (tt0) cc_final: 0.8354 (tp30) REVERT: C 386 ARG cc_start: 0.8479 (tpt-90) cc_final: 0.7216 (ttt180) REVERT: C 449 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: C 514 ARG cc_start: 0.8064 (mmt90) cc_final: 0.6740 (pmt-80) REVERT: C 527 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8844 (ttpt) REVERT: C 531 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8356 (p90) REVERT: A 329 PHE cc_start: 0.9033 (t80) cc_final: 0.8809 (t80) REVERT: A 454 CYS cc_start: 0.6530 (OUTLIER) cc_final: 0.6288 (t) REVERT: A 497 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8915 (mt-10) outliers start: 33 outliers final: 14 residues processed: 160 average time/residue: 0.5482 time to fit residues: 95.0173 Evaluate side-chains 145 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 531 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 561 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [40, 108, 42, 55, 84, 115, 18, 87, 80, 101, 78] chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 84 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 87 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 447 GLN A 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089362 restraints weight = 19794.437| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.41 r_work: 0.3031 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11559 Z= 0.141 Angle : 0.555 8.523 15707 Z= 0.283 Chirality : 0.042 0.160 1752 Planarity : 0.004 0.055 1997 Dihedral : 5.591 55.138 1802 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.49 % Allowed : 11.98 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.22), residues: 1362 helix: 1.26 (0.23), residues: 490 sheet: -0.69 (0.33), residues: 240 loop : 0.60 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 313 TYR 0.023 0.002 TYR C 445 PHE 0.014 0.001 PHE B 170 TRP 0.010 0.001 TRP C 118 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11520) covalent geometry : angle 0.54465 / 0.28 (15614) SS BOND : bond 0.00246 / 0.16 ( 24) SS BOND : angle 1.01848 / 0.88 ( 48) hydrogen bonds : bond 0.03590 / 2.35 ( 506) hydrogen bonds : angle 5.02442 / 3.61 ( 1410) link_BETA1-4 : bond 0.00368 / 0.17 ( 8) link_BETA1-4 : angle 1.90091 / 1.32 ( 24) link_NAG-ASN : bond 0.00265 / 0.11 ( 7) link_NAG-ASN : angle 1.88282 / 1.24 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 109 THR cc_start: 0.8378 (m) cc_final: 0.7933 (t) REVERT: B 488 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: B 511 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8184 (pp30) REVERT: B 513 LYS cc_start: 0.9087 (mtmm) cc_final: 0.8643 (mtmm) REVERT: C 112 LYS cc_start: 0.8223 (tttt) cc_final: 0.7657 (tptp) REVERT: C 119 ASP cc_start: 0.8255 (t0) cc_final: 0.7547 (m-30) REVERT: C 133 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8794 (mtmm) REVERT: C 286 MET cc_start: 0.6890 (tmm) cc_final: 0.6597 (ttt) REVERT: C 386 ARG cc_start: 0.8499 (tpt-90) cc_final: 0.7119 (ttt180) REVERT: C 449 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8015 (tp30) REVERT: C 514 ARG cc_start: 0.8073 (mmt90) cc_final: 0.6725 (pmt-80) REVERT: C 531 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8385 (p90) REVERT: A 454 CYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6337 (t) REVERT: A 497 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8926 (mt-10) outliers start: 31 outliers final: 12 residues processed: 151 average time/residue: 0.5576 time to fit residues: 91.2593 Evaluate side-chains 140 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 531 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 561 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [25, 103, 115, 13, 26, 46, 112, 123, 119, 101, 80] chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 447 GLN A 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.088491 restraints weight = 19757.344| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.40 r_work: 0.3009 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11559 Z= 0.157 Angle : 0.545 6.863 15707 Z= 0.280 Chirality : 0.042 0.167 1752 Planarity : 0.004 0.056 1997 Dihedral : 5.378 54.994 1800 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.97 % Allowed : 12.06 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.23), residues: 1362 helix: 1.50 (0.24), residues: 484 sheet: -0.60 (0.33), residues: 239 loop : 0.68 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 313 TYR 0.024 0.002 TYR C 445 PHE 0.012 0.001 PHE B 170 TRP 0.010 0.001 TRP B 118 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (11520) covalent geometry : angle 0.53507 / 0.28 (15614) SS BOND : bond 0.00248 / 0.17 ( 24) SS BOND : angle 1.05498 / 0.90 ( 48) hydrogen bonds : bond 0.03579 / 2.35 ( 506) hydrogen bonds : angle 4.93534 / 3.55 ( 1410) link_BETA1-4 : bond 0.00353 / 0.17 ( 8) link_BETA1-4 : angle 1.65757 / 1.13 ( 24) link_NAG-ASN : bond 0.00343 / 0.15 ( 7) link_NAG-ASN : angle 1.94995 / 1.28 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 109 THR cc_start: 0.8469 (m) cc_final: 0.8114 (t) REVERT: B 488 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: C 112 LYS cc_start: 0.8250 (tttt) cc_final: 0.7676 (tptp) REVERT: C 119 ASP cc_start: 0.8245 (t0) cc_final: 0.7524 (m-30) REVERT: C 133 LYS cc_start: 0.8997 (mtpp) cc_final: 0.8795 (mtmm) REVERT: C 286 MET cc_start: 0.6829 (tmm) cc_final: 0.6571 (ttt) REVERT: C 386 ARG cc_start: 0.8643 (tpt-90) cc_final: 0.7171 (ttt180) REVERT: C 449 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: C 514 ARG cc_start: 0.8035 (mmt90) cc_final: 0.7015 (pmt-80) REVERT: C 515 GLN cc_start: 0.8387 (tp-100) cc_final: 0.7846 (pm20) REVERT: C 531 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8394 (p90) REVERT: A 100 ILE cc_start: 0.9088 (mt) cc_final: 0.8754 (tp) REVERT: A 454 CYS cc_start: 0.6702 (OUTLIER) cc_final: 0.6375 (t) outliers start: 37 outliers final: 16 residues processed: 152 average time/residue: 0.5509 time to fit residues: 91.1149 Evaluate side-chains 143 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 531 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 561 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [74, 40, 89, 130, 115, 26, 132, 50, 87, 120, 12] chunk 74 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 120 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 447 GLN C 491 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.089031 restraints weight = 19794.834| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.40 r_work: 0.3020 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11559 Z= 0.137 Angle : 0.542 9.905 15707 Z= 0.276 Chirality : 0.041 0.161 1752 Planarity : 0.004 0.062 1997 Dihedral : 5.309 54.594 1800 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.73 % Allowed : 13.10 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.23), residues: 1362 helix: 1.60 (0.24), residues: 484 sheet: -0.53 (0.32), residues: 248 loop : 0.70 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 313 TYR 0.024 0.001 TYR C 445 PHE 0.013 0.001 PHE C 494 TRP 0.009 0.001 TRP B 118 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (11520) covalent geometry : angle 0.53357 / 0.27 (15614) SS BOND : bond 0.00242 / 0.16 ( 24) SS BOND : angle 0.99523 / 0.86 ( 48) hydrogen bonds : bond 0.03398 / 2.23 ( 506) hydrogen bonds : angle 4.84536 / 3.49 ( 1410) link_BETA1-4 : bond 0.00348 / 0.17 ( 8) link_BETA1-4 : angle 1.51558 / 1.03 ( 24) link_NAG-ASN : bond 0.00292 / 0.13 ( 7) link_NAG-ASN : angle 1.84316 / 1.20 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.460 Fit side-chains REVERT: B 109 THR cc_start: 0.8414 (m) cc_final: 0.7960 (t) REVERT: B 371 LYS cc_start: 0.9135 (mmtt) cc_final: 0.8923 (mmtt) REVERT: B 488 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: B 511 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8265 (pp30) REVERT: B 513 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8677 (mtmm) REVERT: C 112 LYS cc_start: 0.8231 (tttt) cc_final: 0.7647 (tptp) REVERT: C 119 ASP cc_start: 0.8255 (t0) cc_final: 0.7537 (m-30) REVERT: C 204 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8535 (mt) REVERT: C 286 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6621 (ttt) REVERT: C 386 ARG cc_start: 0.8475 (tpt-90) cc_final: 0.7047 (ttt180) REVERT: C 449 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: C 495 ASP cc_start: 0.8243 (t0) cc_final: 0.7711 (t0) REVERT: C 514 ARG cc_start: 0.8027 (mmt90) cc_final: 0.7003 (pmt-80) REVERT: C 515 GLN cc_start: 0.8378 (tp-100) cc_final: 0.7874 (pm20) REVERT: C 531 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8383 (p90) REVERT: A 100 ILE cc_start: 0.9106 (mt) cc_final: 0.8776 (tp) REVERT: A 454 CYS cc_start: 0.6568 (OUTLIER) cc_final: 0.6304 (t) outliers start: 34 outliers final: 15 residues processed: 145 average time/residue: 0.5320 time to fit residues: 84.0412 Evaluate side-chains 141 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 531 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 532 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [86, 50, 1, 72, 20, 44, 83, 134, 118, 84, 49] chunk 86 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 118 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.105917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.088889 restraints weight = 19850.021| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.39 r_work: 0.3019 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11559 Z= 0.141 Angle : 0.534 7.847 15707 Z= 0.272 Chirality : 0.041 0.159 1752 Planarity : 0.004 0.058 1997 Dihedral : 5.252 54.676 1800 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.57 % Allowed : 13.59 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.23), residues: 1362 helix: 1.66 (0.24), residues: 484 sheet: -0.49 (0.32), residues: 247 loop : 0.70 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 313 TYR 0.024 0.002 TYR C 445 PHE 0.022 0.001 PHE A 236 TRP 0.008 0.001 TRP C 118 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11520) covalent geometry : angle 0.52554 / 0.27 (15614) SS BOND : bond 0.00240 / 0.16 ( 24) SS BOND : angle 1.00016 / 0.86 ( 48) hydrogen bonds : bond 0.03372 / 2.22 ( 506) hydrogen bonds : angle 4.80423 / 3.46 ( 1410) link_BETA1-4 : bond 0.00340 / 0.16 ( 8) link_BETA1-4 : angle 1.48655 / 1.01 ( 24) link_NAG-ASN : bond 0.00311 / 0.14 ( 7) link_NAG-ASN : angle 1.85282 / 1.21 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: B 109 THR cc_start: 0.8411 (m) cc_final: 0.7944 (t) REVERT: B 488 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: B 513 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8675 (mtmm) REVERT: C 112 LYS cc_start: 0.8228 (tttt) cc_final: 0.7645 (tptp) REVERT: C 119 ASP cc_start: 0.8282 (t0) cc_final: 0.7577 (m-30) REVERT: C 133 LYS cc_start: 0.9055 (mtmm) cc_final: 0.8757 (ttpt) REVERT: C 204 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8485 (mt) REVERT: C 286 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6635 (ttt) REVERT: C 386 ARG cc_start: 0.8456 (tpt-90) cc_final: 0.7021 (ttt180) REVERT: C 461 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8632 (mp) REVERT: C 515 GLN cc_start: 0.8399 (tp-100) cc_final: 0.7924 (pm20) REVERT: C 531 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8346 (p90) REVERT: A 454 CYS cc_start: 0.6584 (OUTLIER) cc_final: 0.6289 (t) outliers start: 32 outliers final: 17 residues processed: 140 average time/residue: 0.5250 time to fit residues: 80.0341 Evaluate side-chains 142 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 561 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [108, 4, 120, 12, 33, 109, 25, 60, 83, 50, 80] chunk 108 optimal weight: 0.9980 chunk 4 optimal weight: 0.0770 chunk 120 optimal weight: 0.5980 chunk 12 optimal weight: 0.0060 chunk 33 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.090592 restraints weight = 19708.103| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.36 r_work: 0.3052 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11559 Z= 0.107 Angle : 0.528 8.055 15707 Z= 0.270 Chirality : 0.040 0.151 1752 Planarity : 0.004 0.057 1997 Dihedral : 5.106 54.046 1800 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.41 % Allowed : 14.47 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.23), residues: 1362 helix: 1.80 (0.24), residues: 478 sheet: -0.49 (0.32), residues: 250 loop : 0.72 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 313 TYR 0.024 0.001 TYR C 445 PHE 0.025 0.001 PHE A 236 TRP 0.009 0.001 TRP A 292 HIS 0.003 0.000 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (11520) covalent geometry : angle 0.52043 / 0.27 (15614) SS BOND : bond 0.00236 / 0.15 ( 24) SS BOND : angle 0.95192 / 0.82 ( 48) hydrogen bonds : bond 0.03172 / 2.08 ( 506) hydrogen bonds : angle 4.78947 / 3.49 ( 1410) link_BETA1-4 : bond 0.00407 / 0.18 ( 8) link_BETA1-4 : angle 1.34938 / 0.92 ( 24) link_NAG-ASN : bond 0.00198 / 0.08 ( 7) link_NAG-ASN : angle 1.63975 / 1.06 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.360 Fit side-chains REVERT: B 109 THR cc_start: 0.8359 (m) cc_final: 0.7895 (t) REVERT: B 371 LYS cc_start: 0.9252 (mmtt) cc_final: 0.9003 (mmtt) REVERT: B 488 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: B 511 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8259 (pp30) REVERT: B 513 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8697 (mtmm) REVERT: C 112 LYS cc_start: 0.8252 (tttt) cc_final: 0.7688 (tptp) REVERT: C 133 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8697 (ttpt) REVERT: C 204 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8537 (mt) REVERT: C 386 ARG cc_start: 0.8399 (tpt-90) cc_final: 0.6991 (ttt180) REVERT: C 461 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8617 (mp) REVERT: C 514 ARG cc_start: 0.8019 (mmt90) cc_final: 0.6942 (pmt-80) REVERT: C 515 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7953 (pm20) REVERT: C 531 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8322 (p90) REVERT: A 454 CYS cc_start: 0.6568 (OUTLIER) cc_final: 0.6312 (t) outliers start: 30 outliers final: 13 residues processed: 149 average time/residue: 0.5265 time to fit residues: 85.3983 Evaluate side-chains 138 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 561 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [48, 8, 22, 105, 87, 106, 3, 93, 1, 53, 6] chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 0.1980 chunk 106 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 93 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.090402 restraints weight = 19659.316| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.37 r_work: 0.3046 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11559 Z= 0.123 Angle : 0.547 11.819 15707 Z= 0.277 Chirality : 0.041 0.152 1752 Planarity : 0.004 0.051 1997 Dihedral : 5.089 54.129 1800 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.77 % Allowed : 15.51 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.23), residues: 1362 helix: 1.83 (0.24), residues: 478 sheet: -0.51 (0.32), residues: 247 loop : 0.71 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 313 TYR 0.024 0.002 TYR C 445 PHE 0.012 0.001 PHE A 229 TRP 0.008 0.001 TRP B 118 HIS 0.002 0.000 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (11520) covalent geometry : angle 0.54006 / 0.28 (15614) SS BOND : bond 0.00242 / 0.16 ( 24) SS BOND : angle 0.96062 / 0.83 ( 48) hydrogen bonds : bond 0.03205 / 2.11 ( 506) hydrogen bonds : angle 4.79385 / 3.50 ( 1410) link_BETA1-4 : bond 0.00358 / 0.16 ( 8) link_BETA1-4 : angle 1.38068 / 0.93 ( 24) link_NAG-ASN : bond 0.00254 / 0.11 ( 7) link_NAG-ASN : angle 1.71030 / 1.11 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: B 109 THR cc_start: 0.8354 (m) cc_final: 0.7894 (t) REVERT: B 371 LYS cc_start: 0.9250 (mmtt) cc_final: 0.8999 (mmtt) REVERT: B 488 GLU cc_start: 0.8702 (mp0) cc_final: 0.8245 (mp0) REVERT: B 511 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8265 (pp30) REVERT: C 112 LYS cc_start: 0.8258 (tttt) cc_final: 0.7692 (tptp) REVERT: C 119 ASP cc_start: 0.8396 (t0) cc_final: 0.7589 (m-30) REVERT: C 133 LYS cc_start: 0.8991 (mtmm) cc_final: 0.8713 (ttpt) REVERT: C 386 ARG cc_start: 0.8414 (tpt-90) cc_final: 0.7007 (ttt180) REVERT: C 461 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8610 (mp) REVERT: C 515 GLN cc_start: 0.8445 (tp-100) cc_final: 0.7994 (pm20) REVERT: C 531 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8350 (p90) REVERT: C 553 LEU cc_start: 0.8591 (tp) cc_final: 0.8136 (mp) REVERT: A 454 CYS cc_start: 0.6470 (OUTLIER) cc_final: 0.6261 (t) outliers start: 22 outliers final: 11 residues processed: 136 average time/residue: 0.5497 time to fit residues: 81.2785 Evaluate side-chains 132 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 561 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [62, 122, 61, 18, 101, 78, 83, 23, 21, 118, 58] chunk 62 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 78 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.107370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.090489 restraints weight = 19732.116| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.39 r_work: 0.3053 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11559 Z= 0.120 Angle : 0.535 9.808 15707 Z= 0.271 Chirality : 0.041 0.152 1752 Planarity : 0.004 0.054 1997 Dihedral : 5.057 54.324 1800 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.53 % Allowed : 15.92 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.23), residues: 1362 helix: 1.77 (0.24), residues: 484 sheet: -0.53 (0.32), residues: 253 loop : 0.76 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 313 TYR 0.025 0.001 TYR C 445 PHE 0.011 0.001 PHE B 457 TRP 0.009 0.001 TRP B 118 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11520) covalent geometry : angle 0.52807 / 0.27 (15614) SS BOND : bond 0.00233 / 0.15 ( 24) SS BOND : angle 0.96381 / 0.83 ( 48) hydrogen bonds : bond 0.03183 / 2.10 ( 506) hydrogen bonds : angle 4.75920 / 3.48 ( 1410) link_BETA1-4 : bond 0.00354 / 0.16 ( 8) link_BETA1-4 : angle 1.35338 / 0.92 ( 24) link_NAG-ASN : bond 0.00255 / 0.11 ( 7) link_NAG-ASN : angle 1.67922 / 1.09 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.410 Fit side-chains REVERT: B 109 THR cc_start: 0.8343 (m) cc_final: 0.7881 (t) REVERT: B 374 THR cc_start: 0.9175 (m) cc_final: 0.8865 (p) REVERT: B 488 GLU cc_start: 0.8694 (mp0) cc_final: 0.8296 (mp0) REVERT: B 511 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8239 (pp30) REVERT: C 112 LYS cc_start: 0.8228 (tttt) cc_final: 0.7661 (tptp) REVERT: C 119 ASP cc_start: 0.8342 (t0) cc_final: 0.7538 (m-30) REVERT: C 133 LYS cc_start: 0.8985 (mtmm) cc_final: 0.8696 (ttpt) REVERT: C 386 ARG cc_start: 0.8415 (tpt-90) cc_final: 0.7013 (ttt180) REVERT: C 461 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8606 (mp) REVERT: C 515 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8059 (pm20) REVERT: C 531 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8339 (p90) REVERT: C 553 LEU cc_start: 0.8531 (tp) cc_final: 0.8124 (mp) REVERT: A 454 CYS cc_start: 0.6484 (OUTLIER) cc_final: 0.6262 (t) outliers start: 19 outliers final: 10 residues processed: 137 average time/residue: 0.5251 time to fit residues: 78.3471 Evaluate side-chains 134 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 524 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [46, 38, 75, 10, 81, 88, 102, 71, 4, 35, 51] chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 10 optimal weight: 0.0030 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.107683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.090818 restraints weight = 19862.566| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.40 r_work: 0.3045 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11559 Z= 0.117 Angle : 0.550 9.703 15707 Z= 0.277 Chirality : 0.041 0.148 1752 Planarity : 0.004 0.054 1997 Dihedral : 5.022 54.184 1800 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.21 % Allowed : 16.40 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.23), residues: 1362 helix: 1.78 (0.24), residues: 484 sheet: -0.49 (0.32), residues: 246 loop : 0.75 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 313 TYR 0.024 0.001 TYR C 445 PHE 0.011 0.001 PHE C 494 TRP 0.009 0.001 TRP B 118 HIS 0.006 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11520) covalent geometry : angle 0.54358 / 0.28 (15614) SS BOND : bond 0.00236 / 0.15 ( 24) SS BOND : angle 0.94722 / 0.81 ( 48) hydrogen bonds : bond 0.03156 / 2.09 ( 506) hydrogen bonds : angle 4.71083 / 3.44 ( 1410) link_BETA1-4 : bond 0.00366 / 0.17 ( 8) link_BETA1-4 : angle 1.33854 / 0.91 ( 24) link_NAG-ASN : bond 0.00241 / 0.11 ( 7) link_NAG-ASN : angle 1.65413 / 1.07 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3635.10 seconds wall clock time: 63 minutes 16.23 seconds (3796.23 seconds total)