Starting phenix.real_space_refine on Fri Aug 22 23:06:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwk_35769/08_2025/8iwk_35769.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwk_35769/08_2025/8iwk_35769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iwk_35769/08_2025/8iwk_35769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwk_35769/08_2025/8iwk_35769.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwk_35769/08_2025/8iwk_35769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwk_35769/08_2025/8iwk_35769.cif" } resolution = 3.0 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= 0.007 sd= 0.143 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 52 5.16 5 C 5523 2.51 5 N 1414 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8479 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4230 Classifications: {'peptide': 545} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 526} Chain breaks: 4 Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'A8S': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C Time building chain proxies: 3.33, per 1000 atoms: 0.39 Number of scatterers: 8479 At special positions: 0 Unit cell: (100.1, 93.5, 122.1, 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 52 16.00 O 1490 8.00 N 1414 7.00 C 5523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 462.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1996 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 56.9% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.677A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.784A pdb=" N LEU A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 140 " --> pdb=" O GLN A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 140' Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.600A pdb=" N LEU A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 189 removed outlier: 3.895A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.734A pdb=" N LYS A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 256 removed outlier: 3.635A pdb=" N ARG A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.683A pdb=" N PHE A 275 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.538A pdb=" N PHE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 removed outlier: 3.849A pdb=" N LEU A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.813A pdb=" N THR A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.663A pdb=" N VAL A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N THR A 355 " --> pdb=" O PRO A 351 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.563A pdb=" N ALA A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 395 " --> pdb=" O CYS A 391 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.624A pdb=" N GLU A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.503A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 454 removed outlier: 3.749A pdb=" N ARG A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.616A pdb=" N ALA A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.761A pdb=" N MET A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 removed outlier: 3.639A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 542 removed outlier: 3.576A pdb=" N PHE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 removed outlier: 3.694A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 561 removed outlier: 3.539A pdb=" N THR A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.950A pdb=" N LYS A 577 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 579 " --> pdb=" O MET A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 4.035A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 658 removed outlier: 3.748A pdb=" N LEU A 642 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 653 " --> pdb=" O TYR A 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.677A pdb=" N LEU C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.784A pdb=" N LEU C 139 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 140 " --> pdb=" O GLN C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 140' Processing helix chain 'C' and resid 156 through 169 removed outlier: 3.601A pdb=" N LEU C 167 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.896A pdb=" N SER C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 removed outlier: 3.734A pdb=" N LYS C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 256 removed outlier: 3.635A pdb=" N ARG C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.684A pdb=" N PHE C 275 " --> pdb=" O PHE C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.538A pdb=" N PHE C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.849A pdb=" N LEU C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.812A pdb=" N THR C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 349 " --> pdb=" O TYR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 357 removed outlier: 3.664A pdb=" N VAL C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR C 355 " --> pdb=" O PRO C 351 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 397 removed outlier: 3.563A pdb=" N ALA C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP C 386 " --> pdb=" O CYS C 382 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 387 " --> pdb=" O ILE C 383 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS C 395 " --> pdb=" O CYS C 391 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.623A pdb=" N GLU C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 425 removed outlier: 3.503A pdb=" N PHE C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 454 removed outlier: 3.750A pdb=" N ARG C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 438 " --> pdb=" O HIS C 434 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Proline residue: C 451 - end of helix Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 471 removed outlier: 3.617A pdb=" N ALA C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 492 removed outlier: 3.761A pdb=" N MET C 482 " --> pdb=" O SER C 478 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 484 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 505 removed outlier: 3.639A pdb=" N ALA C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TRP C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 542 removed outlier: 3.576A pdb=" N PHE C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 518 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 528 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY C 532 " --> pdb=" O LEU C 528 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 533 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 549 removed outlier: 3.694A pdb=" N THR C 549 " --> pdb=" O LYS C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 561 removed outlier: 3.539A pdb=" N THR C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.949A pdb=" N LYS C 577 " --> pdb=" O VAL C 574 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 579 " --> pdb=" O MET C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 594 removed outlier: 4.036A pdb=" N TYR C 584 " --> pdb=" O SER C 580 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 591 " --> pdb=" O ARG C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 658 removed outlier: 3.748A pdb=" N LEU C 642 " --> pdb=" O SER C 638 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 643 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 644 " --> pdb=" O GLY C 640 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG C 650 " --> pdb=" O PHE C 646 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 653 " --> pdb=" O TYR C 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 145 removed outlier: 6.227A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 290 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AA4, first strand: chain 'C' and resid 143 through 145 removed outlier: 6.227A pdb=" N GLY C 143 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N MET C 97 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 290 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE C 288 " --> pdb=" O LEU C 280 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 918 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: 1.34 Time building geometry restraints manager: 0.93 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: 1796 1.33 - 1.45: 1933 1.45 - 1.57: 4842 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 8655 Sorted by residual: bond pdb=" CB ARG C 396 " pdb=" CG ARG C 396 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.41e+00 bond pdb=" CB ARG A 396 " pdb=" CG ARG A 396 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.38e+00 bond pdb=" CB CYS A 421 " pdb=" SG CYS A 421 " ideal model delta sigma weight residual 1.808 1.749 0.059 3.30e-02 9.18e+02 3.23e+00 bond pdb=" CB CYS C 421 " pdb=" SG CYS C 421 " ideal model delta sigma weight residual 1.808 1.749 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB ARG A 510 " pdb=" CG ARG A 510 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.80e+00 ... (remaining 8650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 11181 2.30 - 4.61: 451 4.61 - 6.91: 87 6.91 - 9.22: 12 9.22 - 11.52: 4 Bond angle restraints: 11735 Sorted by residual: angle pdb=" N ILE A 550 " pdb=" CA ILE A 550 " pdb=" C ILE A 550 " ideal model delta sigma weight residual 112.96 107.25 5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" N ILE C 550 " pdb=" CA ILE C 550 " pdb=" C ILE C 550 " ideal model delta sigma weight residual 112.96 107.29 5.67 1.00e+00 1.00e+00 3.22e+01 angle pdb=" N SER A 571 " pdb=" CA SER A 571 " pdb=" C SER A 571 " ideal model delta sigma weight residual 110.80 118.32 -7.52 2.13e+00 2.20e-01 1.25e+01 angle pdb=" N SER C 571 " pdb=" CA SER C 571 " pdb=" C SER C 571 " ideal model delta sigma weight residual 110.80 118.26 -7.46 2.13e+00 2.20e-01 1.23e+01 angle pdb=" C ALA A 350 " pdb=" N PRO A 351 " pdb=" CA PRO A 351 " ideal model delta sigma weight residual 121.91 117.41 4.50 1.35e+00 5.49e-01 1.11e+01 ... (remaining 11730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 4790 15.04 - 30.09: 256 30.09 - 45.13: 42 45.13 - 60.17: 2 60.17 - 75.22: 6 Dihedral angle restraints: 5096 sinusoidal: 1984 harmonic: 3112 Sorted by residual: dihedral pdb=" CA PRO C 570 " pdb=" C PRO C 570 " pdb=" N SER C 571 " pdb=" CA SER C 571 " ideal model delta harmonic sigma weight residual 180.00 154.14 25.86 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PRO A 570 " pdb=" C PRO A 570 " pdb=" N SER A 571 " pdb=" CA SER A 571 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA THR A 202 " pdb=" C THR A 202 " pdb=" N PHE A 203 " pdb=" CA PHE A 203 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1101 0.073 - 0.146: 256 0.146 - 0.219: 32 0.219 - 0.292: 4 0.292 - 0.365: 2 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CB ILE A 134 " pdb=" CA ILE A 134 " pdb=" CG1 ILE A 134 " pdb=" CG2 ILE A 134 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE C 134 " pdb=" CA ILE C 134 " pdb=" CG1 ILE C 134 " pdb=" CG2 ILE C 134 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB VAL C 114 " pdb=" CA VAL C 114 " pdb=" CG1 VAL C 114 " pdb=" CG2 VAL C 114 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1392 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 514 " -0.046 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO A 515 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 515 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 515 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 514 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO C 515 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 515 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 515 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 427 " 0.017 2.00e-02 2.50e+03 1.98e-02 5.86e+00 pdb=" CG HIS A 427 " -0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS A 427 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 427 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS A 427 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 427 " 0.008 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2676 2.83 - 3.35: 7002 3.35 - 3.87: 12432 3.87 - 4.38: 14996 4.38 - 4.90: 26979 Nonbonded interactions: 64085 Sorted by model distance: nonbonded pdb=" O SER A 282 " pdb=" OG SER A 282 " model vdw 2.313 3.040 nonbonded pdb=" O SER C 282 " pdb=" OG SER C 282 " model vdw 2.313 3.040 nonbonded pdb=" O ILE C 550 " pdb=" OG1 THR C 554 " model vdw 2.371 3.040 nonbonded pdb=" O ILE A 550 " pdb=" OG1 THR A 554 " model vdw 2.372 3.040 nonbonded pdb=" O SER C 444 " pdb=" OH TYR C 526 " model vdw 2.373 3.040 ... (remaining 64080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 33 through 662) } 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.620 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:8.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.010 0.083 8655 Z= 0.396 Angle : 1.096 11.522 11735 Z= 0.567 Chirality : 0.063 0.365 1395 Planarity : 0.007 0.068 1440 Dihedral : 10.003 75.217 3100 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.57 (0.15), residues: 1070 helix: -4.64 (0.08), residues: 610 sheet: -2.82 (0.47), residues: 96 loop : -3.81 (0.22), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 117 TYR 0.026 0.003 TYR A 508 PHE 0.031 0.004 PHE A 96 TRP 0.024 0.004 TRP A 426 HIS 0.022 0.004 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00966 ( 8655) covalent geometry : angle 1.09597 (11735) hydrogen bonds : bond 0.35387 ( 320) hydrogen bonds : angle 10.37958 ( 918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.323 Fit side-chains REVERT: A 310 MET cc_start: 0.8052 (ptm) cc_final: 0.7574 (ptp) REVERT: A 599 GLU cc_start: 0.8113 (tt0) cc_final: 0.7419 (pm20) REVERT: C 117 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7276 (mtp85) REVERT: C 310 MET cc_start: 0.8199 (ptm) cc_final: 0.7834 (ptp) REVERT: C 599 GLU cc_start: 0.8065 (tt0) cc_final: 0.7160 (pm20) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.6887 time to fit residues: 108.7936 Evaluate side-chains 96 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN C 434 HIS C 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126597 restraints weight = 9160.974| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.91 r_work: 0.3205 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8655 Z= 0.116 Angle : 0.608 6.288 11735 Z= 0.312 Chirality : 0.040 0.148 1395 Planarity : 0.005 0.048 1440 Dihedral : 5.496 33.980 1202 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.49 % Allowed : 5.97 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (0.19), residues: 1070 helix: -2.84 (0.15), residues: 608 sheet: -2.76 (0.47), residues: 94 loop : -3.25 (0.26), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 180 TYR 0.016 0.001 TYR C 526 PHE 0.017 0.001 PHE A 203 TRP 0.011 0.002 TRP A 447 HIS 0.005 0.001 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8655) covalent geometry : angle 0.60817 (11735) hydrogen bonds : bond 0.05150 ( 320) hydrogen bonds : angle 4.57220 ( 918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.326 Fit side-chains REVERT: A 117 ARG cc_start: 0.7316 (mtp180) cc_final: 0.7102 (mtp85) REVERT: A 599 GLU cc_start: 0.8253 (tt0) cc_final: 0.7059 (pm20) REVERT: C 171 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7800 (mmm160) REVERT: C 274 MET cc_start: 0.8113 (mtt) cc_final: 0.7893 (mtt) REVERT: C 482 MET cc_start: 0.8768 (mmm) cc_final: 0.8505 (mmm) REVERT: C 599 GLU cc_start: 0.8178 (tt0) cc_final: 0.6978 (pm20) REVERT: C 635 MET cc_start: 0.7438 (mtp) cc_final: 0.6810 (mpt) outliers start: 23 outliers final: 10 residues processed: 121 average time/residue: 0.5877 time to fit residues: 75.5126 Evaluate side-chains 106 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 545 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.162380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.119431 restraints weight = 9037.161| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.97 r_work: 0.3058 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8655 Z= 0.223 Angle : 0.700 7.844 11735 Z= 0.351 Chirality : 0.046 0.156 1395 Planarity : 0.005 0.041 1440 Dihedral : 5.676 34.509 1202 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.25 % Allowed : 8.57 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.75 (0.22), residues: 1070 helix: -2.00 (0.18), residues: 616 sheet: -2.92 (0.43), residues: 94 loop : -2.96 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 410 TYR 0.018 0.002 TYR A 526 PHE 0.014 0.002 PHE A 502 TRP 0.016 0.002 TRP C 426 HIS 0.007 0.002 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 8655) covalent geometry : angle 0.69956 (11735) hydrogen bonds : bond 0.06653 ( 320) hydrogen bonds : angle 4.32400 ( 918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.381 Fit side-chains REVERT: A 117 ARG cc_start: 0.7336 (mtp180) cc_final: 0.7064 (mtp85) REVERT: C 205 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6988 (ttp80) REVERT: C 468 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8214 (ttp-170) REVERT: C 599 GLU cc_start: 0.8231 (tt0) cc_final: 0.7984 (tt0) outliers start: 30 outliers final: 19 residues processed: 115 average time/residue: 0.6546 time to fit residues: 79.6088 Evaluate side-chains 114 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 545 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.166127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123851 restraints weight = 9159.275| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.91 r_work: 0.3114 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8655 Z= 0.121 Angle : 0.579 6.269 11735 Z= 0.293 Chirality : 0.041 0.151 1395 Planarity : 0.004 0.037 1440 Dihedral : 5.149 34.124 1202 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.93 % Allowed : 10.09 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.01 (0.23), residues: 1070 helix: -1.35 (0.19), residues: 616 sheet: -2.60 (0.45), residues: 92 loop : -2.75 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.012 0.001 TYR C 526 PHE 0.022 0.001 PHE A 203 TRP 0.011 0.002 TRP A 426 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8655) covalent geometry : angle 0.57907 (11735) hydrogen bonds : bond 0.04742 ( 320) hydrogen bonds : angle 3.89786 ( 918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.332 Fit side-chains REVERT: A 90 MET cc_start: 0.8047 (ptm) cc_final: 0.7791 (ttt) REVERT: A 117 ARG cc_start: 0.7357 (mtp180) cc_final: 0.7074 (mtp85) REVERT: A 211 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8185 (mt-10) REVERT: A 482 MET cc_start: 0.8790 (mmm) cc_final: 0.8573 (mmm) REVERT: C 211 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: C 468 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7978 (ttp-170) REVERT: C 635 MET cc_start: 0.7418 (mtp) cc_final: 0.6736 (mpt) outliers start: 27 outliers final: 18 residues processed: 124 average time/residue: 0.6367 time to fit residues: 83.7746 Evaluate side-chains 117 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 468 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.164765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121212 restraints weight = 9091.964| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.90 r_work: 0.3050 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8655 Z= 0.150 Angle : 0.609 6.989 11735 Z= 0.306 Chirality : 0.042 0.153 1395 Planarity : 0.004 0.038 1440 Dihedral : 5.137 33.475 1202 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.93 % Allowed : 11.61 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.24), residues: 1070 helix: -1.01 (0.20), residues: 606 sheet: -2.49 (0.47), residues: 94 loop : -2.38 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 158 TYR 0.013 0.001 TYR C 586 PHE 0.020 0.001 PHE A 203 TRP 0.013 0.002 TRP C 426 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8655) covalent geometry : angle 0.60874 (11735) hydrogen bonds : bond 0.05202 ( 320) hydrogen bonds : angle 3.87587 ( 918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.284 Fit side-chains REVERT: A 117 ARG cc_start: 0.7367 (mtp180) cc_final: 0.7082 (mtp85) REVERT: A 211 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8127 (mt-10) REVERT: C 90 MET cc_start: 0.8114 (ptm) cc_final: 0.7832 (ttt) REVERT: C 211 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: C 468 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8294 (ttp-170) outliers start: 27 outliers final: 22 residues processed: 123 average time/residue: 0.5995 time to fit residues: 78.5958 Evaluate side-chains 120 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 468 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119615 restraints weight = 9103.322| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.87 r_work: 0.3093 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8655 Z= 0.118 Angle : 0.565 6.392 11735 Z= 0.285 Chirality : 0.040 0.148 1395 Planarity : 0.004 0.038 1440 Dihedral : 4.909 33.527 1202 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.15 % Allowed : 11.50 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.25), residues: 1070 helix: -0.65 (0.21), residues: 602 sheet: -2.10 (0.47), residues: 102 loop : -2.18 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 158 TYR 0.011 0.001 TYR C 586 PHE 0.016 0.001 PHE A 502 TRP 0.011 0.002 TRP A 426 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8655) covalent geometry : angle 0.56534 (11735) hydrogen bonds : bond 0.04451 ( 320) hydrogen bonds : angle 3.72815 ( 918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.360 Fit side-chains REVERT: A 117 ARG cc_start: 0.7360 (mtp180) cc_final: 0.7070 (mtp85) REVERT: A 211 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8079 (mt-10) REVERT: C 90 MET cc_start: 0.8112 (ptm) cc_final: 0.7794 (ttt) REVERT: C 211 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: C 468 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7969 (ttp-170) REVERT: C 635 MET cc_start: 0.7434 (mtp) cc_final: 0.6672 (mpt) outliers start: 29 outliers final: 23 residues processed: 134 average time/residue: 0.5695 time to fit residues: 81.3098 Evaluate side-chains 126 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 545 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.164459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120288 restraints weight = 9207.175| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.91 r_work: 0.3046 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8655 Z= 0.154 Angle : 0.609 6.708 11735 Z= 0.305 Chirality : 0.042 0.153 1395 Planarity : 0.004 0.040 1440 Dihedral : 5.047 33.306 1202 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.36 % Allowed : 11.71 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.25), residues: 1070 helix: -0.63 (0.21), residues: 604 sheet: -1.62 (0.52), residues: 84 loop : -2.11 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 158 TYR 0.012 0.001 TYR C 586 PHE 0.018 0.002 PHE A 502 TRP 0.014 0.002 TRP C 426 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8655) covalent geometry : angle 0.60935 (11735) hydrogen bonds : bond 0.05205 ( 320) hydrogen bonds : angle 3.81774 ( 918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.337 Fit side-chains REVERT: A 117 ARG cc_start: 0.7404 (mtp180) cc_final: 0.7045 (mtp85) REVERT: A 211 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8116 (mt-10) REVERT: C 211 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8153 (mt-10) REVERT: C 468 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8208 (ttp-170) outliers start: 31 outliers final: 25 residues processed: 127 average time/residue: 0.5438 time to fit residues: 73.8591 Evaluate side-chains 128 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 545 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.0050 chunk 7 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN C 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.164430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117557 restraints weight = 8993.459| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.81 r_work: 0.3039 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8655 Z= 0.155 Angle : 0.607 6.591 11735 Z= 0.305 Chirality : 0.042 0.150 1395 Planarity : 0.004 0.040 1440 Dihedral : 5.059 32.735 1202 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.25 % Allowed : 12.26 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.25), residues: 1070 helix: -0.53 (0.21), residues: 602 sheet: -1.99 (0.47), residues: 102 loop : -2.09 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 158 TYR 0.012 0.001 TYR C 586 PHE 0.021 0.001 PHE A 502 TRP 0.013 0.002 TRP C 426 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8655) covalent geometry : angle 0.60722 (11735) hydrogen bonds : bond 0.05161 ( 320) hydrogen bonds : angle 3.80764 ( 918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.343 Fit side-chains REVERT: A 117 ARG cc_start: 0.7398 (mtp180) cc_final: 0.7023 (mtp85) REVERT: A 211 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8127 (mt-10) REVERT: C 90 MET cc_start: 0.8105 (ptm) cc_final: 0.7823 (ttt) REVERT: C 211 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8157 (mt-10) REVERT: C 468 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8303 (ttp-170) outliers start: 30 outliers final: 25 residues processed: 128 average time/residue: 0.5548 time to fit residues: 75.9301 Evaluate side-chains 129 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 545 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN C 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.162831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117874 restraints weight = 9087.511| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.00 r_work: 0.3031 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8655 Z= 0.165 Angle : 0.622 6.819 11735 Z= 0.312 Chirality : 0.043 0.152 1395 Planarity : 0.004 0.042 1440 Dihedral : 5.107 32.916 1202 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.15 % Allowed : 12.47 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.25), residues: 1070 helix: -0.52 (0.21), residues: 604 sheet: -2.11 (0.47), residues: 104 loop : -2.02 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 158 TYR 0.011 0.001 TYR A 526 PHE 0.029 0.002 PHE C 203 TRP 0.014 0.002 TRP C 426 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8655) covalent geometry : angle 0.62240 (11735) hydrogen bonds : bond 0.05368 ( 320) hydrogen bonds : angle 3.83794 ( 918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.409 Fit side-chains REVERT: A 117 ARG cc_start: 0.7398 (mtp180) cc_final: 0.7023 (mtp85) REVERT: A 211 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 397 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8523 (mt) REVERT: C 90 MET cc_start: 0.8086 (ptm) cc_final: 0.7794 (ttt) REVERT: C 211 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8126 (mt-10) REVERT: C 397 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8544 (mt) REVERT: C 468 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8302 (ttp-170) outliers start: 29 outliers final: 25 residues processed: 129 average time/residue: 0.5625 time to fit residues: 77.5805 Evaluate side-chains 134 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 545 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 71 optimal weight: 0.0060 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN C 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.168022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120867 restraints weight = 9059.350| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.85 r_work: 0.3096 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8655 Z= 0.095 Angle : 0.531 5.695 11735 Z= 0.271 Chirality : 0.039 0.138 1395 Planarity : 0.004 0.042 1440 Dihedral : 4.650 33.469 1202 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.39 % Allowed : 13.77 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.26), residues: 1070 helix: -0.10 (0.21), residues: 604 sheet: -1.79 (0.50), residues: 102 loop : -1.92 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 180 TYR 0.009 0.001 TYR C 586 PHE 0.033 0.001 PHE C 203 TRP 0.009 0.001 TRP A 447 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 8655) covalent geometry : angle 0.53138 (11735) hydrogen bonds : bond 0.03679 ( 320) hydrogen bonds : angle 3.53578 ( 918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.264 Fit side-chains REVERT: A 117 ARG cc_start: 0.7378 (mtp180) cc_final: 0.7123 (mtp85) REVERT: A 188 GLU cc_start: 0.7229 (tt0) cc_final: 0.6794 (tm-30) REVERT: A 211 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8001 (mt-10) REVERT: C 90 MET cc_start: 0.8087 (ptm) cc_final: 0.7808 (ttt) REVERT: C 188 GLU cc_start: 0.7240 (tt0) cc_final: 0.6824 (tm-30) REVERT: C 211 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8104 (mt-10) REVERT: C 468 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7967 (ttp-170) REVERT: C 635 MET cc_start: 0.7351 (mtp) cc_final: 0.6596 (mpt) outliers start: 22 outliers final: 16 residues processed: 129 average time/residue: 0.5504 time to fit residues: 76.1684 Evaluate side-chains 131 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 476 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 147 GLN C 130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122388 restraints weight = 9047.440| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.96 r_work: 0.3076 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8655 Z= 0.123 Angle : 0.569 6.093 11735 Z= 0.287 Chirality : 0.041 0.148 1395 Planarity : 0.004 0.043 1440 Dihedral : 4.743 33.981 1202 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.39 % Allowed : 14.53 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.26), residues: 1070 helix: -0.06 (0.21), residues: 604 sheet: -1.84 (0.53), residues: 92 loop : -1.89 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 158 TYR 0.011 0.001 TYR C 586 PHE 0.024 0.001 PHE A 502 TRP 0.013 0.002 TRP C 426 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8655) covalent geometry : angle 0.56909 (11735) hydrogen bonds : bond 0.04471 ( 320) hydrogen bonds : angle 3.60871 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3048.05 seconds wall clock time: 52 minutes 44.53 seconds (3164.53 seconds total)