Starting phenix.real_space_refine on Sun Sep 29 14:29:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/09_2024/7mik_23854.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/09_2024/7mik_23854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/09_2024/7mik_23854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/09_2024/7mik_23854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/09_2024/7mik_23854.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/09_2024/7mik_23854.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 124 5.16 5 Na 4 4.78 5 C 15064 2.51 5 N 3476 2.21 5 O 4024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22728 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "B" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "C" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "D" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "A" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 524 Unusual residues: {' NA': 4, 'POV': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 13.27, per 1000 atoms: 0.58 Number of scatterers: 22728 At special positions: 0 Unit cell: (127.842, 127.842, 130.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 36 15.00 Na 4 11.00 O 4024 8.00 N 3476 7.00 C 15064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.02 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.02 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.02 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.02 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: 5.29 Conformation dependent library (CDL) restraints added in 3.0 seconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4904 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 63.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.535A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.542A pdb=" N GLN A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.558A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.602A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.669A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.627A pdb=" N THR A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.636A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.518A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.703A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.676A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.574A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.610A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.520A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.810A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.532A pdb=" N PHE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 507 removed outlier: 3.694A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 497 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 Processing helix chain 'A' and resid 520 through 543 removed outlier: 3.746A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.632A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.732A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 568' Processing helix chain 'A' and resid 569 through 574 Processing helix chain 'A' and resid 574 through 586 removed outlier: 3.687A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 3.589A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.588A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 removed outlier: 3.510A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 685 removed outlier: 3.975A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.774A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.637A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.534A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.541A pdb=" N GLN B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.559A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.602A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.669A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.627A pdb=" N THR B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.636A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.517A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.703A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.676A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.574A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.610A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.520A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.810A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.531A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 507 removed outlier: 3.694A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 520 Processing helix chain 'B' and resid 520 through 543 removed outlier: 3.746A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 removed outlier: 3.631A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.733A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 568' Processing helix chain 'B' and resid 569 through 574 Processing helix chain 'B' and resid 574 through 586 removed outlier: 3.687A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 3.590A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.588A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 removed outlier: 3.509A pdb=" N LEU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.975A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 705 removed outlier: 3.774A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.637A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.534A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.542A pdb=" N GLN C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.559A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.603A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.669A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.627A pdb=" N THR C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 271 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.636A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.518A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.703A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.676A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.574A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.610A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.520A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.811A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 434 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.532A pdb=" N PHE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 507 removed outlier: 3.694A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 497 " --> pdb=" O TRP C 493 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 520 Processing helix chain 'C' and resid 520 through 543 removed outlier: 3.746A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 removed outlier: 3.631A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 568 removed outlier: 3.733A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 563 through 568' Processing helix chain 'C' and resid 569 through 574 Processing helix chain 'C' and resid 574 through 586 removed outlier: 3.688A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 3.590A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.587A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 removed outlier: 3.510A pdb=" N LEU C 655 " --> pdb=" O PRO C 651 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 685 removed outlier: 3.975A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 705 removed outlier: 3.774A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.638A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.535A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.541A pdb=" N GLN D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 158 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.558A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.603A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.669A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.627A pdb=" N THR D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 271 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.636A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.518A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.703A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.675A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.575A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.610A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.520A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.811A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS D 434 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.532A pdb=" N PHE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 457 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 507 removed outlier: 3.694A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 497 " --> pdb=" O TRP D 493 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 520 Processing helix chain 'D' and resid 520 through 543 removed outlier: 3.746A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 560 removed outlier: 3.631A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 removed outlier: 3.734A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 563 through 568' Processing helix chain 'D' and resid 569 through 574 Processing helix chain 'D' and resid 574 through 586 removed outlier: 3.687A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 3.589A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 595 " --> pdb=" O LEU D 591 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.588A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 removed outlier: 3.510A pdb=" N LEU D 655 " --> pdb=" O PRO D 651 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 662 " --> pdb=" O LEU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 685 removed outlier: 3.975A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 705 removed outlier: 3.774A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.638A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.777A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 722 through 724 removed outlier: 6.970A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.777A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 722 through 724 removed outlier: 6.970A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.777A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 722 through 724 removed outlier: 6.970A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.778A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 722 through 724 removed outlier: 6.970A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2592 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: 6.07 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3432 1.31 - 1.44: 6000 1.44 - 1.56: 13436 1.56 - 1.69: 72 1.69 - 1.82: 204 Bond restraints: 23144 Sorted by residual: bond pdb=" C21 POV A 909 " pdb=" O21 POV A 909 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C21 POV B 902 " pdb=" O21 POV B 902 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C21 POV D 903 " pdb=" O21 POV D 903 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C21 POV C 902 " pdb=" O21 POV C 902 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C21 POV D 906 " pdb=" O21 POV D 906 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 23139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 29516 2.70 - 5.40: 956 5.40 - 8.09: 274 8.09 - 10.79: 122 10.79 - 13.49: 100 Bond angle restraints: 30968 Sorted by residual: angle pdb=" C12 POV A 905 " pdb=" N POV A 905 " pdb=" C14 POV A 905 " ideal model delta sigma weight residual 107.13 120.62 -13.49 3.00e+00 1.11e-01 2.02e+01 angle pdb=" C12 POV B 907 " pdb=" N POV B 907 " pdb=" C14 POV B 907 " ideal model delta sigma weight residual 107.13 120.59 -13.46 3.00e+00 1.11e-01 2.01e+01 angle pdb=" C GLY D 262 " pdb=" N GLU D 263 " pdb=" CA GLU D 263 " ideal model delta sigma weight residual 121.54 130.10 -8.56 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C GLY A 262 " pdb=" N GLU A 263 " pdb=" CA GLU A 263 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C12 POV C 907 " pdb=" N POV C 907 " pdb=" C14 POV C 907 " ideal model delta sigma weight residual 107.13 120.53 -13.40 3.00e+00 1.11e-01 2.00e+01 ... (remaining 30963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.47: 13266 30.47 - 60.94: 855 60.94 - 91.40: 129 91.40 - 121.87: 30 121.87 - 152.34: 20 Dihedral angle restraints: 14300 sinusoidal: 6744 harmonic: 7556 Sorted by residual: dihedral pdb=" CA GLN C 313 " pdb=" C GLN C 313 " pdb=" N ASN C 314 " pdb=" CA ASN C 314 " ideal model delta harmonic sigma weight residual -180.00 -131.17 -48.83 0 5.00e+00 4.00e-02 9.54e+01 dihedral pdb=" CA GLN D 313 " pdb=" C GLN D 313 " pdb=" N ASN D 314 " pdb=" CA ASN D 314 " ideal model delta harmonic sigma weight residual -180.00 -131.20 -48.80 0 5.00e+00 4.00e-02 9.52e+01 dihedral pdb=" CA GLN B 313 " pdb=" C GLN B 313 " pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta harmonic sigma weight residual 180.00 -131.23 -48.77 0 5.00e+00 4.00e-02 9.51e+01 ... (remaining 14297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2761 0.065 - 0.130: 479 0.130 - 0.195: 76 0.195 - 0.259: 8 0.259 - 0.324: 4 Chirality restraints: 3328 Sorted by residual: chirality pdb=" CG LEU B 469 " pdb=" CB LEU B 469 " pdb=" CD1 LEU B 469 " pdb=" CD2 LEU B 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CG LEU D 469 " pdb=" CB LEU D 469 " pdb=" CD1 LEU D 469 " pdb=" CD2 LEU D 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CG LEU A 469 " pdb=" CB LEU A 469 " pdb=" CD1 LEU A 469 " pdb=" CD2 LEU A 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 3325 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 343 " 0.038 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO A 344 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 343 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO D 344 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 344 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 344 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 343 " -0.038 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO C 344 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 344 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 344 " -0.032 5.00e-02 4.00e+02 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 994 2.72 - 3.26: 19629 3.26 - 3.81: 32180 3.81 - 4.35: 44455 4.35 - 4.90: 75098 Nonbonded interactions: 172356 Sorted by model distance: nonbonded pdb="NA NA A 911 " pdb="NA NA A 912 " model vdw 2.170 1.900 nonbonded pdb=" OH TYR B 650 " pdb=" O LYS C 545 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR A 650 " pdb=" O LYS B 545 " model vdw 2.333 3.040 nonbonded pdb=" O LYS A 545 " pdb=" OH TYR D 650 " model vdw 2.344 3.040 nonbonded pdb=" OD1 ASN C 298 " pdb=" ND1 HIS C 301 " model vdw 2.355 3.120 ... (remaining 172351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 118 through 757 or resid 901 through 908)) selection = (chain 'B' and (resid 118 through 757 or resid 901 through 908)) selection = (chain 'C' and (resid 118 through 757 or resid 901 through 908)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 0.680 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: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 48.370 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.093 23144 Z= 0.618 Angle : 1.473 13.491 30968 Z= 0.651 Chirality : 0.052 0.324 3328 Planarity : 0.006 0.057 3712 Dihedral : 20.360 152.341 9384 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.53 % Allowed : 4.47 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -6.20 (0.10), residues: 2552 helix: -4.84 (0.04), residues: 1540 sheet: -1.74 (0.57), residues: 76 loop : -2.56 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 710 HIS 0.010 0.002 HIS D 301 PHE 0.028 0.003 PHE C 526 TYR 0.017 0.003 TYR B 461 ARG 0.007 0.001 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 471 time to evaluate : 2.245 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7150 (pt0) REVERT: A 229 ASP cc_start: 0.7764 (m-30) cc_final: 0.7552 (m-30) REVERT: A 257 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 322 ASP cc_start: 0.7640 (t70) cc_final: 0.7302 (t0) REVERT: A 337 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.7451 (mtt-85) REVERT: A 434 LYS cc_start: 0.8026 (mtpm) cc_final: 0.7652 (mmtt) REVERT: A 647 ASN cc_start: 0.8221 (t160) cc_final: 0.7936 (t0) REVERT: A 683 ASN cc_start: 0.7706 (m110) cc_final: 0.7342 (m-40) REVERT: B 211 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7352 (pt0) REVERT: B 257 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7006 (mt-10) REVERT: B 322 ASP cc_start: 0.7677 (t70) cc_final: 0.7454 (t0) REVERT: C 257 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6954 (mt-10) REVERT: C 322 ASP cc_start: 0.7504 (t70) cc_final: 0.7299 (t0) REVERT: C 337 ARG cc_start: 0.7909 (mtp-110) cc_final: 0.7498 (mtt-85) REVERT: C 434 LYS cc_start: 0.8037 (mtpm) cc_final: 0.7777 (mmtp) REVERT: C 545 LYS cc_start: 0.7267 (mtmm) cc_final: 0.7066 (mptt) REVERT: C 647 ASN cc_start: 0.8247 (t160) cc_final: 0.7971 (t0) REVERT: C 683 ASN cc_start: 0.7739 (m110) cc_final: 0.7480 (m-40) REVERT: C 687 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6959 (pt0) REVERT: C 738 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8331 (tttm) REVERT: C 744 THR cc_start: 0.8667 (t) cc_final: 0.8461 (m) REVERT: D 211 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7203 (pt0) REVERT: D 257 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6868 (mt-10) REVERT: D 322 ASP cc_start: 0.7615 (t70) cc_final: 0.7338 (t0) REVERT: D 337 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7496 (mtt-85) REVERT: D 434 LYS cc_start: 0.8045 (mtpm) cc_final: 0.7735 (mmtt) REVERT: D 647 ASN cc_start: 0.8197 (t160) cc_final: 0.7970 (t0) REVERT: D 683 ASN cc_start: 0.7776 (m110) cc_final: 0.7440 (m-40) REVERT: D 738 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8397 (tttm) outliers start: 12 outliers final: 5 residues processed: 479 average time/residue: 0.3622 time to fit residues: 259.5685 Evaluate side-chains 319 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 314 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 469 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 232 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 284 ASN A 314 ASN A 471 HIS A 646 GLN A 647 ASN B 178 ASN B 251 ASN B 284 ASN B 314 ASN B 330 ASN B 471 HIS B 646 GLN B 647 ASN C 178 ASN C 251 ASN C 314 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN C 647 ASN D 178 ASN D 314 ASN D 471 HIS D 646 GLN D 647 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23144 Z= 0.186 Angle : 0.573 6.244 30968 Z= 0.295 Chirality : 0.040 0.160 3328 Planarity : 0.004 0.035 3712 Dihedral : 21.967 177.187 4346 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.31 % Allowed : 7.14 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.98 (0.13), residues: 2552 helix: -2.66 (0.10), residues: 1552 sheet: -1.07 (0.55), residues: 76 loop : -2.41 (0.17), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 559 HIS 0.004 0.001 HIS B 301 PHE 0.014 0.001 PHE A 193 TYR 0.017 0.002 TYR B 575 ARG 0.002 0.000 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 326 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7070 (tt0) REVERT: A 257 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6805 (mt-10) REVERT: A 283 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6763 (mt-10) REVERT: A 337 ARG cc_start: 0.7935 (mtp-110) cc_final: 0.7448 (mtt-85) REVERT: A 434 LYS cc_start: 0.7751 (mtpm) cc_final: 0.7360 (mmtp) REVERT: A 683 ASN cc_start: 0.7577 (m110) cc_final: 0.7133 (m-40) REVERT: A 712 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.7603 (mtm-85) REVERT: B 257 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6943 (mt-10) REVERT: B 283 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6833 (mt-10) REVERT: B 311 LYS cc_start: 0.8373 (ttpp) cc_final: 0.7959 (mtpp) REVERT: C 160 HIS cc_start: 0.6109 (t-90) cc_final: 0.5364 (m170) REVERT: C 161 LYS cc_start: 0.7380 (mmtt) cc_final: 0.6970 (mmmt) REVERT: C 257 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6911 (mt-10) REVERT: C 337 ARG cc_start: 0.7968 (mtp-110) cc_final: 0.7478 (mtt-85) REVERT: C 434 LYS cc_start: 0.7751 (mtpm) cc_final: 0.7415 (mmtp) REVERT: C 496 CYS cc_start: 0.7955 (t) cc_final: 0.7643 (t) REVERT: C 683 ASN cc_start: 0.7740 (m110) cc_final: 0.7332 (m-40) REVERT: D 211 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7137 (tt0) REVERT: D 257 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6801 (mt-10) REVERT: D 337 ARG cc_start: 0.7885 (mtp-110) cc_final: 0.7472 (mtt-85) REVERT: D 434 LYS cc_start: 0.7746 (mtpm) cc_final: 0.7391 (mmtp) REVERT: D 683 ASN cc_start: 0.7683 (m110) cc_final: 0.7285 (m-40) outliers start: 30 outliers final: 10 residues processed: 354 average time/residue: 0.3853 time to fit residues: 202.5593 Evaluate side-chains 289 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 279 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 495 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 251 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 646 GLN B 160 HIS B 646 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN D 160 HIS D 646 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23144 Z= 0.345 Angle : 0.669 6.834 30968 Z= 0.332 Chirality : 0.045 0.155 3328 Planarity : 0.004 0.035 3712 Dihedral : 21.135 123.767 4336 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.15 % Allowed : 8.36 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.68 (0.15), residues: 2552 helix: -1.41 (0.12), residues: 1540 sheet: -0.82 (0.53), residues: 84 loop : -2.32 (0.17), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 692 HIS 0.008 0.001 HIS B 301 PHE 0.025 0.002 PHE C 526 TYR 0.017 0.002 TYR D 451 ARG 0.003 0.000 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 293 time to evaluate : 2.452 Fit side-chains REVERT: A 214 GLU cc_start: 0.7444 (tt0) cc_final: 0.6564 (pt0) REVERT: A 257 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6934 (mt-10) REVERT: A 283 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6983 (mt-10) REVERT: A 337 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7453 (mtt-85) REVERT: A 434 LYS cc_start: 0.7844 (mtpm) cc_final: 0.7353 (mmtt) REVERT: A 683 ASN cc_start: 0.7652 (m110) cc_final: 0.7212 (m-40) REVERT: A 738 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8124 (mtpp) REVERT: B 214 GLU cc_start: 0.7543 (tt0) cc_final: 0.7029 (pt0) REVERT: B 283 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7152 (mt-10) REVERT: C 161 LYS cc_start: 0.7480 (mmtt) cc_final: 0.7103 (mmmt) REVERT: C 257 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7031 (mt-10) REVERT: C 337 ARG cc_start: 0.7931 (mtp-110) cc_final: 0.7528 (mtt-85) REVERT: C 434 LYS cc_start: 0.7920 (mtpm) cc_final: 0.7495 (mmtt) REVERT: C 683 ASN cc_start: 0.7699 (m110) cc_final: 0.7466 (m-40) REVERT: C 738 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8218 (mtpp) REVERT: D 214 GLU cc_start: 0.7469 (tt0) cc_final: 0.6650 (pt0) REVERT: D 257 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6958 (mt-10) REVERT: D 337 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7511 (mtt-85) REVERT: D 434 LYS cc_start: 0.7912 (mtpm) cc_final: 0.7471 (mmtt) REVERT: D 683 ASN cc_start: 0.7722 (m110) cc_final: 0.7315 (m-40) REVERT: D 738 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8203 (mtpp) outliers start: 49 outliers final: 26 residues processed: 330 average time/residue: 0.3852 time to fit residues: 189.5926 Evaluate side-chains 298 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 272 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN A 647 ASN B 330 ASN B 646 GLN C 330 ASN C 471 HIS C 646 GLN C 647 ASN D 646 GLN D 647 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23144 Z= 0.209 Angle : 0.568 13.273 30968 Z= 0.280 Chirality : 0.040 0.156 3328 Planarity : 0.003 0.029 3712 Dihedral : 19.708 102.009 4336 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.01 % Allowed : 9.81 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.92 (0.15), residues: 2552 helix: -0.69 (0.13), residues: 1544 sheet: -0.51 (0.57), residues: 76 loop : -2.22 (0.17), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 692 HIS 0.005 0.001 HIS D 301 PHE 0.017 0.001 PHE B 316 TYR 0.013 0.002 TYR A 575 ARG 0.003 0.000 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 277 time to evaluate : 2.373 Fit side-chains REVERT: A 214 GLU cc_start: 0.7452 (tt0) cc_final: 0.6555 (pt0) REVERT: A 257 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6836 (mt-10) REVERT: A 283 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6975 (mt-10) REVERT: A 337 ARG cc_start: 0.7919 (mtp-110) cc_final: 0.7468 (mtt-85) REVERT: A 434 LYS cc_start: 0.7787 (mtpm) cc_final: 0.7321 (mmtp) REVERT: A 683 ASN cc_start: 0.7615 (m110) cc_final: 0.7153 (m-40) REVERT: A 712 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7632 (mmm-85) REVERT: A 722 LYS cc_start: 0.8416 (tttt) cc_final: 0.8213 (tttm) REVERT: A 738 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8129 (mtpp) REVERT: B 283 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7167 (mt-10) REVERT: B 311 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7866 (mtpp) REVERT: C 161 LYS cc_start: 0.7480 (mmtt) cc_final: 0.7110 (mmmt) REVERT: C 214 GLU cc_start: 0.7641 (tt0) cc_final: 0.6836 (pt0) REVERT: C 257 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6889 (mt-10) REVERT: C 337 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.7526 (mtt-85) REVERT: C 350 LYS cc_start: 0.8166 (tppt) cc_final: 0.7883 (tttt) REVERT: C 434 LYS cc_start: 0.7847 (mtpm) cc_final: 0.7438 (mmtp) REVERT: C 496 CYS cc_start: 0.7855 (t) cc_final: 0.7557 (t) REVERT: C 683 ASN cc_start: 0.7675 (m110) cc_final: 0.7185 (m-40) REVERT: C 738 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8215 (mtpp) REVERT: D 141 ASP cc_start: 0.5959 (t70) cc_final: 0.5754 (t70) REVERT: D 214 GLU cc_start: 0.7468 (tt0) cc_final: 0.6628 (pt0) REVERT: D 257 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6865 (mt-10) REVERT: D 337 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7516 (mtt-85) REVERT: D 434 LYS cc_start: 0.7827 (mtpm) cc_final: 0.7412 (mmtp) REVERT: D 469 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5428 (mt) REVERT: D 683 ASN cc_start: 0.7696 (m110) cc_final: 0.7209 (m-40) REVERT: D 738 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8165 (mtpp) outliers start: 46 outliers final: 26 residues processed: 312 average time/residue: 0.3903 time to fit residues: 183.6113 Evaluate side-chains 282 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 255 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 732 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 211 optimal weight: 0.5980 chunk 171 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN B 646 GLN B 647 ASN C 646 GLN D 646 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23144 Z= 0.223 Angle : 0.568 12.205 30968 Z= 0.281 Chirality : 0.041 0.226 3328 Planarity : 0.003 0.030 3712 Dihedral : 19.098 101.841 4336 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.88 % Allowed : 10.68 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.43 (0.16), residues: 2552 helix: -0.26 (0.13), residues: 1548 sheet: -0.46 (0.57), residues: 76 loop : -2.08 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 710 HIS 0.005 0.001 HIS D 301 PHE 0.017 0.001 PHE A 316 TYR 0.013 0.002 TYR C 451 ARG 0.003 0.000 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 269 time to evaluate : 2.414 Fit side-chains REVERT: A 257 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6775 (mt-10) REVERT: A 283 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6954 (mt-10) REVERT: A 337 ARG cc_start: 0.7911 (mtp-110) cc_final: 0.7427 (mtt-85) REVERT: A 434 LYS cc_start: 0.7803 (mtpm) cc_final: 0.7335 (mmtp) REVERT: A 683 ASN cc_start: 0.7660 (m110) cc_final: 0.7162 (m-40) REVERT: A 712 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7453 (mmm-85) REVERT: A 717 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6159 (mtm) REVERT: A 722 LYS cc_start: 0.8413 (tttt) cc_final: 0.8191 (tttm) REVERT: A 738 LYS cc_start: 0.8484 (ttmm) cc_final: 0.8154 (mtpp) REVERT: B 283 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7160 (mt-10) REVERT: B 311 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7877 (mtpp) REVERT: B 717 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6333 (mtm) REVERT: C 141 ASP cc_start: 0.6069 (t70) cc_final: 0.5849 (t0) REVERT: C 161 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7386 (mmmt) REVERT: C 257 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6871 (mt-10) REVERT: C 337 ARG cc_start: 0.7923 (mtp-110) cc_final: 0.7537 (mtt-85) REVERT: C 434 LYS cc_start: 0.7853 (mtpm) cc_final: 0.7408 (mmtt) REVERT: C 496 CYS cc_start: 0.7863 (t) cc_final: 0.7572 (t) REVERT: C 683 ASN cc_start: 0.7714 (m110) cc_final: 0.7260 (m-40) REVERT: C 738 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8187 (mtpp) REVERT: D 257 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6807 (mt-10) REVERT: D 337 ARG cc_start: 0.7888 (mtp-110) cc_final: 0.7504 (mtt-85) REVERT: D 434 LYS cc_start: 0.7830 (mtpm) cc_final: 0.7410 (mmtp) REVERT: D 469 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5717 (mt) REVERT: D 683 ASN cc_start: 0.7727 (m110) cc_final: 0.7257 (m-40) REVERT: D 738 LYS cc_start: 0.8473 (ttmm) cc_final: 0.8173 (mtpp) outliers start: 43 outliers final: 30 residues processed: 300 average time/residue: 0.3138 time to fit residues: 144.3735 Evaluate side-chains 288 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 255 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 2.9990 chunk 222 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 205 optimal weight: 0.1980 chunk 114 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN B 646 GLN C 646 GLN D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23144 Z= 0.208 Angle : 0.559 13.110 30968 Z= 0.275 Chirality : 0.040 0.142 3328 Planarity : 0.003 0.030 3712 Dihedral : 18.609 98.838 4336 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.62 % Allowed : 11.56 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.12 (0.16), residues: 2552 helix: 0.02 (0.13), residues: 1548 sheet: -0.34 (0.58), residues: 76 loop : -2.01 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 710 HIS 0.005 0.001 HIS A 301 PHE 0.017 0.001 PHE D 316 TYR 0.012 0.001 TYR D 451 ARG 0.005 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 260 time to evaluate : 2.569 Fit side-chains REVERT: A 283 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6991 (mt-10) REVERT: A 337 ARG cc_start: 0.7940 (mtp-110) cc_final: 0.7514 (mtt-85) REVERT: A 434 LYS cc_start: 0.7794 (mtpm) cc_final: 0.7325 (mmtp) REVERT: A 469 LEU cc_start: 0.5075 (OUTLIER) cc_final: 0.4848 (mt) REVERT: A 683 ASN cc_start: 0.7660 (m110) cc_final: 0.7137 (m-40) REVERT: A 712 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7445 (mmm-85) REVERT: A 717 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6193 (mtm) REVERT: A 722 LYS cc_start: 0.8404 (tttt) cc_final: 0.8181 (tttm) REVERT: A 738 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8143 (mtpp) REVERT: B 283 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7149 (mt-10) REVERT: B 311 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7854 (mtpp) REVERT: B 717 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6340 (mtm) REVERT: C 161 LYS cc_start: 0.7610 (mmtt) cc_final: 0.7279 (mmmt) REVERT: C 257 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6837 (mt-10) REVERT: C 337 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7526 (mtt-85) REVERT: C 350 LYS cc_start: 0.8148 (tppt) cc_final: 0.7878 (tttt) REVERT: C 434 LYS cc_start: 0.7847 (mtpm) cc_final: 0.7426 (mmtp) REVERT: C 683 ASN cc_start: 0.7708 (m110) cc_final: 0.7237 (m-40) REVERT: C 738 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8170 (mtpp) REVERT: D 162 LEU cc_start: 0.6532 (mt) cc_final: 0.6298 (mt) REVERT: D 337 ARG cc_start: 0.7923 (mtp-110) cc_final: 0.7521 (mtt-85) REVERT: D 434 LYS cc_start: 0.7813 (mtpm) cc_final: 0.7395 (mmtp) REVERT: D 469 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5753 (mt) REVERT: D 683 ASN cc_start: 0.7713 (m110) cc_final: 0.7210 (m-40) REVERT: D 738 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8155 (mtpp) outliers start: 37 outliers final: 27 residues processed: 287 average time/residue: 0.3835 time to fit residues: 167.3893 Evaluate side-chains 282 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 113 optimal weight: 0.0060 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN B 646 GLN C 646 GLN D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23144 Z= 0.146 Angle : 0.500 13.126 30968 Z= 0.248 Chirality : 0.038 0.144 3328 Planarity : 0.003 0.029 3712 Dihedral : 17.885 91.445 4336 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.05 % Allowed : 12.57 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2552 helix: 0.39 (0.14), residues: 1560 sheet: -0.26 (0.58), residues: 76 loop : -1.93 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 710 HIS 0.003 0.001 HIS B 301 PHE 0.017 0.001 PHE A 316 TYR 0.010 0.001 TYR C 575 ARG 0.004 0.000 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 2.383 Fit side-chains revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6961 (mt-10) REVERT: A 337 ARG cc_start: 0.7934 (mtp-110) cc_final: 0.7470 (mtt-85) REVERT: A 434 LYS cc_start: 0.7780 (mtpm) cc_final: 0.7280 (mmtp) REVERT: A 683 ASN cc_start: 0.7609 (m110) cc_final: 0.7103 (m-40) REVERT: A 712 ARG cc_start: 0.7793 (mtm-85) cc_final: 0.7441 (mmm-85) REVERT: A 717 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6245 (mtm) REVERT: A 722 LYS cc_start: 0.8363 (tttt) cc_final: 0.8131 (tttm) REVERT: A 738 LYS cc_start: 0.8409 (ttmm) cc_final: 0.7860 (mtpp) REVERT: A 741 GLU cc_start: 0.7201 (mp0) cc_final: 0.6827 (mp0) REVERT: B 283 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7104 (mt-10) REVERT: B 311 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7576 (mtmm) REVERT: B 717 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6411 (mtm) REVERT: C 257 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6757 (mt-10) REVERT: C 337 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.7503 (mtt-85) REVERT: C 350 LYS cc_start: 0.8077 (tppt) cc_final: 0.7803 (tttt) REVERT: C 434 LYS cc_start: 0.7792 (mtpm) cc_final: 0.7373 (mmtp) REVERT: C 496 CYS cc_start: 0.7798 (t) cc_final: 0.7507 (t) REVERT: C 683 ASN cc_start: 0.7651 (m110) cc_final: 0.7179 (m-40) REVERT: C 738 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8025 (mtpp) REVERT: D 337 ARG cc_start: 0.7911 (mtp-110) cc_final: 0.7497 (mtt-85) REVERT: D 434 LYS cc_start: 0.7769 (mtpm) cc_final: 0.7353 (mmtp) REVERT: D 469 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5732 (mt) REVERT: D 683 ASN cc_start: 0.7650 (m110) cc_final: 0.7178 (m-40) REVERT: D 738 LYS cc_start: 0.8414 (ttmm) cc_final: 0.8039 (mtpp) outliers start: 24 outliers final: 16 residues processed: 279 average time/residue: 0.3827 time to fit residues: 160.2790 Evaluate side-chains 263 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 244 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 525 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN D 646 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23144 Z= 0.143 Angle : 0.513 13.267 30968 Z= 0.250 Chirality : 0.038 0.177 3328 Planarity : 0.003 0.028 3712 Dihedral : 17.678 89.035 4336 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.14 % Allowed : 12.52 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2552 helix: 0.63 (0.14), residues: 1560 sheet: -0.21 (0.57), residues: 76 loop : -1.83 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 710 HIS 0.003 0.001 HIS B 301 PHE 0.017 0.001 PHE D 316 TYR 0.010 0.001 TYR B 575 ARG 0.005 0.000 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 248 time to evaluate : 2.518 Fit side-chains revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 337 ARG cc_start: 0.7945 (mtp-110) cc_final: 0.7477 (mtt-85) REVERT: A 434 LYS cc_start: 0.7765 (mtpm) cc_final: 0.7274 (mmtp) REVERT: A 683 ASN cc_start: 0.7632 (m110) cc_final: 0.7129 (m-40) REVERT: A 712 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7398 (mmm-85) REVERT: A 717 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6329 (mtm) REVERT: A 722 LYS cc_start: 0.8367 (tttt) cc_final: 0.8129 (tttm) REVERT: A 738 LYS cc_start: 0.8366 (ttmm) cc_final: 0.8010 (mtpp) REVERT: B 283 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7102 (mt-10) REVERT: B 311 LYS cc_start: 0.7960 (ttpp) cc_final: 0.7569 (mtmm) REVERT: B 717 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6492 (mtm) REVERT: C 257 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6734 (mt-10) REVERT: C 337 ARG cc_start: 0.7905 (mtp-110) cc_final: 0.7508 (mtt-85) REVERT: C 434 LYS cc_start: 0.7787 (mtpm) cc_final: 0.7362 (mmtp) REVERT: C 469 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.4780 (mt) REVERT: C 683 ASN cc_start: 0.7663 (m110) cc_final: 0.7208 (m-40) REVERT: C 738 LYS cc_start: 0.8295 (ttmm) cc_final: 0.8032 (mtpp) REVERT: D 337 ARG cc_start: 0.7916 (mtp-110) cc_final: 0.7507 (mtt-85) REVERT: D 434 LYS cc_start: 0.7791 (mtpm) cc_final: 0.7380 (mmtp) REVERT: D 683 ASN cc_start: 0.7670 (m110) cc_final: 0.7196 (m-40) REVERT: D 738 LYS cc_start: 0.8308 (ttmm) cc_final: 0.8037 (mtpp) outliers start: 26 outliers final: 17 residues processed: 270 average time/residue: 0.3752 time to fit residues: 153.4113 Evaluate side-chains 266 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 246 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 180 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23144 Z= 0.131 Angle : 0.502 13.735 30968 Z= 0.244 Chirality : 0.038 0.156 3328 Planarity : 0.003 0.028 3712 Dihedral : 17.368 88.852 4336 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.96 % Allowed : 12.70 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2552 helix: 0.86 (0.14), residues: 1560 sheet: -0.17 (0.57), residues: 76 loop : -1.77 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 710 HIS 0.003 0.001 HIS C 301 PHE 0.016 0.001 PHE D 316 TYR 0.009 0.001 TYR B 575 ARG 0.005 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 244 time to evaluate : 2.289 Fit side-chains revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6940 (mt-10) REVERT: A 337 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7453 (mtt-85) REVERT: A 434 LYS cc_start: 0.7750 (mtpm) cc_final: 0.7273 (mmtp) REVERT: A 683 ASN cc_start: 0.7644 (m110) cc_final: 0.7157 (m-40) REVERT: A 712 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7362 (mmm-85) REVERT: A 717 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6335 (mtm) REVERT: A 722 LYS cc_start: 0.8362 (tttt) cc_final: 0.8116 (tttm) REVERT: A 738 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7999 (mtpp) REVERT: B 283 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7071 (mt-10) REVERT: B 311 LYS cc_start: 0.7875 (ttpp) cc_final: 0.7535 (mtmm) REVERT: B 717 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6481 (mtm) REVERT: C 337 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7489 (mtt-85) REVERT: C 434 LYS cc_start: 0.7773 (mtpm) cc_final: 0.7350 (mmtp) REVERT: C 469 LEU cc_start: 0.5495 (OUTLIER) cc_final: 0.4800 (mt) REVERT: C 496 CYS cc_start: 0.7720 (t) cc_final: 0.7412 (t) REVERT: C 683 ASN cc_start: 0.7603 (m110) cc_final: 0.7118 (m-40) REVERT: C 738 LYS cc_start: 0.8331 (ttmm) cc_final: 0.8036 (mtpp) REVERT: D 337 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.7484 (mtt-85) REVERT: D 434 LYS cc_start: 0.7783 (mtpm) cc_final: 0.7367 (mmtp) REVERT: D 683 ASN cc_start: 0.7675 (m110) cc_final: 0.7223 (m-40) REVERT: D 738 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8029 (mtpp) outliers start: 22 outliers final: 16 residues processed: 261 average time/residue: 0.3571 time to fit residues: 141.6467 Evaluate side-chains 257 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 238 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 255 optimal weight: 0.5980 chunk 234 optimal weight: 5.9990 chunk 203 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 156 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23144 Z= 0.118 Angle : 0.481 11.291 30968 Z= 0.236 Chirality : 0.037 0.140 3328 Planarity : 0.003 0.028 3712 Dihedral : 16.913 89.400 4336 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.79 % Allowed : 12.57 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2552 helix: 1.09 (0.14), residues: 1560 sheet: -0.14 (0.57), residues: 76 loop : -1.72 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 710 HIS 0.002 0.000 HIS B 301 PHE 0.016 0.001 PHE D 316 TYR 0.008 0.001 TYR B 575 ARG 0.004 0.000 ARG D 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 2.433 Fit side-chains revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6859 (mt-10) REVERT: A 311 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7021 (mtmm) REVERT: A 337 ARG cc_start: 0.7905 (mtp-110) cc_final: 0.7427 (mtt-85) REVERT: A 434 LYS cc_start: 0.7760 (mtpm) cc_final: 0.7310 (mmtp) REVERT: A 450 PHE cc_start: 0.7053 (m-10) cc_final: 0.6247 (t80) REVERT: A 683 ASN cc_start: 0.7594 (m110) cc_final: 0.7125 (m-40) REVERT: A 722 LYS cc_start: 0.8392 (tttt) cc_final: 0.8138 (tttm) REVERT: A 738 LYS cc_start: 0.8318 (ttmm) cc_final: 0.8004 (mtpp) REVERT: B 283 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7065 (mt-10) REVERT: B 311 LYS cc_start: 0.7737 (ttpp) cc_final: 0.7454 (mtmm) REVERT: B 450 PHE cc_start: 0.7404 (m-10) cc_final: 0.6843 (t80) REVERT: B 479 MET cc_start: 0.4872 (mtt) cc_final: 0.4639 (mtm) REVERT: C 311 LYS cc_start: 0.7661 (mtpp) cc_final: 0.7087 (mtmm) REVERT: C 337 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7498 (mtt-85) REVERT: C 434 LYS cc_start: 0.7760 (mtpm) cc_final: 0.7340 (mmtp) REVERT: C 450 PHE cc_start: 0.7134 (m-10) cc_final: 0.6398 (t80) REVERT: C 469 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.4782 (mp) REVERT: C 496 CYS cc_start: 0.7752 (t) cc_final: 0.7446 (t) REVERT: C 683 ASN cc_start: 0.7650 (m110) cc_final: 0.7185 (m-40) REVERT: C 738 LYS cc_start: 0.8244 (ttmm) cc_final: 0.7969 (mtpp) REVERT: D 311 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7046 (mtmm) REVERT: D 337 ARG cc_start: 0.7897 (mtp-110) cc_final: 0.7506 (mtt-85) REVERT: D 434 LYS cc_start: 0.7753 (mtpm) cc_final: 0.7326 (mmtp) REVERT: D 450 PHE cc_start: 0.7158 (m-10) cc_final: 0.6390 (t80) REVERT: D 683 ASN cc_start: 0.7628 (m110) cc_final: 0.7191 (m-40) REVERT: D 738 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7979 (mtpp) outliers start: 18 outliers final: 15 residues processed: 251 average time/residue: 0.3660 time to fit residues: 139.5371 Evaluate side-chains 247 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 231 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 29 optimal weight: 0.0070 chunk 56 optimal weight: 2.9990 chunk 203 optimal weight: 0.0870 chunk 85 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.166432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.118012 restraints weight = 24298.395| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.97 r_work: 0.3051 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23144 Z= 0.103 Angle : 0.470 11.936 30968 Z= 0.229 Chirality : 0.037 0.137 3328 Planarity : 0.002 0.027 3712 Dihedral : 16.247 89.940 4336 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.88 % Allowed : 12.74 % Favored : 86.38 % 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: 0.40 (0.17), residues: 2552 helix: 1.35 (0.14), residues: 1560 sheet: -0.06 (0.57), residues: 76 loop : -1.65 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 710 HIS 0.002 0.000 HIS B 301 PHE 0.016 0.001 PHE D 316 TYR 0.007 0.001 TYR D 575 ARG 0.004 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4687.25 seconds wall clock time: 88 minutes 42.80 seconds (5322.80 seconds total)