Starting phenix.real_space_refine on Fri Sep 19 03:24:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mik_23854/09_2025/7mik_23854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mik_23854/09_2025/7mik_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/cci-nas-00/data/ceres_data/7mik_23854/09_2025/7mik_23854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mik_23854/09_2025/7mik_23854.map" model { file = "/net/cci-nas-00/data/ceres_data/7mik_23854/09_2025/7mik_23854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mik_23854/09_2025/7mik_23854.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.66, per 1000 atoms: 0.25 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: 2.04 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.75 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: 3.79 Time building geometry restraints manager: 2.70 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 908) selection = (chain 'B' and resid 118 through 908) selection = (chain 'C' and resid 118 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.560 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- 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 23148 Z= 0.491 Angle : 1.473 13.491 30976 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.20 (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 ARG 0.007 0.001 ARG B 363 TYR 0.017 0.003 TYR B 461 PHE 0.028 0.003 PHE C 526 TRP 0.014 0.002 TRP D 710 HIS 0.010 0.002 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.01034 (23144) covalent geometry : angle 1.47300 (30968) SS BOND : bond 0.00839 ( 4) SS BOND : angle 0.79124 ( 8) hydrogen bonds : bond 0.37697 ( 868) hydrogen bonds : angle 9.56362 ( 2592) *********************** 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 to be fit. rotamer outliers: 12 poor density : 471 time to evaluate : 0.960 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: 0.1883 time to fit residues: 135.6566 Evaluate side-chains 319 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 314 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.166206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.117206 restraints weight = 24424.831| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.03 r_work: 0.3020 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23148 Z= 0.116 Angle : 0.555 5.787 30976 Z= 0.286 Chirality : 0.039 0.159 3328 Planarity : 0.004 0.036 3712 Dihedral : 22.017 173.452 4346 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.09 % Allowed : 7.40 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.02 (0.13), residues: 2552 helix: -2.72 (0.10), residues: 1556 sheet: -1.08 (0.54), residues: 76 loop : -2.38 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 363 TYR 0.014 0.001 TYR C 575 PHE 0.015 0.001 PHE A 193 TRP 0.010 0.001 TRP C 559 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00251 (23144) covalent geometry : angle 0.55550 (30968) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.34109 ( 8) hydrogen bonds : bond 0.05799 ( 868) hydrogen bonds : angle 4.21353 ( 2592) *********************** 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 to be fit. rotamer outliers: 25 poor density : 331 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7504 (tt0) REVERT: A 257 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7330 (mt-10) REVERT: A 337 ARG cc_start: 0.8406 (mtp-110) cc_final: 0.7879 (mtt-85) REVERT: A 434 LYS cc_start: 0.8142 (mtpm) cc_final: 0.7792 (mmtp) REVERT: A 647 ASN cc_start: 0.8196 (t0) cc_final: 0.7974 (t0) REVERT: A 683 ASN cc_start: 0.7908 (m110) cc_final: 0.7514 (m-40) REVERT: A 712 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7832 (mtm-85) REVERT: B 160 HIS cc_start: 0.6223 (t-90) cc_final: 0.5577 (m170) REVERT: B 257 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7320 (mt-10) REVERT: B 283 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6995 (mt-10) REVERT: B 311 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7955 (mtpp) REVERT: C 160 HIS cc_start: 0.6270 (t-90) cc_final: 0.5617 (m170) REVERT: C 161 LYS cc_start: 0.7502 (mmtt) cc_final: 0.7114 (mmmt) REVERT: C 257 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7393 (mt-10) REVERT: C 337 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.7828 (mtt-85) REVERT: C 434 LYS cc_start: 0.8116 (mtpm) cc_final: 0.7779 (mmtp) REVERT: C 496 CYS cc_start: 0.8286 (t) cc_final: 0.7933 (t) REVERT: C 683 ASN cc_start: 0.8008 (m110) cc_final: 0.7600 (m-40) REVERT: D 211 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7507 (tt0) REVERT: D 257 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7359 (mt-10) REVERT: D 337 ARG cc_start: 0.8428 (mtp-110) cc_final: 0.7894 (mtt-85) REVERT: D 434 LYS cc_start: 0.8144 (mtpm) cc_final: 0.7784 (mmtp) REVERT: D 647 ASN cc_start: 0.8224 (t0) cc_final: 0.8016 (t0) REVERT: D 683 ASN cc_start: 0.7929 (m110) cc_final: 0.7559 (m-40) REVERT: D 712 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7881 (mtm-85) outliers start: 25 outliers final: 5 residues processed: 355 average time/residue: 0.1897 time to fit residues: 100.1431 Evaluate side-chains 289 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 284 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 398 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 241 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 114 optimal weight: 0.1980 chunk 233 optimal weight: 0.0470 chunk 106 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- 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 646 GLN C 471 HIS C 646 GLN C 647 ASN D 160 HIS D 646 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.157167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.110656 restraints weight = 24513.335| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.14 r_work: 0.2936 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23148 Z= 0.125 Angle : 0.545 8.804 30976 Z= 0.273 Chirality : 0.040 0.145 3328 Planarity : 0.003 0.029 3712 Dihedral : 20.103 109.515 4336 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.62 % Allowed : 8.58 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.15), residues: 2552 helix: -1.11 (0.12), residues: 1552 sheet: -0.74 (0.55), residues: 76 loop : -2.18 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 567 TYR 0.013 0.002 TYR A 575 PHE 0.015 0.001 PHE C 316 TRP 0.008 0.001 TRP C 692 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00293 (23144) covalent geometry : angle 0.54487 (30968) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.27821 ( 8) hydrogen bonds : bond 0.05419 ( 868) hydrogen bonds : angle 3.83562 ( 2592) *********************** 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 328 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 0.890 Fit side-chains REVERT: A 257 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7393 (mt-10) REVERT: A 337 ARG cc_start: 0.8608 (mtp-110) cc_final: 0.7936 (mtt-85) REVERT: A 434 LYS cc_start: 0.8395 (mtpm) cc_final: 0.7995 (mmtp) REVERT: A 683 ASN cc_start: 0.8176 (m110) cc_final: 0.7679 (m-40) REVERT: A 738 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8593 (mtpp) REVERT: B 257 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7403 (mt-10) REVERT: B 311 LYS cc_start: 0.8314 (ttpp) cc_final: 0.7940 (mtpp) REVERT: C 161 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7311 (mmmt) REVERT: C 214 GLU cc_start: 0.8273 (tt0) cc_final: 0.7407 (pt0) REVERT: C 257 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7396 (mt-10) REVERT: C 337 ARG cc_start: 0.8634 (mtp-110) cc_final: 0.7958 (mtt-85) REVERT: C 434 LYS cc_start: 0.8364 (mtpm) cc_final: 0.7975 (mmtp) REVERT: C 496 CYS cc_start: 0.8338 (t) cc_final: 0.7989 (t) REVERT: C 610 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7100 (mt-10) REVERT: C 647 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7410 (t0) REVERT: C 683 ASN cc_start: 0.8161 (m110) cc_final: 0.7642 (m-40) REVERT: C 738 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8622 (mtpp) REVERT: D 257 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7395 (mt-10) REVERT: D 337 ARG cc_start: 0.8591 (mtp-110) cc_final: 0.7940 (mtt-85) REVERT: D 434 LYS cc_start: 0.8364 (mtpm) cc_final: 0.7952 (mmtp) REVERT: D 683 ASN cc_start: 0.8169 (m110) cc_final: 0.7672 (m-40) REVERT: D 738 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8608 (mtpp) outliers start: 37 outliers final: 14 residues processed: 323 average time/residue: 0.1917 time to fit residues: 93.2358 Evaluate side-chains 276 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 261 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 398 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 C residue 647 ASN Chi-restraints excluded: chain D residue 166 ASP 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 495 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 109 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 195 optimal weight: 7.9990 chunk 219 optimal weight: 0.1980 chunk 242 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 646 GLN C 646 GLN C 647 ASN D 646 GLN D 647 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.157592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.112224 restraints weight = 24661.288| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.17 r_work: 0.2924 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23148 Z= 0.112 Angle : 0.530 12.809 30976 Z= 0.260 Chirality : 0.039 0.143 3328 Planarity : 0.003 0.026 3712 Dihedral : 18.950 93.162 4336 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.49 % Allowed : 9.46 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.16), residues: 2552 helix: -0.35 (0.13), residues: 1556 sheet: -0.46 (0.57), residues: 76 loop : -1.99 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.011 0.001 TYR C 575 PHE 0.015 0.001 PHE D 316 TRP 0.007 0.001 TRP C 692 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00260 (23144) covalent geometry : angle 0.52991 (30968) SS BOND : bond 0.00107 ( 4) SS BOND : angle 0.30668 ( 8) hydrogen bonds : bond 0.04665 ( 868) hydrogen bonds : angle 3.65170 ( 2592) *********************** 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 320 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 0.848 Fit side-chains REVERT: A 141 ASP cc_start: 0.6035 (t70) cc_final: 0.5819 (t70) REVERT: A 214 GLU cc_start: 0.8263 (tt0) cc_final: 0.7422 (pt0) REVERT: A 257 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7299 (mt-10) REVERT: A 286 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7746 (mp10) REVERT: A 337 ARG cc_start: 0.8608 (mtp-110) cc_final: 0.7975 (mtt-85) REVERT: A 434 LYS cc_start: 0.8382 (mtpm) cc_final: 0.7959 (mmtp) REVERT: A 683 ASN cc_start: 0.8122 (m110) cc_final: 0.7630 (m-40) REVERT: A 738 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8539 (mtpp) REVERT: B 214 GLU cc_start: 0.8269 (tt0) cc_final: 0.7436 (pt0) REVERT: B 257 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7317 (mt-10) REVERT: B 311 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7911 (mtpp) REVERT: C 161 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7462 (mmmt) REVERT: C 214 GLU cc_start: 0.8292 (tt0) cc_final: 0.7378 (pt0) REVERT: C 257 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7342 (mt-10) REVERT: C 337 ARG cc_start: 0.8591 (mtp-110) cc_final: 0.7925 (mtt-85) REVERT: C 434 LYS cc_start: 0.8380 (mtpm) cc_final: 0.7964 (mmtp) REVERT: C 496 CYS cc_start: 0.8157 (t) cc_final: 0.7775 (t) REVERT: C 683 ASN cc_start: 0.8063 (m110) cc_final: 0.7560 (m-40) REVERT: C 738 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8546 (mtpp) REVERT: D 141 ASP cc_start: 0.6074 (t70) cc_final: 0.5855 (t70) REVERT: D 214 GLU cc_start: 0.8253 (tt0) cc_final: 0.7350 (pt0) REVERT: D 257 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7325 (mt-10) REVERT: D 337 ARG cc_start: 0.8560 (mtp-110) cc_final: 0.7914 (mtt-85) REVERT: D 434 LYS cc_start: 0.8388 (mtpm) cc_final: 0.7970 (mmtp) REVERT: D 469 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5133 (mt) REVERT: D 683 ASN cc_start: 0.8080 (m110) cc_final: 0.7594 (m-40) REVERT: D 738 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8542 (mtpp) outliers start: 34 outliers final: 16 residues processed: 313 average time/residue: 0.1905 time to fit residues: 90.1145 Evaluate side-chains 281 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 264 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 603 VAL 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 495 THR 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 469 LEU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 97 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.152096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.107499 restraints weight = 24475.444| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.95 r_work: 0.2872 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 23148 Z= 0.227 Angle : 0.682 10.680 30976 Z= 0.333 Chirality : 0.045 0.175 3328 Planarity : 0.004 0.031 3712 Dihedral : 19.927 112.737 4336 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.01 % Allowed : 10.46 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.16), residues: 2552 helix: -0.44 (0.13), residues: 1548 sheet: -0.45 (0.56), residues: 84 loop : -2.10 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.017 0.002 TYR C 451 PHE 0.021 0.002 PHE C 526 TRP 0.009 0.002 TRP C 692 HIS 0.008 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00568 (23144) covalent geometry : angle 0.68213 (30968) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.24765 ( 8) hydrogen bonds : bond 0.06749 ( 868) hydrogen bonds : angle 4.04885 ( 2592) *********************** 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 314 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 0.900 Fit side-chains REVERT: A 257 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7437 (mt-10) REVERT: A 337 ARG cc_start: 0.8577 (mtp-110) cc_final: 0.7932 (mtt-85) REVERT: A 434 LYS cc_start: 0.8488 (mtpm) cc_final: 0.7983 (mmtt) REVERT: A 469 LEU cc_start: 0.5273 (OUTLIER) cc_final: 0.4566 (mt) REVERT: A 683 ASN cc_start: 0.8112 (m110) cc_final: 0.7585 (m-40) REVERT: A 738 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8523 (mtpp) REVERT: B 257 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7445 (mt-10) REVERT: C 161 LYS cc_start: 0.7864 (mmtt) cc_final: 0.7594 (mmmt) REVERT: C 257 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7465 (mt-10) REVERT: C 337 ARG cc_start: 0.8544 (mtp-110) cc_final: 0.7932 (mtt-85) REVERT: C 434 LYS cc_start: 0.8476 (mtpm) cc_final: 0.7963 (mmtt) REVERT: C 683 ASN cc_start: 0.8111 (m110) cc_final: 0.7604 (m-40) REVERT: C 738 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8534 (mtpp) REVERT: D 257 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7423 (mt-10) REVERT: D 337 ARG cc_start: 0.8543 (mtp-110) cc_final: 0.7931 (mtt-85) REVERT: D 434 LYS cc_start: 0.8480 (mtpm) cc_final: 0.7977 (mmtt) REVERT: D 469 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5392 (mt) REVERT: D 683 ASN cc_start: 0.8112 (m110) cc_final: 0.7581 (m-40) REVERT: D 738 LYS cc_start: 0.8828 (ttmm) cc_final: 0.8539 (mtpp) outliers start: 46 outliers final: 34 residues processed: 298 average time/residue: 0.1821 time to fit residues: 82.8618 Evaluate side-chains 286 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL 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 469 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 MET 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 525 VAL Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 127 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 495 THR Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 235 ILE 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 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 79 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 167 optimal weight: 0.0570 chunk 164 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 99 optimal weight: 0.0870 chunk 127 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 D 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.159581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.113728 restraints weight = 24487.109| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.11 r_work: 0.2988 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23148 Z= 0.086 Angle : 0.478 7.879 30976 Z= 0.239 Chirality : 0.038 0.160 3328 Planarity : 0.003 0.026 3712 Dihedral : 18.035 87.000 4336 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.23 % Allowed : 11.08 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.16), residues: 2552 helix: 0.30 (0.13), residues: 1552 sheet: -0.08 (0.59), residues: 76 loop : -1.94 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.009 0.001 TYR B 575 PHE 0.015 0.001 PHE D 316 TRP 0.008 0.001 TRP C 710 HIS 0.002 0.000 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00183 (23144) covalent geometry : angle 0.47847 (30968) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.23529 ( 8) hydrogen bonds : bond 0.03613 ( 868) hydrogen bonds : angle 3.51877 ( 2592) *********************** 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 to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 0.864 Fit side-chains REVERT: A 337 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.7981 (mtt-85) REVERT: A 434 LYS cc_start: 0.8326 (mtpm) cc_final: 0.7880 (mmtp) REVERT: A 683 ASN cc_start: 0.8030 (m110) cc_final: 0.7509 (m-40) REVERT: A 738 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8421 (mtpp) REVERT: B 311 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7937 (mtpp) REVERT: C 161 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7589 (mmmt) REVERT: C 337 ARG cc_start: 0.8537 (mtp-110) cc_final: 0.7890 (mtt-85) REVERT: C 434 LYS cc_start: 0.8321 (mtpm) cc_final: 0.7881 (mmtp) REVERT: C 496 CYS cc_start: 0.8159 (t) cc_final: 0.7855 (t) REVERT: C 683 ASN cc_start: 0.8009 (m110) cc_final: 0.7487 (m-40) REVERT: C 738 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8327 (mtpp) REVERT: C 741 GLU cc_start: 0.7692 (mp0) cc_final: 0.7352 (mp0) REVERT: D 337 ARG cc_start: 0.8535 (mtp-110) cc_final: 0.7900 (mtt-85) REVERT: D 434 LYS cc_start: 0.8336 (mtpm) cc_final: 0.7887 (mmtp) REVERT: D 469 LEU cc_start: 0.5666 (OUTLIER) cc_final: 0.5293 (mt) REVERT: D 683 ASN cc_start: 0.8012 (m110) cc_final: 0.7484 (m-40) REVERT: D 738 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8440 (mtpp) outliers start: 28 outliers final: 10 residues processed: 292 average time/residue: 0.1774 time to fit residues: 80.0625 Evaluate side-chains 259 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 248 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 469 LEU 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 9 optimal weight: 0.4980 chunk 72 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 254 optimal weight: 0.9990 chunk 225 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 214 optimal weight: 0.0670 chunk 87 optimal weight: 6.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.160485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.113688 restraints weight = 24377.399| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.39 r_work: 0.3004 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 0.025 23148 Z= 0.083 Angle : 0.477 10.496 30976 Z= 0.235 Chirality : 0.038 0.147 3328 Planarity : 0.003 0.025 3712 Dihedral : 17.451 87.987 4336 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.48 % Allowed : 12.04 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.17), residues: 2552 helix: 0.72 (0.14), residues: 1564 sheet: -0.04 (0.57), residues: 76 loop : -1.72 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.008 0.001 TYR A 575 PHE 0.016 0.001 PHE D 316 TRP 0.007 0.001 TRP C 710 HIS 0.002 0.000 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00175 (23144) covalent geometry : angle 0.47734 (30968) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.25402 ( 8) hydrogen bonds : bond 0.03558 ( 868) hydrogen bonds : angle 3.41498 ( 2592) *********************** 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 264 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 253 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.8414 (mtp-110) cc_final: 0.7937 (mtt-85) REVERT: A 434 LYS cc_start: 0.8165 (mtpm) cc_final: 0.7832 (mmtp) REVERT: A 450 PHE cc_start: 0.7667 (m-10) cc_final: 0.6910 (t80) REVERT: A 469 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4805 (mt) REVERT: A 683 ASN cc_start: 0.7928 (m110) cc_final: 0.7467 (m-40) REVERT: A 738 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8315 (mtpp) REVERT: B 311 LYS cc_start: 0.8165 (ttpp) cc_final: 0.7634 (mtmm) REVERT: B 450 PHE cc_start: 0.7669 (m-10) cc_final: 0.6910 (t80) REVERT: C 161 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7448 (mmmt) REVERT: C 337 ARG cc_start: 0.8355 (mtp-110) cc_final: 0.7866 (mtt-85) REVERT: C 434 LYS cc_start: 0.8195 (mtpm) cc_final: 0.7848 (mmtp) REVERT: C 496 CYS cc_start: 0.8205 (t) cc_final: 0.7905 (t) REVERT: C 683 ASN cc_start: 0.7900 (m110) cc_final: 0.7446 (m-40) REVERT: C 738 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8254 (mtpp) REVERT: C 741 GLU cc_start: 0.7373 (mp0) cc_final: 0.7118 (mp0) REVERT: D 337 ARG cc_start: 0.8338 (mtp-110) cc_final: 0.7871 (mtt-85) REVERT: D 434 LYS cc_start: 0.8171 (mtpm) cc_final: 0.7836 (mmtp) REVERT: D 450 PHE cc_start: 0.7661 (m-10) cc_final: 0.6907 (t80) REVERT: D 469 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.5251 (mp) REVERT: D 683 ASN cc_start: 0.7910 (m110) cc_final: 0.7459 (m-40) REVERT: D 738 LYS cc_start: 0.8557 (ttmm) cc_final: 0.8321 (mtpp) outliers start: 11 outliers final: 7 residues processed: 262 average time/residue: 0.1823 time to fit residues: 73.4961 Evaluate side-chains 254 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 245 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 603 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 159 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 252 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 208 optimal weight: 0.2980 chunk 2 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.154472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.105135 restraints weight = 24372.665| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.98 r_work: 0.2918 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23148 Z= 0.164 Angle : 0.593 12.120 30976 Z= 0.290 Chirality : 0.042 0.153 3328 Planarity : 0.003 0.030 3712 Dihedral : 18.200 96.537 4336 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.96 % Allowed : 11.91 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.16), residues: 2552 helix: 0.49 (0.13), residues: 1548 sheet: -0.26 (0.57), residues: 76 loop : -1.82 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.015 0.002 TYR B 451 PHE 0.017 0.002 PHE D 316 TRP 0.007 0.001 TRP D 710 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00404 (23144) covalent geometry : angle 0.59321 (30968) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.30430 ( 8) hydrogen bonds : bond 0.05556 ( 868) hydrogen bonds : angle 3.74524 ( 2592) *********************** 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 269 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.902 Fit side-chains REVERT: A 337 ARG cc_start: 0.8421 (mtp-110) cc_final: 0.7993 (mtt-85) REVERT: A 434 LYS cc_start: 0.8275 (mtpm) cc_final: 0.7862 (mmtt) REVERT: A 469 LEU cc_start: 0.5311 (OUTLIER) cc_final: 0.5099 (mt) REVERT: A 683 ASN cc_start: 0.8089 (m110) cc_final: 0.7678 (m-40) REVERT: A 738 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8423 (mtpp) REVERT: B 311 LYS cc_start: 0.8373 (ttpp) cc_final: 0.8029 (mtpp) REVERT: C 337 ARG cc_start: 0.8393 (mtp-110) cc_final: 0.7933 (mtt-85) REVERT: C 434 LYS cc_start: 0.8293 (mtpm) cc_final: 0.7874 (mmtt) REVERT: C 469 LEU cc_start: 0.5310 (OUTLIER) cc_final: 0.4688 (mt) REVERT: C 683 ASN cc_start: 0.8105 (m110) cc_final: 0.7688 (m-40) REVERT: C 738 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8298 (mtpp) REVERT: C 741 GLU cc_start: 0.7481 (mp0) cc_final: 0.7246 (mp0) REVERT: D 337 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.7931 (mtt-85) REVERT: D 434 LYS cc_start: 0.8274 (mtpm) cc_final: 0.7865 (mmtt) REVERT: D 469 LEU cc_start: 0.5633 (OUTLIER) cc_final: 0.5338 (mp) REVERT: D 683 ASN cc_start: 0.8081 (m110) cc_final: 0.7667 (m-40) REVERT: D 738 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8435 (mtpp) outliers start: 22 outliers final: 14 residues processed: 266 average time/residue: 0.1860 time to fit residues: 75.7559 Evaluate side-chains 259 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 603 VAL 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 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 469 LEU Chi-restraints excluded: chain C residue 603 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 18 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 D 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.159224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.110400 restraints weight = 24468.462| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.99 r_work: 0.2992 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23148 Z= 0.092 Angle : 0.499 13.419 30976 Z= 0.245 Chirality : 0.039 0.141 3328 Planarity : 0.003 0.028 3712 Dihedral : 17.429 89.632 4336 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.57 % Allowed : 12.13 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.17), residues: 2552 helix: 0.78 (0.14), residues: 1560 sheet: -0.10 (0.57), residues: 76 loop : -1.76 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.009 0.001 TYR B 575 PHE 0.016 0.001 PHE D 316 TRP 0.007 0.001 TRP D 710 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00206 (23144) covalent geometry : angle 0.49932 (30968) SS BOND : bond 0.00111 ( 4) SS BOND : angle 0.23621 ( 8) hydrogen bonds : bond 0.03913 ( 868) hydrogen bonds : angle 3.50335 ( 2592) *********************** 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 255 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.8429 (mtp-110) cc_final: 0.7949 (mtt-85) REVERT: A 434 LYS cc_start: 0.8177 (mtpm) cc_final: 0.7792 (mmtp) REVERT: A 683 ASN cc_start: 0.7998 (m110) cc_final: 0.7525 (m-40) REVERT: A 738 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8380 (mtpp) REVERT: B 311 LYS cc_start: 0.8250 (ttpp) cc_final: 0.7922 (mtpp) REVERT: C 337 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.7873 (mtt-85) REVERT: C 434 LYS cc_start: 0.8207 (mtpm) cc_final: 0.7816 (mmtp) REVERT: C 469 LEU cc_start: 0.5085 (OUTLIER) cc_final: 0.4834 (mt) REVERT: C 496 CYS cc_start: 0.8158 (t) cc_final: 0.7866 (t) REVERT: C 683 ASN cc_start: 0.7963 (m110) cc_final: 0.7494 (m-40) REVERT: C 738 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8232 (mtpp) REVERT: C 741 GLU cc_start: 0.7414 (mp0) cc_final: 0.7166 (mp0) REVERT: D 337 ARG cc_start: 0.8358 (mtp-110) cc_final: 0.7875 (mtt-85) REVERT: D 434 LYS cc_start: 0.8188 (mtpm) cc_final: 0.7803 (mmtp) REVERT: D 469 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.5165 (mp) REVERT: D 683 ASN cc_start: 0.7988 (m110) cc_final: 0.7510 (m-40) REVERT: D 738 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8312 (mtpp) outliers start: 13 outliers final: 10 residues processed: 253 average time/residue: 0.1840 time to fit residues: 71.5442 Evaluate side-chains 252 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 127 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 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 398 THR Chi-restraints excluded: chain D residue 469 LEU 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 82 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 123 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.156684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.107386 restraints weight = 24430.571| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.99 r_work: 0.2950 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23148 Z= 0.118 Angle : 0.535 13.167 30976 Z= 0.262 Chirality : 0.040 0.197 3328 Planarity : 0.003 0.030 3712 Dihedral : 17.524 89.943 4336 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.57 % Allowed : 12.26 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.17), residues: 2552 helix: 0.77 (0.14), residues: 1560 sheet: -0.11 (0.57), residues: 76 loop : -1.77 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.012 0.001 TYR B 451 PHE 0.017 0.001 PHE D 316 TRP 0.007 0.001 TRP C 710 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00281 (23144) covalent geometry : angle 0.53526 (30968) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.25373 ( 8) hydrogen bonds : bond 0.04624 ( 868) hydrogen bonds : angle 3.58669 ( 2592) ********************** 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 255 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.8419 (mtp-110) cc_final: 0.7955 (mtt-85) REVERT: A 434 LYS cc_start: 0.8238 (mtpm) cc_final: 0.7839 (mmtp) REVERT: A 683 ASN cc_start: 0.8035 (m110) cc_final: 0.7581 (m-40) REVERT: A 738 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8395 (mtpp) REVERT: B 311 LYS cc_start: 0.8272 (ttpp) cc_final: 0.7947 (mtpp) REVERT: C 337 ARG cc_start: 0.8379 (mtp-110) cc_final: 0.7890 (mtt-85) REVERT: C 434 LYS cc_start: 0.8228 (mtpm) cc_final: 0.7841 (mmtp) REVERT: C 496 CYS cc_start: 0.8158 (t) cc_final: 0.7891 (t) REVERT: C 683 ASN cc_start: 0.8038 (m110) cc_final: 0.7587 (m-40) REVERT: C 738 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8240 (mtpp) REVERT: C 741 GLU cc_start: 0.7503 (mp0) cc_final: 0.7247 (mp0) REVERT: D 337 ARG cc_start: 0.8376 (mtp-110) cc_final: 0.7892 (mtt-85) REVERT: D 434 LYS cc_start: 0.8240 (mtpm) cc_final: 0.7843 (mmtp) REVERT: D 469 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.5137 (mp) REVERT: D 683 ASN cc_start: 0.8029 (m110) cc_final: 0.7574 (m-40) REVERT: D 738 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8363 (mtpp) outliers start: 13 outliers final: 11 residues processed: 253 average time/residue: 0.1697 time to fit residues: 66.2763 Evaluate side-chains 250 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 238 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 127 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 C residue 127 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 603 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 66 optimal weight: 8.9990 chunk 209 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 217 optimal weight: 0.1980 chunk 212 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.158984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.112996 restraints weight = 24346.793| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.12 r_work: 0.2946 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23148 Z= 0.099 Angle : 0.511 13.903 30976 Z= 0.248 Chirality : 0.039 0.148 3328 Planarity : 0.003 0.029 3712 Dihedral : 17.113 88.202 4336 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.61 % Allowed : 12.08 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.17), residues: 2552 helix: 0.91 (0.14), residues: 1560 sheet: -0.10 (0.57), residues: 76 loop : -1.72 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.009 0.001 TYR A 575 PHE 0.017 0.001 PHE D 316 TRP 0.007 0.001 TRP A 710 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00228 (23144) covalent geometry : angle 0.51090 (30968) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.24606 ( 8) hydrogen bonds : bond 0.04074 ( 868) hydrogen bonds : angle 3.50354 ( 2592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6281.19 seconds wall clock time: 108 minutes 6.06 seconds (6486.06 seconds total)