Starting phenix.real_space_refine on Tue Mar 19 01:12:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/03_2024/7mik_23854_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/03_2024/7mik_23854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/03_2024/7mik_23854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/03_2024/7mik_23854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/03_2024/7mik_23854_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mik_23854/03_2024/7mik_23854_updated.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 124 5.16 5 Na 4 4.78 5 C 15064 2.51 5 N 3476 2.21 5 O 4024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 149": "NH1" <-> "NH2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 757": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 757": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 757": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 757": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22728 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "B" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "C" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "D" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "A" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 524 Unusual residues: {' NA': 4, 'POV': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 11.19, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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: 8.29 Conformation dependent library (CDL) restraints added in 3.8 seconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 4 sheets defined 54.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.535A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 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) Processing helix chain 'A' and resid 154 through 157 No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.558A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 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) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 230 through 237 removed outlier: 3.515A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 299 through 305 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 316 through 328 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 344 through 351 removed outlier: 3.676A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.574A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.520A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.556A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 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 437 through 460 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 485 through 506 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 513 through 519 Processing helix chain 'A' and resid 521 through 542 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 548 through 559 removed outlier: 3.632A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 568 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 564 through 568' Processing helix chain 'A' and resid 570 through 573 No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 575 through 585 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 587 through 608 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) removed outlier: 3.830A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 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 651 through 665 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 669 through 686 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) removed outlier: 4.618A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 704 removed outlier: 3.774A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 712 No H-bonds generated for 'chain 'A' and resid 709 through 712' Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.534A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 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) Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.559A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 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) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 230 through 237 removed outlier: 3.515A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 299 through 305 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 316 through 328 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 344 through 351 removed outlier: 3.676A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 removed outlier: 3.574A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.520A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.555A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 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 437 through 460 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 485 through 506 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 513 through 519 Processing helix chain 'B' and resid 521 through 542 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 548 through 559 removed outlier: 3.631A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 568 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 564 through 568' Processing helix chain 'B' and resid 570 through 573 No H-bonds generated for 'chain 'B' and resid 570 through 573' Processing helix chain 'B' and resid 575 through 585 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 587 through 608 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) removed outlier: 3.830A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 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 651 through 665 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 669 through 686 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) removed outlier: 4.618A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 704 removed outlier: 3.774A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 712 No H-bonds generated for 'chain 'B' and resid 709 through 712' Processing helix chain 'C' and resid 120 through 129 removed outlier: 3.534A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 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) Processing helix chain 'C' and resid 154 through 157 No H-bonds generated for 'chain 'C' and resid 154 through 157' Processing helix chain 'C' and resid 171 through 177 removed outlier: 3.559A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 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) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 230 through 237 removed outlier: 3.516A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 275 through 282 Processing helix chain 'C' and resid 299 through 305 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 316 through 328 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 344 through 351 removed outlier: 3.676A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 3.574A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.520A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.555A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 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 437 through 460 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 485 through 506 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 513 through 519 Processing helix chain 'C' and resid 521 through 542 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 548 through 559 removed outlier: 3.631A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 568 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 564 through 568' Processing helix chain 'C' and resid 570 through 573 No H-bonds generated for 'chain 'C' and resid 570 through 573' Processing helix chain 'C' and resid 575 through 585 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 587 through 608 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) removed outlier: 3.829A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 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 651 through 665 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 669 through 686 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) removed outlier: 4.618A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 704 removed outlier: 3.774A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 712 No H-bonds generated for 'chain 'C' and resid 709 through 712' Processing helix chain 'D' and resid 120 through 129 removed outlier: 3.535A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 147 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) Processing helix chain 'D' and resid 154 through 157 No H-bonds generated for 'chain 'D' and resid 154 through 157' Processing helix chain 'D' and resid 171 through 177 removed outlier: 3.558A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 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) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 230 through 237 removed outlier: 3.516A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 275 through 282 Processing helix chain 'D' and resid 299 through 305 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 316 through 328 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 344 through 351 removed outlier: 3.675A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 removed outlier: 3.575A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.520A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.555A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 435 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 437 through 460 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 485 through 506 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 513 through 519 Processing helix chain 'D' and resid 521 through 542 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 548 through 559 removed outlier: 3.631A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 568 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 564 through 568' Processing helix chain 'D' and resid 570 through 573 No H-bonds generated for 'chain 'D' and resid 570 through 573' Processing helix chain 'D' and resid 575 through 585 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 587 through 608 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) removed outlier: 3.830A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 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 651 through 665 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 669 through 686 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) removed outlier: 4.619A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 704 removed outlier: 3.774A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 712 No H-bonds generated for 'chain 'D' and resid 709 through 712' Processing sheet with id= A, first strand: chain 'A' and resid 731 through 737 removed outlier: 6.652A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP A 391 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS A 376 " --> pdb=" O ASP A 391 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 731 through 737 removed outlier: 6.652A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP B 391 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS B 376 " --> pdb=" O ASP B 391 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 731 through 737 removed outlier: 6.652A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP C 391 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS C 376 " --> pdb=" O ASP C 391 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 731 through 737 removed outlier: 6.651A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP D 391 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS D 376 " --> pdb=" O ASP D 391 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 8.99 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: 99.07 - 106.07: 377 106.07 - 113.07: 12794 113.07 - 120.08: 8100 120.08 - 127.08: 9465 127.08 - 134.08: 232 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: 1002 2.72 - 3.26: 19733 3.26 - 3.81: 32336 3.81 - 4.35: 44823 4.35 - 4.90: 75182 Nonbonded interactions: 173076 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 2.440 nonbonded pdb=" OH TYR A 650 " pdb=" O LYS B 545 " model vdw 2.333 2.440 nonbonded pdb=" O LYS A 545 " pdb=" OH TYR D 650 " model vdw 2.344 2.440 nonbonded pdb=" OD1 ASN C 298 " pdb=" ND1 HIS C 301 " model vdw 2.355 2.520 ... (remaining 173071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 118 through 757 or resid 901 through 908)) selection = (chain 'B' and (resid 118 through 757 or resid 901 through 908)) selection = (chain 'C' and (resid 118 through 757 or resid 901 through 908)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.850 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 56.100 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.093 23144 Z= 0.604 Angle : 1.473 13.491 30968 Z= 0.651 Chirality : 0.052 0.324 3328 Planarity : 0.006 0.057 3712 Dihedral : 20.360 152.341 9384 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.53 % Allowed : 4.47 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.20 (0.10), residues: 2552 helix: -4.84 (0.04), residues: 1540 sheet: -1.74 (0.57), residues: 76 loop : -2.56 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 710 HIS 0.010 0.002 HIS D 301 PHE 0.028 0.003 PHE C 526 TYR 0.017 0.003 TYR B 461 ARG 0.007 0.001 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 471 time to evaluate : 2.388 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: 0.3692 time to fit residues: 264.0336 Evaluate side-chains 319 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 314 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 469 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 103 optimal weight: 0.0060 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 0.4980 chunk 149 optimal weight: 5.9990 chunk 232 optimal weight: 0.8980 overall best weight: 0.4954 ------------------------------------------------------------------------------- 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 A 735 ASN B 178 ASN B 251 ASN B 284 ASN B 314 ASN B 330 ASN B 471 HIS B 646 GLN B 647 ASN B 735 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 C 735 ASN D 178 ASN D 314 ASN D 471 HIS D 646 GLN D 647 ASN D 735 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 23144 Z= 0.114 Angle : 0.503 5.359 30968 Z= 0.257 Chirality : 0.037 0.169 3328 Planarity : 0.004 0.030 3712 Dihedral : 21.697 172.975 4346 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.44 % Allowed : 6.83 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.13), residues: 2552 helix: -2.97 (0.09), residues: 1500 sheet: -1.07 (0.59), residues: 76 loop : -2.23 (0.17), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 559 HIS 0.002 0.000 HIS C 301 PHE 0.016 0.001 PHE A 193 TYR 0.011 0.001 TYR C 575 ARG 0.003 0.000 ARG D 136 *********************** 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 378 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 345 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7185 (tt0) REVERT: A 257 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6726 (mt-10) REVERT: A 283 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6398 (mt-10) REVERT: A 337 ARG cc_start: 0.7923 (mtp-110) cc_final: 0.7455 (mtt-85) REVERT: A 434 LYS cc_start: 0.7588 (mtpm) cc_final: 0.7234 (mmtp) REVERT: A 647 ASN cc_start: 0.8140 (t0) cc_final: 0.7904 (t0) REVERT: A 683 ASN cc_start: 0.7513 (m110) cc_final: 0.7101 (m-40) REVERT: B 257 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6920 (mt-10) REVERT: B 283 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6733 (mt-10) REVERT: B 311 LYS cc_start: 0.8277 (ttpp) cc_final: 0.7902 (mtpp) REVERT: C 161 LYS cc_start: 0.7325 (mmtt) cc_final: 0.6918 (mmmt) REVERT: C 257 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6848 (mt-10) REVERT: C 311 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7437 (mtmm) REVERT: C 337 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7456 (mtt-85) REVERT: C 434 LYS cc_start: 0.7597 (mtpm) cc_final: 0.7315 (mmtp) REVERT: C 488 MET cc_start: 0.7539 (mtp) cc_final: 0.7298 (mtm) REVERT: C 683 ASN cc_start: 0.7583 (m110) cc_final: 0.7164 (m-40) REVERT: D 199 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6198 (mt) REVERT: D 211 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7244 (tt0) REVERT: D 257 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6769 (mt-10) REVERT: D 283 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6542 (mt-10) REVERT: D 337 ARG cc_start: 0.7925 (mtp-110) cc_final: 0.7508 (mtt-85) REVERT: D 434 LYS cc_start: 0.7627 (mtpm) cc_final: 0.7340 (mmtt) REVERT: D 647 ASN cc_start: 0.8176 (t0) cc_final: 0.7960 (t0) REVERT: D 683 ASN cc_start: 0.7528 (m110) cc_final: 0.7139 (m-40) outliers start: 33 outliers final: 12 residues processed: 371 average time/residue: 0.3811 time to fit residues: 212.0053 Evaluate side-chains 287 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 274 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 309 ASP 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 D residue 156 ASP Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 309 ASP 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 129 optimal weight: 5.9990 chunk 72 optimal weight: 0.0270 chunk 193 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 186 optimal weight: 0.5980 overall best weight: 1.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 646 GLN B 160 HIS C 160 HIS C 471 HIS C 646 GLN D 160 HIS D 646 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23144 Z= 0.207 Angle : 0.567 8.896 30968 Z= 0.277 Chirality : 0.040 0.141 3328 Planarity : 0.003 0.029 3712 Dihedral : 20.187 112.929 4336 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.71 % Allowed : 9.37 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.15), residues: 2552 helix: -1.51 (0.12), residues: 1520 sheet: -0.92 (0.57), residues: 84 loop : -2.05 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 692 HIS 0.013 0.001 HIS A 160 PHE 0.020 0.001 PHE C 316 TYR 0.014 0.002 TYR C 451 ARG 0.002 0.000 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 272 time to evaluate : 2.398 Fit side-chains REVERT: A 160 HIS cc_start: 0.5988 (t-90) cc_final: 0.5477 (m170) REVERT: A 257 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6815 (mt-10) REVERT: A 337 ARG cc_start: 0.7900 (mtp-110) cc_final: 0.7475 (mtt-85) REVERT: A 434 LYS cc_start: 0.7737 (mtpm) cc_final: 0.7317 (mmtp) REVERT: A 683 ASN cc_start: 0.7696 (m110) cc_final: 0.7172 (m-40) REVERT: A 738 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8184 (mtpp) REVERT: B 214 GLU cc_start: 0.7529 (tt0) cc_final: 0.7038 (pt0) REVERT: B 257 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6988 (mt-10) REVERT: B 283 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6965 (mt-10) REVERT: B 311 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7657 (mtmm) REVERT: C 161 LYS cc_start: 0.7342 (mmtt) cc_final: 0.6992 (mmmt) REVERT: C 214 GLU cc_start: 0.7450 (tt0) cc_final: 0.6666 (pt0) REVERT: C 257 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6929 (mt-10) REVERT: C 283 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7036 (mt-10) REVERT: C 315 ASP cc_start: 0.7406 (t0) cc_final: 0.7192 (t0) REVERT: C 337 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7526 (mtt-85) REVERT: C 434 LYS cc_start: 0.7755 (mtpm) cc_final: 0.7394 (mmtp) REVERT: C 488 MET cc_start: 0.7433 (mtp) cc_final: 0.7212 (mtm) REVERT: C 545 LYS cc_start: 0.7776 (mttm) cc_final: 0.7477 (mmtt) REVERT: C 683 ASN cc_start: 0.7718 (m110) cc_final: 0.7314 (m-40) REVERT: C 722 LYS cc_start: 0.8408 (tttt) cc_final: 0.8205 (tttm) REVERT: C 738 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8283 (mtpp) REVERT: D 160 HIS cc_start: 0.6022 (t-90) cc_final: 0.5596 (m170) REVERT: D 199 ILE cc_start: 0.6450 (OUTLIER) cc_final: 0.6058 (mt) REVERT: D 211 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7057 (mt-10) REVERT: D 214 GLU cc_start: 0.7340 (tt0) cc_final: 0.6563 (pt0) REVERT: D 257 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6822 (mt-10) REVERT: D 337 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7528 (mtt-85) REVERT: D 434 LYS cc_start: 0.7745 (mtpm) cc_final: 0.7373 (mmtp) REVERT: D 683 ASN cc_start: 0.7757 (m110) cc_final: 0.7265 (m-40) REVERT: D 722 LYS cc_start: 0.8428 (tttt) cc_final: 0.8184 (tttm) REVERT: D 738 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8238 (mtpp) outliers start: 39 outliers final: 18 residues processed: 299 average time/residue: 0.3649 time to fit residues: 164.7594 Evaluate side-chains 272 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 253 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP 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 B residue 166 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 199 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 247 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 221 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN B 646 GLN C 646 GLN D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 23144 Z= 0.109 Angle : 0.479 11.723 30968 Z= 0.230 Chirality : 0.037 0.156 3328 Planarity : 0.003 0.026 3712 Dihedral : 18.546 86.351 4336 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.92 % Allowed : 10.60 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2552 helix: -0.50 (0.13), residues: 1516 sheet: -0.89 (0.58), residues: 84 loop : -1.75 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 692 HIS 0.002 0.000 HIS A 301 PHE 0.014 0.001 PHE C 316 TYR 0.010 0.001 TYR A 650 ARG 0.004 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 255 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.5988 (t70) cc_final: 0.5771 (t70) REVERT: A 160 HIS cc_start: 0.6132 (t-90) cc_final: 0.5556 (m-70) REVERT: A 257 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6700 (mt-10) REVERT: A 283 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6693 (mt-10) REVERT: A 337 ARG cc_start: 0.7915 (mtp-110) cc_final: 0.7446 (mtt-85) REVERT: A 434 LYS cc_start: 0.7619 (mtpm) cc_final: 0.7245 (mmtt) REVERT: A 683 ASN cc_start: 0.7586 (m110) cc_final: 0.7052 (m-40) REVERT: A 722 LYS cc_start: 0.8404 (tttt) cc_final: 0.8142 (tttm) REVERT: A 738 LYS cc_start: 0.8487 (ttmm) cc_final: 0.7847 (mtpp) REVERT: B 257 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6876 (mt-10) REVERT: B 311 LYS cc_start: 0.8084 (ttpp) cc_final: 0.7653 (mtmm) REVERT: C 161 LYS cc_start: 0.7369 (mmtt) cc_final: 0.7050 (mmmt) REVERT: C 257 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6800 (mt-10) REVERT: C 283 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7014 (mt-10) REVERT: C 337 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.7520 (mtt-85) REVERT: C 434 LYS cc_start: 0.7650 (mtpm) cc_final: 0.7346 (mmtt) REVERT: C 683 ASN cc_start: 0.7580 (m110) cc_final: 0.7131 (m-40) REVERT: C 738 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8193 (mtpp) REVERT: D 141 ASP cc_start: 0.5922 (t70) cc_final: 0.5701 (t70) REVERT: D 160 HIS cc_start: 0.6217 (t-90) cc_final: 0.5687 (m-70) REVERT: D 199 ILE cc_start: 0.6459 (OUTLIER) cc_final: 0.6070 (mt) REVERT: D 257 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6730 (mt-10) REVERT: D 337 ARG cc_start: 0.7890 (mtp-110) cc_final: 0.7485 (mtt-85) REVERT: D 434 LYS cc_start: 0.7640 (mtpm) cc_final: 0.7319 (mmtt) REVERT: D 469 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5188 (mt) REVERT: D 488 MET cc_start: 0.7306 (mtm) cc_final: 0.6849 (mtp) REVERT: D 683 ASN cc_start: 0.7634 (m110) cc_final: 0.7141 (m-40) REVERT: D 722 LYS cc_start: 0.8419 (tttt) cc_final: 0.8209 (tttm) REVERT: D 738 LYS cc_start: 0.8521 (ttmm) cc_final: 0.7894 (mtpp) outliers start: 21 outliers final: 7 residues processed: 271 average time/residue: 0.3866 time to fit residues: 156.4814 Evaluate side-chains 263 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 254 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 525 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 3 optimal weight: 0.0470 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 222 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 overall best weight: 2.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN B 647 ASN C 647 ASN D 647 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23144 Z= 0.214 Angle : 0.542 10.440 30968 Z= 0.266 Chirality : 0.041 0.183 3328 Planarity : 0.003 0.026 3712 Dihedral : 18.777 96.625 4336 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.53 % Allowed : 10.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.16), residues: 2552 helix: -0.24 (0.13), residues: 1516 sheet: -0.87 (0.58), residues: 84 loop : -1.75 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 692 HIS 0.006 0.001 HIS D 301 PHE 0.018 0.001 PHE C 316 TYR 0.014 0.002 TYR C 451 ARG 0.004 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 257 time to evaluate : 2.199 Fit side-chains REVERT: A 257 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6705 (mt-10) REVERT: A 337 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7463 (mtt-85) REVERT: A 350 LYS cc_start: 0.8105 (tppt) cc_final: 0.7749 (tttt) REVERT: A 434 LYS cc_start: 0.7734 (mtpm) cc_final: 0.7274 (mmtp) REVERT: A 683 ASN cc_start: 0.7673 (m110) cc_final: 0.7134 (m-40) REVERT: A 722 LYS cc_start: 0.8417 (tttt) cc_final: 0.8192 (tttm) REVERT: A 738 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7945 (ttmt) REVERT: B 257 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6897 (mt-10) REVERT: B 311 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7710 (mtmm) REVERT: B 350 LYS cc_start: 0.8288 (tppt) cc_final: 0.7879 (tttt) REVERT: C 161 LYS cc_start: 0.7455 (mmtt) cc_final: 0.7089 (mmmt) REVERT: C 257 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6776 (mt-10) REVERT: C 315 ASP cc_start: 0.7527 (t0) cc_final: 0.7119 (t0) REVERT: C 337 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7537 (mtt-85) REVERT: C 350 LYS cc_start: 0.8176 (tppt) cc_final: 0.7785 (tttt) REVERT: C 434 LYS cc_start: 0.7779 (mtpm) cc_final: 0.7389 (mmtp) REVERT: C 496 CYS cc_start: 0.7789 (t) cc_final: 0.7528 (t) REVERT: C 683 ASN cc_start: 0.7688 (m110) cc_final: 0.7268 (m-40) REVERT: C 738 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8184 (mtpp) REVERT: D 199 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.6243 (mt) REVERT: D 257 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6728 (mt-10) REVERT: D 337 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7559 (mtt-85) REVERT: D 350 LYS cc_start: 0.8156 (tppt) cc_final: 0.7787 (tttt) REVERT: D 434 LYS cc_start: 0.7759 (mtpm) cc_final: 0.7359 (mmtp) REVERT: D 469 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5252 (mt) REVERT: D 683 ASN cc_start: 0.7720 (m110) cc_final: 0.7245 (m-40) REVERT: D 722 LYS cc_start: 0.8417 (tttt) cc_final: 0.8203 (tttm) REVERT: D 738 LYS cc_start: 0.8387 (ttmm) cc_final: 0.7967 (ttmt) outliers start: 35 outliers final: 30 residues processed: 281 average time/residue: 0.3703 time to fit residues: 157.1046 Evaluate side-chains 282 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 250 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 166 ASP 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 515 SER Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 282 MET 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 515 SER Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 282 MET 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 525 VAL Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 732 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 247 optimal weight: 4.9990 chunk 205 optimal weight: 0.0470 chunk 114 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 overall best weight: 3.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN B 646 GLN C 646 GLN D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.005 0.037 23144 Z= 0.302 Angle : 0.626 11.782 30968 Z= 0.306 Chirality : 0.043 0.178 3328 Planarity : 0.004 0.033 3712 Dihedral : 19.315 107.577 4336 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.06 % Allowed : 11.47 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.16), residues: 2552 helix: -0.32 (0.13), residues: 1524 sheet: -0.90 (0.57), residues: 84 loop : -1.86 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 692 HIS 0.008 0.001 HIS C 301 PHE 0.019 0.002 PHE C 316 TYR 0.016 0.002 TYR B 451 ARG 0.004 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 264 time to evaluate : 2.481 Fit side-chains REVERT: A 257 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6827 (mt-10) REVERT: A 283 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6892 (mt-10) REVERT: A 337 ARG cc_start: 0.7934 (mtp-110) cc_final: 0.7471 (mtt-85) REVERT: A 350 LYS cc_start: 0.8149 (tppt) cc_final: 0.7753 (tttt) REVERT: A 434 LYS cc_start: 0.7816 (mtpm) cc_final: 0.7317 (mmtp) REVERT: A 469 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.4816 (mt) REVERT: A 683 ASN cc_start: 0.7627 (m110) cc_final: 0.7178 (m-40) REVERT: A 722 LYS cc_start: 0.8400 (tttt) cc_final: 0.8187 (tttm) REVERT: A 738 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8233 (mtpp) REVERT: B 141 ASP cc_start: 0.6102 (t70) cc_final: 0.5869 (t70) REVERT: B 311 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8043 (mtpp) REVERT: B 350 LYS cc_start: 0.8334 (tppt) cc_final: 0.7892 (tttt) REVERT: B 469 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.4817 (mt) REVERT: C 141 ASP cc_start: 0.5959 (t70) cc_final: 0.5702 (t70) REVERT: C 161 LYS cc_start: 0.7443 (mmtt) cc_final: 0.7062 (mmmt) REVERT: C 257 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6921 (mt-10) REVERT: C 315 ASP cc_start: 0.7967 (t0) cc_final: 0.7646 (t0) REVERT: C 337 ARG cc_start: 0.7952 (mtp-110) cc_final: 0.7578 (mtt-85) REVERT: C 350 LYS cc_start: 0.8219 (tppt) cc_final: 0.7811 (tttt) REVERT: C 434 LYS cc_start: 0.7875 (mtpm) cc_final: 0.7413 (mmtt) REVERT: C 683 ASN cc_start: 0.7678 (m110) cc_final: 0.7268 (m-40) REVERT: C 738 LYS cc_start: 0.8464 (ttmm) cc_final: 0.8205 (mtpp) REVERT: D 199 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.5888 (mt) REVERT: D 257 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6868 (mt-10) REVERT: D 337 ARG cc_start: 0.7979 (mtp-110) cc_final: 0.7584 (mtt-85) REVERT: D 350 LYS cc_start: 0.8194 (tppt) cc_final: 0.7782 (tttt) REVERT: D 434 LYS cc_start: 0.7850 (mtpm) cc_final: 0.7362 (mmtt) REVERT: D 469 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5581 (mt) REVERT: D 683 ASN cc_start: 0.7676 (m110) cc_final: 0.7264 (m-40) REVERT: D 738 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8261 (mtpp) outliers start: 47 outliers final: 34 residues processed: 293 average time/residue: 0.3643 time to fit residues: 161.0683 Evaluate side-chains 283 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 245 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 217 THR 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 469 LEU Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 282 MET 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 Chi-restraints excluded: chain D residue 732 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 113 optimal weight: 0.0370 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN B 646 GLN C 646 GLN D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23144 Z= 0.142 Angle : 0.483 6.972 30968 Z= 0.241 Chirality : 0.038 0.142 3328 Planarity : 0.003 0.031 3712 Dihedral : 18.086 91.934 4336 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.58 % Allowed : 11.60 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2552 helix: 0.26 (0.14), residues: 1520 sheet: -0.91 (0.58), residues: 84 loop : -1.78 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 692 HIS 0.004 0.001 HIS D 301 PHE 0.017 0.001 PHE D 316 TYR 0.010 0.001 TYR C 451 ARG 0.005 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 246 time to evaluate : 2.366 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.7964 (mtp-110) cc_final: 0.7499 (mtt-85) REVERT: A 350 LYS cc_start: 0.8035 (tppt) cc_final: 0.7695 (tttt) REVERT: A 434 LYS cc_start: 0.7703 (mtpm) cc_final: 0.7209 (mmtp) REVERT: A 469 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.4715 (mt) REVERT: A 683 ASN cc_start: 0.7567 (m110) cc_final: 0.7019 (m-40) REVERT: A 722 LYS cc_start: 0.8359 (tttt) cc_final: 0.8146 (tttm) REVERT: A 738 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8220 (mtpp) REVERT: B 311 LYS cc_start: 0.8270 (ttpp) cc_final: 0.7724 (mtmm) REVERT: B 350 LYS cc_start: 0.8242 (tppt) cc_final: 0.7850 (tttt) REVERT: B 469 LEU cc_start: 0.5485 (OUTLIER) cc_final: 0.4873 (mt) REVERT: C 161 LYS cc_start: 0.7531 (mmtt) cc_final: 0.7188 (mmmt) REVERT: C 257 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6788 (mt-10) REVERT: C 315 ASP cc_start: 0.7602 (t0) cc_final: 0.7188 (t0) REVERT: C 337 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7543 (mtt-85) REVERT: C 350 LYS cc_start: 0.8126 (tppt) cc_final: 0.7766 (tttt) REVERT: C 434 LYS cc_start: 0.7765 (mtpm) cc_final: 0.7325 (mmtp) REVERT: C 683 ASN cc_start: 0.7564 (m110) cc_final: 0.7121 (m-40) REVERT: C 738 LYS cc_start: 0.8399 (ttmm) cc_final: 0.8163 (mtpp) REVERT: D 199 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6058 (mt) REVERT: D 337 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7544 (mtt-85) REVERT: D 350 LYS cc_start: 0.8101 (tppt) cc_final: 0.7742 (tttt) REVERT: D 434 LYS cc_start: 0.7758 (mtpm) cc_final: 0.7305 (mmtp) REVERT: D 469 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5634 (mt) REVERT: D 683 ASN cc_start: 0.7606 (m110) cc_final: 0.7099 (m-40) REVERT: D 738 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8263 (mtpp) outliers start: 36 outliers final: 20 residues processed: 268 average time/residue: 0.3677 time to fit residues: 150.2071 Evaluate side-chains 267 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 243 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP 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 525 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 3.9990 chunk 98 optimal weight: 0.0980 chunk 147 optimal weight: 0.0670 chunk 74 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN B 646 GLN C 646 GLN D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23144 Z= 0.129 Angle : 0.468 6.908 30968 Z= 0.232 Chirality : 0.038 0.137 3328 Planarity : 0.003 0.028 3712 Dihedral : 17.377 89.575 4336 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.23 % Allowed : 11.82 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2552 helix: 0.63 (0.14), residues: 1520 sheet: -0.87 (0.57), residues: 84 loop : -1.68 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 692 HIS 0.004 0.001 HIS C 301 PHE 0.017 0.001 PHE D 316 TYR 0.009 0.001 TYR A 451 ARG 0.004 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 244 time to evaluate : 2.214 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7490 (mtt-85) REVERT: A 350 LYS cc_start: 0.8014 (tppt) cc_final: 0.7720 (tttt) REVERT: A 434 LYS cc_start: 0.7628 (mtpm) cc_final: 0.7164 (mmtp) REVERT: A 469 LEU cc_start: 0.5384 (OUTLIER) cc_final: 0.4807 (mt) REVERT: A 683 ASN cc_start: 0.7529 (m110) cc_final: 0.7008 (m-40) REVERT: A 722 LYS cc_start: 0.8384 (tttt) cc_final: 0.8155 (tttm) REVERT: A 738 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8185 (mtpp) REVERT: B 311 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7708 (mtmm) REVERT: B 350 LYS cc_start: 0.8217 (tppt) cc_final: 0.7855 (tttt) REVERT: B 469 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.4817 (mt) REVERT: C 161 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7274 (mmmt) REVERT: C 283 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7119 (pt0) REVERT: C 337 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7535 (mtt-85) REVERT: C 350 LYS cc_start: 0.8096 (tppt) cc_final: 0.7768 (tttt) REVERT: C 434 LYS cc_start: 0.7702 (mtpm) cc_final: 0.7299 (mmtp) REVERT: C 683 ASN cc_start: 0.7552 (m110) cc_final: 0.7098 (m-40) REVERT: C 738 LYS cc_start: 0.8399 (ttmm) cc_final: 0.8179 (mtpp) REVERT: D 199 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6070 (mt) REVERT: D 337 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7515 (mtt-85) REVERT: D 350 LYS cc_start: 0.8075 (tppt) cc_final: 0.7748 (tttt) REVERT: D 434 LYS cc_start: 0.7661 (mtpm) cc_final: 0.7250 (mmtp) REVERT: D 469 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5744 (mt) REVERT: D 683 ASN cc_start: 0.7564 (m110) cc_final: 0.7088 (m-40) REVERT: D 738 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8236 (mtpp) outliers start: 28 outliers final: 13 residues processed: 261 average time/residue: 0.3619 time to fit residues: 144.9558 Evaluate side-chains 257 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 240 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 603 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 309 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 199 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 603 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 180 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23144 Z= 0.101 Angle : 0.457 13.498 30968 Z= 0.222 Chirality : 0.037 0.138 3328 Planarity : 0.002 0.026 3712 Dihedral : 16.946 89.609 4336 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.88 % Allowed : 12.48 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.17), residues: 2552 helix: 0.98 (0.14), residues: 1524 sheet: -0.86 (0.57), residues: 84 loop : -1.54 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 739 HIS 0.002 0.000 HIS A 301 PHE 0.015 0.001 PHE D 316 TYR 0.006 0.001 TYR C 451 ARG 0.006 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 243 time to evaluate : 2.505 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.7947 (mtp-110) cc_final: 0.7465 (mtt-85) REVERT: A 350 LYS cc_start: 0.7998 (tppt) cc_final: 0.7699 (tttt) REVERT: A 434 LYS cc_start: 0.7641 (mtpm) cc_final: 0.7202 (mmtt) REVERT: A 469 LEU cc_start: 0.5337 (OUTLIER) cc_final: 0.5124 (mt) REVERT: A 683 ASN cc_start: 0.7508 (m110) cc_final: 0.6984 (m-40) REVERT: A 722 LYS cc_start: 0.8408 (tttt) cc_final: 0.8151 (tttm) REVERT: A 738 LYS cc_start: 0.8437 (ttmm) cc_final: 0.8157 (mtpp) REVERT: B 311 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7631 (mtmm) REVERT: B 350 LYS cc_start: 0.8204 (tppt) cc_final: 0.7856 (tttt) REVERT: B 469 LEU cc_start: 0.5356 (OUTLIER) cc_final: 0.4810 (mt) REVERT: C 161 LYS cc_start: 0.7628 (mmtt) cc_final: 0.7298 (mmmt) REVERT: C 283 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7135 (pt0) REVERT: C 337 ARG cc_start: 0.7931 (mtp-110) cc_final: 0.7497 (mtt-85) REVERT: C 350 LYS cc_start: 0.8087 (tppt) cc_final: 0.7773 (tttt) REVERT: C 434 LYS cc_start: 0.7650 (mtpm) cc_final: 0.7285 (mmtt) REVERT: C 683 ASN cc_start: 0.7527 (m110) cc_final: 0.7091 (m-40) REVERT: C 738 LYS cc_start: 0.8353 (ttmm) cc_final: 0.8131 (mtpp) REVERT: D 199 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.6158 (mt) REVERT: D 337 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.7494 (mtt-85) REVERT: D 350 LYS cc_start: 0.8075 (tppt) cc_final: 0.7770 (tttt) REVERT: D 434 LYS cc_start: 0.7661 (mtpm) cc_final: 0.7280 (mmtt) REVERT: D 683 ASN cc_start: 0.7558 (m110) cc_final: 0.7082 (m-40) REVERT: D 738 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8196 (mtpp) outliers start: 20 outliers final: 13 residues processed: 253 average time/residue: 0.3534 time to fit residues: 137.3912 Evaluate side-chains 254 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 238 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 603 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 chunk 255 optimal weight: 0.0370 chunk 234 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 156 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23144 Z= 0.105 Angle : 0.463 13.267 30968 Z= 0.224 Chirality : 0.037 0.193 3328 Planarity : 0.002 0.025 3712 Dihedral : 16.660 89.713 4336 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.74 % Allowed : 12.70 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2552 helix: 1.13 (0.14), residues: 1536 sheet: -0.82 (0.57), residues: 84 loop : -1.44 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 739 HIS 0.002 0.000 HIS C 301 PHE 0.016 0.001 PHE D 316 TYR 0.008 0.001 TYR C 451 ARG 0.005 0.000 ARG A 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 2.635 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7475 (mtt-85) REVERT: A 434 LYS cc_start: 0.7633 (mtpm) cc_final: 0.7221 (mmtp) REVERT: A 683 ASN cc_start: 0.7540 (m110) cc_final: 0.7002 (m-40) REVERT: A 722 LYS cc_start: 0.8402 (tttt) cc_final: 0.8145 (tttm) REVERT: A 738 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8107 (mtpp) REVERT: B 311 LYS cc_start: 0.7904 (ttpp) cc_final: 0.7571 (mtmm) REVERT: B 350 LYS cc_start: 0.8188 (tppt) cc_final: 0.7842 (tttt) REVERT: B 469 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.4831 (mt) REVERT: C 161 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7337 (mmmt) REVERT: C 283 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7199 (pt0) REVERT: C 337 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7496 (mtt-85) REVERT: C 350 LYS cc_start: 0.8077 (tppt) cc_final: 0.7769 (tttt) REVERT: C 434 LYS cc_start: 0.7700 (mtpm) cc_final: 0.7341 (mmtp) REVERT: C 450 PHE cc_start: 0.7100 (m-10) cc_final: 0.6376 (t80) REVERT: C 683 ASN cc_start: 0.7591 (m110) cc_final: 0.7152 (m-40) REVERT: C 738 LYS cc_start: 0.8341 (ttmm) cc_final: 0.8116 (mtpp) REVERT: D 199 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6183 (mt) REVERT: D 337 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7494 (mtt-85) REVERT: D 434 LYS cc_start: 0.7653 (mtpm) cc_final: 0.7301 (mmtp) REVERT: D 683 ASN cc_start: 0.7581 (m110) cc_final: 0.7099 (m-40) REVERT: D 738 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8190 (mtpp) outliers start: 17 outliers final: 13 residues processed: 252 average time/residue: 0.3558 time to fit residues: 137.1803 Evaluate side-chains 251 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 178 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.158387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109880 restraints weight = 24344.598| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.04 r_work: 0.2946 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23144 Z= 0.162 Angle : 0.507 13.311 30968 Z= 0.247 Chirality : 0.039 0.154 3328 Planarity : 0.003 0.027 3712 Dihedral : 16.902 89.069 4336 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.74 % Allowed : 12.57 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2552 helix: 1.00 (0.14), residues: 1540 sheet: 0.16 (0.61), residues: 64 loop : -1.63 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 380 HIS 0.004 0.001 HIS D 301 PHE 0.017 0.001 PHE C 316 TYR 0.012 0.001 TYR C 451 ARG 0.006 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4638.85 seconds wall clock time: 84 minutes 15.58 seconds (5055.58 seconds total)