Starting phenix.real_space_refine on Wed Feb 12 23:56:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwk_35769/02_2025/8iwk_35769.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwk_35769/02_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_35769/02_2025/8iwk_35769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwk_35769/02_2025/8iwk_35769.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwk_35769/02_2025/8iwk_35769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwk_35769/02_2025/8iwk_35769.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 7.60, per 1000 atoms: 0.90 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: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.86 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: 2.21 Time building geometry restraints manager: 2.38 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 23.360 Find NCS groups from input model: 0.320 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.800 ------------------------------------------------------------------------------- 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= 0.620 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 : 1.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.004 TRP A 426 HIS 0.022 0.004 HIS A 427 PHE 0.031 0.004 PHE A 96 TYR 0.026 0.003 TYR A 508 ARG 0.006 0.001 ARG A 117 *********************** 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 : 0.944 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: 1.4950 time to fit residues: 236.6819 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 : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.167379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.123676 restraints weight = 9000.378| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.97 r_work: 0.3158 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8655 Z= 0.180 Angle : 0.619 6.213 11735 Z= 0.317 Chirality : 0.041 0.149 1395 Planarity : 0.005 0.048 1440 Dihedral : 5.541 33.891 1202 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.60 % Allowed : 6.18 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.19), residues: 1070 helix: -2.81 (0.15), residues: 608 sheet: -2.78 (0.46), residues: 94 loop : -3.25 (0.26), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 447 HIS 0.005 0.001 HIS C 427 PHE 0.017 0.001 PHE A 203 TYR 0.016 0.001 TYR C 526 ARG 0.007 0.001 ARG C 180 *********************** 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: 24 poor density : 113 time to evaluate : 0.951 Fit side-chains REVERT: A 117 ARG cc_start: 0.7280 (mtp180) cc_final: 0.7037 (mtp85) REVERT: A 599 GLU cc_start: 0.8261 (tt0) cc_final: 0.7015 (pm20) REVERT: C 117 ARG cc_start: 0.7295 (mtp180) cc_final: 0.7025 (mtp85) REVERT: C 274 MET cc_start: 0.8199 (mtt) cc_final: 0.7981 (mtt) REVERT: C 424 MET cc_start: 0.8875 (mmm) cc_final: 0.8673 (mmm) REVERT: C 599 GLU cc_start: 0.8166 (tt0) cc_final: 0.6923 (pm20) REVERT: C 635 MET cc_start: 0.7428 (mtp) cc_final: 0.6732 (mpt) outliers start: 24 outliers final: 10 residues processed: 120 average time/residue: 1.3028 time to fit residues: 166.2643 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 : 0.897 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 0.0000 chunk 96 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- 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 = 0.166954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124617 restraints weight = 9113.488| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.99 r_work: 0.3124 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2131 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= 0.175 Angle : 0.574 6.326 11735 Z= 0.291 Chirality : 0.040 0.152 1395 Planarity : 0.004 0.035 1440 Dihedral : 5.100 35.022 1202 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.60 % Allowed : 8.57 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.23), residues: 1070 helix: -1.61 (0.19), residues: 604 sheet: -2.84 (0.44), residues: 94 loop : -2.69 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 426 HIS 0.004 0.001 HIS C 219 PHE 0.013 0.001 PHE A 502 TYR 0.014 0.001 TYR A 586 ARG 0.003 0.000 ARG A 158 *********************** 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 133 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.961 Fit side-chains REVERT: A 117 ARG cc_start: 0.7249 (mtp180) cc_final: 0.7035 (mtp85) REVERT: A 482 MET cc_start: 0.8770 (mmm) cc_final: 0.8551 (mmm) REVERT: C 274 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7932 (mtt) REVERT: C 468 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7854 (ttp-170) REVERT: C 482 MET cc_start: 0.8794 (mmm) cc_final: 0.8587 (mmm) REVERT: C 635 MET cc_start: 0.7397 (mtp) cc_final: 0.6726 (mpt) outliers start: 24 outliers final: 12 residues processed: 122 average time/residue: 1.3207 time to fit residues: 171.6699 Evaluate side-chains 113 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 174 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 403 HIS 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 211 GLU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 468 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.162789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120545 restraints weight = 9030.208| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.81 r_work: 0.3071 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8655 Z= 0.349 Angle : 0.693 7.679 11735 Z= 0.347 Chirality : 0.046 0.156 1395 Planarity : 0.005 0.043 1440 Dihedral : 5.520 33.672 1202 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.36 % Allowed : 9.98 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.23), residues: 1070 helix: -1.47 (0.19), residues: 608 sheet: -2.75 (0.45), residues: 94 loop : -2.63 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 426 HIS 0.007 0.002 HIS A 427 PHE 0.026 0.002 PHE A 203 TYR 0.017 0.002 TYR A 526 ARG 0.005 0.001 ARG A 410 *********************** 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 137 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.910 Fit side-chains REVERT: A 90 MET cc_start: 0.8019 (ptm) cc_final: 0.7778 (ttt) REVERT: A 117 ARG cc_start: 0.7365 (mtp180) cc_final: 0.7100 (mtp85) REVERT: A 397 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8547 (mt) REVERT: C 397 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8569 (mt) REVERT: C 468 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8388 (ttp-170) outliers start: 31 outliers final: 24 residues processed: 123 average time/residue: 1.3378 time to fit residues: 174.5904 Evaluate side-chains 124 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 289 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 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 171 ARG 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 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 545 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.163199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119867 restraints weight = 9126.629| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.72 r_work: 0.3053 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2307 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= 0.257 Angle : 0.627 7.333 11735 Z= 0.315 Chirality : 0.043 0.154 1395 Planarity : 0.004 0.042 1440 Dihedral : 5.265 33.448 1202 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.47 % Allowed : 10.85 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.24), residues: 1070 helix: -1.08 (0.20), residues: 602 sheet: -2.59 (0.46), residues: 94 loop : -2.43 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 426 HIS 0.006 0.001 HIS A 219 PHE 0.024 0.002 PHE C 203 TYR 0.013 0.002 TYR C 526 ARG 0.006 0.001 ARG C 180 *********************** 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 135 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.910 Fit side-chains REVERT: A 117 ARG cc_start: 0.7407 (mtp180) cc_final: 0.7072 (mtp85) REVERT: A 211 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: A 482 MET cc_start: 0.8857 (mmm) cc_final: 0.8646 (mmm) REVERT: C 211 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: C 468 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7985 (ttp-170) REVERT: C 482 MET cc_start: 0.8874 (mmm) cc_final: 0.8666 (mmm) outliers start: 32 outliers final: 25 residues processed: 121 average time/residue: 1.2657 time to fit residues: 162.9921 Evaluate side-chains 122 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain A residue 289 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 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 171 ARG 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 Chi-restraints excluded: chain C residue 545 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.166780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.119790 restraints weight = 8973.466| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.83 r_work: 0.3068 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2529 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= 0.172 Angle : 0.564 6.063 11735 Z= 0.286 Chirality : 0.040 0.147 1395 Planarity : 0.004 0.040 1440 Dihedral : 4.930 33.080 1202 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.71 % Allowed : 11.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.25), residues: 1070 helix: -0.68 (0.21), residues: 602 sheet: -2.23 (0.46), residues: 102 loop : -2.20 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 426 HIS 0.004 0.001 HIS C 219 PHE 0.017 0.001 PHE A 502 TYR 0.010 0.001 TYR A 586 ARG 0.006 0.000 ARG A 158 *********************** 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 135 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.878 Fit side-chains REVERT: A 117 ARG cc_start: 0.7397 (mtp180) cc_final: 0.7112 (mtp85) REVERT: A 211 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8088 (mt-10) REVERT: C 211 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8090 (mt-10) REVERT: C 274 MET cc_start: 0.8254 (mtt) cc_final: 0.8012 (mtt) REVERT: C 468 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8170 (ttp-170) REVERT: C 635 MET cc_start: 0.7428 (mtp) cc_final: 0.6668 (mpt) outliers start: 25 outliers final: 20 residues processed: 129 average time/residue: 1.1009 time to fit residues: 152.5643 Evaluate side-chains 122 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 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 = 0.3820 r_free = 0.3820 target = 0.163914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116903 restraints weight = 9163.625| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.84 r_work: 0.3020 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2489 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= 0.258 Angle : 0.622 6.998 11735 Z= 0.314 Chirality : 0.043 0.151 1395 Planarity : 0.004 0.039 1440 Dihedral : 5.124 33.414 1202 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.04 % Allowed : 12.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.25), residues: 1070 helix: -0.67 (0.21), residues: 602 sheet: -2.31 (0.46), residues: 104 loop : -2.13 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 426 HIS 0.005 0.001 HIS A 219 PHE 0.020 0.001 PHE A 502 TYR 0.012 0.001 TYR A 526 ARG 0.007 0.001 ARG A 158 *********************** 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 132 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 1.234 Fit side-chains REVERT: A 117 ARG cc_start: 0.7427 (mtp180) cc_final: 0.7044 (mtp85) REVERT: A 211 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8112 (mt-10) REVERT: C 211 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8109 (mt-10) REVERT: C 468 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8300 (ttp-170) outliers start: 28 outliers final: 21 residues processed: 123 average time/residue: 1.0579 time to fit residues: 140.2502 Evaluate side-chains 122 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 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 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 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 17 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.164341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120413 restraints weight = 9163.935| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.87 r_work: 0.3100 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2602 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= 0.200 Angle : 0.577 6.405 11735 Z= 0.292 Chirality : 0.041 0.147 1395 Planarity : 0.004 0.039 1440 Dihedral : 4.940 33.109 1202 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.04 % Allowed : 12.91 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.25), residues: 1070 helix: -0.46 (0.21), residues: 602 sheet: -2.03 (0.48), residues: 100 loop : -2.09 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 426 HIS 0.005 0.001 HIS A 219 PHE 0.020 0.001 PHE A 502 TYR 0.011 0.001 TYR A 586 ARG 0.007 0.000 ARG C 158 *********************** 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 139 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.938 Fit side-chains REVERT: A 117 ARG cc_start: 0.7406 (mtp180) cc_final: 0.7096 (mtp85) REVERT: A 211 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8081 (mt-10) REVERT: C 211 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8079 (mt-10) REVERT: C 468 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8204 (ttp-170) REVERT: C 635 MET cc_start: 0.7442 (mtp) cc_final: 0.6702 (mpt) outliers start: 28 outliers final: 21 residues processed: 129 average time/residue: 1.1350 time to fit residues: 156.7512 Evaluate side-chains 129 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3820 r_free = 0.3820 target = 0.163959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119980 restraints weight = 9066.331| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.90 r_work: 0.3043 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2577 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= 0.255 Angle : 0.618 6.997 11735 Z= 0.309 Chirality : 0.043 0.149 1395 Planarity : 0.004 0.044 1440 Dihedral : 5.073 33.113 1202 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.60 % Allowed : 13.88 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.25), residues: 1070 helix: -0.52 (0.21), residues: 602 sheet: -2.17 (0.47), residues: 102 loop : -2.03 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 426 HIS 0.005 0.001 HIS A 219 PHE 0.022 0.001 PHE A 502 TYR 0.011 0.001 TYR C 526 ARG 0.009 0.001 ARG A 158 *********************** 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 134 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.012 Fit side-chains REVERT: A 117 ARG cc_start: 0.7404 (mtp180) cc_final: 0.7075 (mtp85) REVERT: A 211 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8090 (mt-10) REVERT: C 211 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8099 (mt-10) REVERT: C 468 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8335 (ttp-170) outliers start: 24 outliers final: 21 residues processed: 128 average time/residue: 1.1297 time to fit residues: 155.0134 Evaluate side-chains 130 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 92 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 64 optimal weight: 0.0870 chunk 52 optimal weight: 0.7980 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.168731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122383 restraints weight = 9080.634| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.83 r_work: 0.3118 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 8655 Z= 0.123 Angle : 0.514 5.609 11735 Z= 0.261 Chirality : 0.039 0.141 1395 Planarity : 0.004 0.037 1440 Dihedral : 4.552 33.746 1202 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.17 % Allowed : 14.53 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.26), residues: 1070 helix: -0.05 (0.21), residues: 602 sheet: -1.94 (0.50), residues: 102 loop : -1.84 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 447 HIS 0.003 0.001 HIS A 219 PHE 0.022 0.001 PHE A 502 TYR 0.007 0.001 TYR C 586 ARG 0.008 0.000 ARG A 158 ********************** 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 137 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.976 Fit side-chains REVERT: A 117 ARG cc_start: 0.7346 (mtp180) cc_final: 0.7083 (mtp85) REVERT: A 211 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8041 (mt-10) REVERT: C 188 GLU cc_start: 0.7193 (tt0) cc_final: 0.6829 (tm-30) REVERT: C 211 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7992 (mt-10) REVERT: C 296 MET cc_start: 0.8284 (tpp) cc_final: 0.8060 (mmm) REVERT: C 468 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8024 (ttp-170) outliers start: 20 outliers final: 14 residues processed: 131 average time/residue: 1.1335 time to fit residues: 159.1852 Evaluate side-chains 128 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 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 174 THR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 382 CYS 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 51 optimal weight: 6.9990 chunk 46 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 24 optimal weight: 0.0040 chunk 44 optimal weight: 3.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- 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 C 147 GLN 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 = 0.166968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120296 restraints weight = 9136.804| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.85 r_work: 0.3086 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8655 Z= 0.171 Angle : 0.551 5.943 11735 Z= 0.276 Chirality : 0.040 0.146 1395 Planarity : 0.004 0.043 1440 Dihedral : 4.642 34.129 1202 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.06 % Allowed : 15.40 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 1070 helix: -0.01 (0.21), residues: 604 sheet: -1.92 (0.53), residues: 92 loop : -1.77 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 426 HIS 0.004 0.001 HIS A 219 PHE 0.024 0.001 PHE A 502 TYR 0.011 0.001 TYR A 586 ARG 0.009 0.000 ARG C 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5698.06 seconds wall clock time: 101 minutes 12.96 seconds (6072.96 seconds total)