Starting phenix.real_space_refine on Sun Feb 18 10:48:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/02_2024/7mil_23855_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/02_2024/7mil_23855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/02_2024/7mil_23855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/02_2024/7mil_23855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/02_2024/7mil_23855_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/02_2024/7mil_23855_updated.pdb" } resolution = 3.86 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= 0.004 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 8 5.49 5 S 132 5.16 5 Na 1 4.78 5 C 14168 2.51 5 N 3552 2.21 5 O 3892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 375": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 375": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 729": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21753 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5347 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 18, 'TRANS': 637} Chain breaks: 1 Chain: "B" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5347 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 18, 'TRANS': 637} Chain breaks: 1 Chain: "C" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5347 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 18, 'TRANS': 637} Chain breaks: 1 Chain: "D" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5347 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 18, 'TRANS': 637} Chain breaks: 1 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {' NA': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 11.11, per 1000 atoms: 0.51 Number of scatterers: 21753 At special positions: 0 Unit cell: (141.57, 139.854, 126.126, 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 132 16.00 P 8 15.00 Na 1 11.00 O 3892 8.00 N 3552 7.00 C 14168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.04 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.04 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.04 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.04 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.03 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: 7.59 Conformation dependent library (CDL) restraints added in 3.8 seconds 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 8 sheets defined 54.7% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 114 through 129 removed outlier: 4.112A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.963A pdb=" N ARG A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 181 through 196 removed outlier: 4.352A pdb=" N LYS A 184 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 185 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 190 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 193 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 194 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 196 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.717A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.709A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 335 No H-bonds generated for 'chain 'A' and resid 332 through 335' Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 423 through 433 removed outlier: 3.650A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 460 removed outlier: 3.533A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 506 removed outlier: 3.928A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 522 through 541 removed outlier: 3.833A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 528 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 568 removed outlier: 3.850A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLY A 568 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 583 removed outlier: 3.794A pdb=" N VAL A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 4.089A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.996A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 removed outlier: 3.790A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 685 removed outlier: 3.644A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 705 removed outlier: 3.778A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 703 " --> pdb=" O THR A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 739 through 750 removed outlier: 4.005A pdb=" N THR A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 749 " --> pdb=" O HIS A 745 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 removed outlier: 4.113A pdb=" N LYS B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 146 removed outlier: 3.962A pdb=" N ARG B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 181 through 196 removed outlier: 4.352A pdb=" N LYS B 184 " --> pdb=" O PRO B 181 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 185 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B 187 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 190 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE B 193 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 194 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU B 196 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 299 through 306 removed outlier: 3.717A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.710A pdb=" N MET B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 335 No H-bonds generated for 'chain 'B' and resid 332 through 335' Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.649A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 460 removed outlier: 3.533A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 506 removed outlier: 3.927A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 522 through 541 removed outlier: 3.834A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 528 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 568 removed outlier: 3.850A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLY B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 583 removed outlier: 3.793A pdb=" N VAL B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 4.089A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.997A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 665 removed outlier: 3.790A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 removed outlier: 3.643A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 705 removed outlier: 3.778A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 703 " --> pdb=" O THR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 739 through 750 removed outlier: 4.005A pdb=" N THR B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 749 " --> pdb=" O HIS B 745 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 removed outlier: 4.112A pdb=" N LYS C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 146 removed outlier: 3.963A pdb=" N ARG C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 181 through 196 removed outlier: 4.353A pdb=" N LYS C 184 " --> pdb=" O PRO C 181 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 185 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL C 187 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 190 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE C 193 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 194 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU C 196 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 276 through 282 Processing helix chain 'C' and resid 299 through 306 removed outlier: 3.717A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.711A pdb=" N MET C 320 " --> pdb=" O PHE C 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 335 No H-bonds generated for 'chain 'C' and resid 332 through 335' Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 423 through 433 removed outlier: 3.650A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 460 removed outlier: 3.533A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 454 " --> pdb=" O PHE C 450 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 506 removed outlier: 3.927A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 522 through 541 removed outlier: 3.833A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 528 " --> pdb=" O PHE C 524 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 568 removed outlier: 3.850A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLY C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 583 removed outlier: 3.794A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 608 removed outlier: 4.090A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.997A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 665 removed outlier: 3.790A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 685 removed outlier: 3.644A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 705 removed outlier: 3.779A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 703 " --> pdb=" O THR C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 739 through 750 removed outlier: 4.005A pdb=" N THR C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU C 749 " --> pdb=" O HIS C 745 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN C 750 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 129 removed outlier: 4.112A pdb=" N LYS D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG D 122 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 126 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 146 removed outlier: 3.962A pdb=" N ARG D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 181 through 196 removed outlier: 4.352A pdb=" N LYS D 184 " --> pdb=" O PRO D 181 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 185 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL D 187 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 190 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE D 193 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 194 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 196 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 276 through 282 Processing helix chain 'D' and resid 299 through 306 removed outlier: 3.717A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.710A pdb=" N MET D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 335 No H-bonds generated for 'chain 'D' and resid 332 through 335' Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 405 through 409 Processing helix chain 'D' and resid 417 through 420 No H-bonds generated for 'chain 'D' and resid 417 through 420' Processing helix chain 'D' and resid 423 through 433 removed outlier: 3.649A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 460 removed outlier: 3.534A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 506 removed outlier: 3.926A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 522 through 541 removed outlier: 3.833A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 528 " --> pdb=" O PHE D 524 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 568 removed outlier: 3.850A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLY D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.793A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 608 removed outlier: 4.090A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE D 595 " --> pdb=" O LEU D 591 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.996A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 665 removed outlier: 3.790A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 685 removed outlier: 3.643A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 705 removed outlier: 3.779A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 703 " --> pdb=" O THR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 739 through 750 removed outlier: 4.006A pdb=" N THR D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU D 749 " --> pdb=" O HIS D 745 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN D 750 " --> pdb=" O VAL D 746 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 376 through 378 removed outlier: 3.623A pdb=" N TYR A 390 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 719 through 721 removed outlier: 3.571A pdb=" N GLU A 719 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 376 through 378 removed outlier: 3.622A pdb=" N TYR B 390 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 719 through 721 removed outlier: 3.571A pdb=" N GLU B 719 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 376 through 378 removed outlier: 3.622A pdb=" N TYR C 390 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 719 through 721 removed outlier: 3.571A pdb=" N GLU C 719 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 376 through 378 removed outlier: 3.622A pdb=" N TYR D 390 " --> pdb=" O LEU D 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 719 through 721 removed outlier: 3.571A pdb=" N GLU D 719 " --> pdb=" O CYS D 731 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1884 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: 5.37 Time building geometry restraints manager: 8.29 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: 3452 1.31 - 1.44: 5928 1.44 - 1.56: 12588 1.56 - 1.69: 20 1.69 - 1.82: 216 Bond restraints: 22204 Sorted by residual: bond pdb=" C21 POV B 902 " pdb=" O21 POV B 902 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C21 POV A 902 " pdb=" O21 POV A 902 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C21 POV C 902 " pdb=" O21 POV C 902 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C21 POV D 902 " pdb=" O21 POV D 902 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C21 POV D 901 " pdb=" O21 POV D 901 " ideal model delta sigma weight residual 1.330 1.418 -0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 22199 not shown) Histogram of bond angle deviations from ideal: 98.87 - 106.25: 448 106.25 - 113.63: 12433 113.63 - 121.01: 11525 121.01 - 128.39: 5378 128.39 - 135.77: 184 Bond angle restraints: 29968 Sorted by residual: angle pdb=" CA LEU C 469 " pdb=" CB LEU C 469 " pdb=" CG LEU C 469 " ideal model delta sigma weight residual 116.30 135.77 -19.47 3.50e+00 8.16e-02 3.09e+01 angle pdb=" CA LEU A 469 " pdb=" CB LEU A 469 " pdb=" CG LEU A 469 " ideal model delta sigma weight residual 116.30 135.76 -19.46 3.50e+00 8.16e-02 3.09e+01 angle pdb=" CA LEU B 469 " pdb=" CB LEU B 469 " pdb=" CG LEU B 469 " ideal model delta sigma weight residual 116.30 135.74 -19.44 3.50e+00 8.16e-02 3.08e+01 angle pdb=" CA LEU D 469 " pdb=" CB LEU D 469 " pdb=" CG LEU D 469 " ideal model delta sigma weight residual 116.30 135.69 -19.39 3.50e+00 8.16e-02 3.07e+01 angle pdb=" C THR D 411 " pdb=" N ASN D 412 " pdb=" CA ASN D 412 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.60e+01 ... (remaining 29963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.19: 12905 27.19 - 54.38: 472 54.38 - 81.57: 39 81.57 - 108.76: 12 108.76 - 135.95: 4 Dihedral angle restraints: 13432 sinusoidal: 5680 harmonic: 7752 Sorted by residual: dihedral pdb=" CB CYS C 721 " pdb=" SG CYS C 721 " pdb=" SG CYS C 731 " pdb=" CB CYS C 731 " ideal model delta sinusoidal sigma weight residual -86.00 -156.62 70.62 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CB CYS B 721 " pdb=" SG CYS B 721 " pdb=" SG CYS B 731 " pdb=" CB CYS B 731 " ideal model delta sinusoidal sigma weight residual -86.00 -156.62 70.62 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CB CYS A 721 " pdb=" SG CYS A 721 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -156.62 70.62 1 1.00e+01 1.00e-02 6.41e+01 ... (remaining 13429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2604 0.054 - 0.108: 656 0.108 - 0.162: 76 0.162 - 0.216: 28 0.216 - 0.270: 12 Chirality restraints: 3376 Sorted by residual: chirality pdb=" CB VAL C 154 " pdb=" CA VAL C 154 " pdb=" CG1 VAL C 154 " pdb=" CG2 VAL C 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL B 154 " pdb=" CA VAL B 154 " pdb=" CG1 VAL B 154 " pdb=" CG2 VAL B 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB VAL D 154 " pdb=" CA VAL D 154 " pdb=" CG1 VAL D 154 " pdb=" CG2 VAL D 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 3373 not shown) Planarity restraints: 3708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 180 " -0.040 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO B 181 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " 0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO C 181 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO A 181 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.034 5.00e-02 4.00e+02 ... (remaining 3705 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6508 2.82 - 3.34: 19197 3.34 - 3.86: 32318 3.86 - 4.38: 38103 4.38 - 4.90: 64534 Nonbonded interactions: 160660 Sorted by model distance: nonbonded pdb=" OD1 ASP A 322 " pdb=" OH TYR A 359 " model vdw 2.304 2.440 nonbonded pdb=" OD1 ASP C 322 " pdb=" OH TYR C 359 " model vdw 2.304 2.440 nonbonded pdb=" OD1 ASP D 322 " pdb=" OH TYR D 359 " model vdw 2.305 2.440 nonbonded pdb=" OD1 ASP B 322 " pdb=" OH TYR B 359 " model vdw 2.305 2.440 nonbonded pdb=" OG SER C 620 " pdb=" NE2 GLN C 646 " model vdw 2.319 2.520 ... (remaining 160655 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' selection = chain 'B' selection = (chain 'C' and (resid 59 through 751 or resid 901 through 902)) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.680 Check model and map are aligned: 0.330 Set scattering table: 0.220 Process input model: 52.040 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.007 0.090 22204 Z= 0.419 Angle : 1.169 19.467 29968 Z= 0.608 Chirality : 0.050 0.270 3376 Planarity : 0.006 0.061 3708 Dihedral : 13.070 135.950 8368 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.45 % Favored : 95.40 % Rotamer: Outliers : 0.68 % Allowed : 5.61 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.90 (0.10), residues: 2608 helix: -4.63 (0.05), residues: 1440 sheet: -3.55 (0.44), residues: 88 loop : -2.61 (0.15), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 742 HIS 0.006 0.002 HIS A 301 PHE 0.018 0.002 PHE D 316 TYR 0.013 0.002 TYR C 544 ARG 0.009 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 621 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8065 (pt0) cc_final: 0.7350 (mm-30) REVERT: A 159 MET cc_start: 0.7002 (tpp) cc_final: 0.6791 (tpp) REVERT: A 193 PHE cc_start: 0.6925 (t80) cc_final: 0.6643 (t80) REVERT: A 201 ASP cc_start: 0.7445 (t70) cc_final: 0.7022 (p0) REVERT: A 318 LYS cc_start: 0.8565 (tttm) cc_final: 0.7907 (ttmt) REVERT: A 358 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7602 (mtpp) REVERT: A 399 THR cc_start: 0.8052 (p) cc_final: 0.7787 (t) REVERT: A 479 MET cc_start: 0.3936 (mmm) cc_final: 0.3678 (mmp) REVERT: A 493 TRP cc_start: 0.7322 (t-100) cc_final: 0.7058 (t-100) REVERT: A 542 PHE cc_start: 0.7288 (m-10) cc_final: 0.5677 (t80) REVERT: A 575 TYR cc_start: 0.7793 (t80) cc_final: 0.7551 (t80) REVERT: A 588 LEU cc_start: 0.9035 (mm) cc_final: 0.8496 (mt) REVERT: A 611 LYS cc_start: 0.6237 (ttpm) cc_final: 0.5726 (mmmm) REVERT: A 627 ASP cc_start: 0.7689 (m-30) cc_final: 0.7445 (m-30) REVERT: A 684 VAL cc_start: 0.7638 (t) cc_final: 0.7274 (t) REVERT: A 688 SER cc_start: 0.7885 (p) cc_final: 0.7279 (m) REVERT: A 743 LYS cc_start: 0.7375 (mtpp) cc_final: 0.6787 (tmtt) REVERT: B 122 ARG cc_start: 0.6909 (mtp85) cc_final: 0.6672 (mtm110) REVERT: B 128 SER cc_start: 0.7025 (m) cc_final: 0.6796 (t) REVERT: B 133 GLU cc_start: 0.7435 (pt0) cc_final: 0.7192 (pt0) REVERT: B 159 MET cc_start: 0.6313 (tpp) cc_final: 0.6042 (tpt) REVERT: B 282 MET cc_start: 0.7213 (mtp) cc_final: 0.6997 (mtp) REVERT: B 358 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7624 (mtpp) REVERT: B 379 ASP cc_start: 0.6184 (p0) cc_final: 0.5917 (t0) REVERT: B 399 THR cc_start: 0.8127 (p) cc_final: 0.7763 (t) REVERT: B 493 TRP cc_start: 0.7374 (t-100) cc_final: 0.7015 (t-100) REVERT: B 542 PHE cc_start: 0.7028 (m-10) cc_final: 0.5550 (t80) REVERT: B 575 TYR cc_start: 0.7808 (t80) cc_final: 0.7600 (t80) REVERT: B 588 LEU cc_start: 0.9051 (mm) cc_final: 0.8514 (mt) REVERT: B 611 LYS cc_start: 0.6295 (ttpm) cc_final: 0.5759 (mmmm) REVERT: B 627 ASP cc_start: 0.7677 (m-30) cc_final: 0.7439 (m-30) REVERT: B 688 SER cc_start: 0.7768 (p) cc_final: 0.7546 (m) REVERT: B 743 LYS cc_start: 0.7581 (mtpp) cc_final: 0.7278 (tmtt) REVERT: C 133 GLU cc_start: 0.7967 (pt0) cc_final: 0.7298 (mm-30) REVERT: C 318 LYS cc_start: 0.8521 (tttm) cc_final: 0.7936 (ttmt) REVERT: C 358 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7901 (ttpp) REVERT: C 399 THR cc_start: 0.8185 (p) cc_final: 0.7912 (t) REVERT: C 435 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7790 (mmmt) REVERT: C 450 PHE cc_start: 0.6834 (t80) cc_final: 0.6505 (t80) REVERT: C 479 MET cc_start: 0.3843 (mmm) cc_final: 0.3442 (mmp) REVERT: C 542 PHE cc_start: 0.7365 (m-10) cc_final: 0.6189 (t80) REVERT: C 555 MET cc_start: 0.8233 (mtm) cc_final: 0.8013 (mtp) REVERT: C 574 MET cc_start: 0.6997 (pp-130) cc_final: 0.6788 (mmt) REVERT: C 588 LEU cc_start: 0.8998 (mm) cc_final: 0.8629 (mt) REVERT: C 611 LYS cc_start: 0.5966 (ttpm) cc_final: 0.5384 (mmmm) REVERT: C 688 SER cc_start: 0.7846 (p) cc_final: 0.6782 (p) REVERT: C 728 PHE cc_start: 0.6832 (m-80) cc_final: 0.6613 (m-80) REVERT: C 743 LYS cc_start: 0.6909 (mtpp) cc_final: 0.6475 (tmtt) REVERT: D 120 LYS cc_start: 0.6720 (mtmp) cc_final: 0.6444 (tttm) REVERT: D 122 ARG cc_start: 0.6899 (mtp85) cc_final: 0.6562 (mtm110) REVERT: D 240 ASP cc_start: 0.7419 (m-30) cc_final: 0.6907 (p0) REVERT: D 356 ILE cc_start: 0.9144 (mm) cc_final: 0.8924 (mt) REVERT: D 358 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7638 (mtpp) REVERT: D 379 ASP cc_start: 0.6168 (p0) cc_final: 0.5629 (t0) REVERT: D 399 THR cc_start: 0.8069 (p) cc_final: 0.7764 (t) REVERT: D 426 HIS cc_start: 0.6704 (t70) cc_final: 0.6452 (t-90) REVERT: D 450 PHE cc_start: 0.7185 (t80) cc_final: 0.6908 (t80) REVERT: D 493 TRP cc_start: 0.7308 (t-100) cc_final: 0.6849 (t-100) REVERT: D 542 PHE cc_start: 0.7145 (m-10) cc_final: 0.5698 (t80) REVERT: D 588 LEU cc_start: 0.9076 (mm) cc_final: 0.8511 (mt) REVERT: D 627 ASP cc_start: 0.7693 (m-30) cc_final: 0.7449 (m-30) REVERT: D 688 SER cc_start: 0.7886 (p) cc_final: 0.7462 (m) REVERT: D 716 ARG cc_start: 0.7233 (tpp-160) cc_final: 0.6938 (tpp80) REVERT: D 743 LYS cc_start: 0.7555 (mtpp) cc_final: 0.6827 (tmtt) outliers start: 16 outliers final: 6 residues processed: 634 average time/residue: 0.3538 time to fit residues: 334.1093 Evaluate side-chains 342 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 336 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 676 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.0170 chunk 197 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 203 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 394 ASN ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 683 ASN A 735 ASN B 160 HIS B 346 GLN B 394 ASN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN B 683 ASN B 735 ASN C 180 ASN C 182 ASN C 346 GLN C 394 ASN ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS C 646 GLN C 683 ASN C 735 ASN D 178 ASN D 292 GLN D 346 GLN D 394 ASN ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN D 683 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22204 Z= 0.174 Angle : 0.622 10.734 29968 Z= 0.313 Chirality : 0.039 0.148 3376 Planarity : 0.005 0.054 3708 Dihedral : 12.245 118.890 3160 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.53 % Favored : 96.32 % Rotamer: Outliers : 3.10 % Allowed : 12.20 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.13), residues: 2608 helix: -2.99 (0.09), residues: 1468 sheet: -3.68 (0.45), residues: 88 loop : -2.16 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 481 HIS 0.004 0.001 HIS D 160 PHE 0.024 0.001 PHE A 489 TYR 0.017 0.001 TYR A 359 ARG 0.006 0.000 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 365 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PRO cc_start: 0.6330 (Cg_endo) cc_final: 0.6089 (Cg_exo) REVERT: A 133 GLU cc_start: 0.7739 (pt0) cc_final: 0.7331 (mm-30) REVERT: A 201 ASP cc_start: 0.7620 (t70) cc_final: 0.7281 (p0) REVERT: A 229 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6189 (m-30) REVERT: A 399 THR cc_start: 0.8285 (p) cc_final: 0.7962 (t) REVERT: A 450 PHE cc_start: 0.6984 (t80) cc_final: 0.6489 (t80) REVERT: A 479 MET cc_start: 0.3958 (mmm) cc_final: 0.3657 (mmp) REVERT: A 491 LEU cc_start: 0.7708 (mt) cc_final: 0.7499 (tp) REVERT: A 493 TRP cc_start: 0.7411 (t-100) cc_final: 0.6868 (t-100) REVERT: A 542 PHE cc_start: 0.7441 (m-10) cc_final: 0.6199 (t80) REVERT: A 561 ASN cc_start: 0.8808 (m110) cc_final: 0.8425 (m110) REVERT: A 588 LEU cc_start: 0.9141 (mm) cc_final: 0.8697 (mt) REVERT: A 611 LYS cc_start: 0.6326 (OUTLIER) cc_final: 0.5895 (mmmt) REVERT: A 702 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7827 (tp30) REVERT: A 743 LYS cc_start: 0.7306 (mtpp) cc_final: 0.6973 (tmtt) REVERT: B 159 MET cc_start: 0.6130 (tpp) cc_final: 0.5799 (tpt) REVERT: B 282 MET cc_start: 0.6979 (mtp) cc_final: 0.6750 (mtp) REVERT: B 358 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7328 (mtpp) REVERT: B 379 ASP cc_start: 0.6212 (p0) cc_final: 0.5877 (t0) REVERT: B 399 THR cc_start: 0.8251 (p) cc_final: 0.7854 (t) REVERT: B 450 PHE cc_start: 0.7086 (t80) cc_final: 0.6393 (t80) REVERT: B 493 TRP cc_start: 0.7345 (t-100) cc_final: 0.6844 (t-100) REVERT: B 542 PHE cc_start: 0.7213 (m-10) cc_final: 0.5616 (t80) REVERT: B 561 ASN cc_start: 0.8796 (m110) cc_final: 0.8413 (m110) REVERT: B 572 MET cc_start: 0.8444 (mmm) cc_final: 0.8233 (tpp) REVERT: B 588 LEU cc_start: 0.9106 (mm) cc_final: 0.8674 (mt) REVERT: B 611 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5872 (mmmt) REVERT: B 743 LYS cc_start: 0.7580 (mtpp) cc_final: 0.7328 (tmtt) REVERT: C 120 LYS cc_start: 0.8053 (mtmp) cc_final: 0.7772 (mtmt) REVERT: C 133 GLU cc_start: 0.8128 (pt0) cc_final: 0.7373 (mm-30) REVERT: C 135 LEU cc_start: 0.7522 (mm) cc_final: 0.7204 (tt) REVERT: C 399 THR cc_start: 0.8243 (p) cc_final: 0.7911 (t) REVERT: C 450 PHE cc_start: 0.6961 (t80) cc_final: 0.6696 (t80) REVERT: C 479 MET cc_start: 0.3747 (mmm) cc_final: 0.3454 (mmp) REVERT: C 484 LEU cc_start: 0.5560 (OUTLIER) cc_final: 0.5290 (mt) REVERT: C 561 ASN cc_start: 0.8804 (m110) cc_final: 0.8430 (m110) REVERT: C 588 LEU cc_start: 0.9089 (mm) cc_final: 0.8603 (mt) REVERT: C 611 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5646 (mmmt) REVERT: C 627 ASP cc_start: 0.7398 (m-30) cc_final: 0.7108 (m-30) REVERT: C 743 LYS cc_start: 0.7107 (mtpp) cc_final: 0.6762 (tmtt) REVERT: D 147 ARG cc_start: 0.4847 (mpt-90) cc_final: 0.4217 (ttp80) REVERT: D 159 MET cc_start: 0.6346 (tpt) cc_final: 0.6069 (tpt) REVERT: D 201 ASP cc_start: 0.7500 (t70) cc_final: 0.6985 (p0) REVERT: D 240 ASP cc_start: 0.7568 (m-30) cc_final: 0.7001 (p0) REVERT: D 358 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7401 (mtpp) REVERT: D 399 THR cc_start: 0.8272 (p) cc_final: 0.7914 (t) REVERT: D 542 PHE cc_start: 0.7305 (m-10) cc_final: 0.5776 (t80) REVERT: D 561 ASN cc_start: 0.8838 (m110) cc_final: 0.8434 (m110) REVERT: D 588 LEU cc_start: 0.9121 (mm) cc_final: 0.8692 (mt) REVERT: D 611 LYS cc_start: 0.6205 (OUTLIER) cc_final: 0.5899 (mmmt) REVERT: D 702 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: D 711 LEU cc_start: 0.7754 (tp) cc_final: 0.7374 (tt) REVERT: D 716 ARG cc_start: 0.7303 (tpp-160) cc_final: 0.6966 (tpp80) REVERT: D 743 LYS cc_start: 0.7513 (mtpp) cc_final: 0.6937 (tmtt) outliers start: 73 outliers final: 31 residues processed: 421 average time/residue: 0.3174 time to fit residues: 207.9533 Evaluate side-chains 336 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 297 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 196 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 236 optimal weight: 0.0020 chunk 255 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 chunk 234 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS B 160 HIS B 178 ASN B 216 GLN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS D 178 ASN D 216 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22204 Z= 0.129 Angle : 0.547 10.561 29968 Z= 0.267 Chirality : 0.038 0.135 3376 Planarity : 0.003 0.051 3708 Dihedral : 11.293 124.840 3158 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.89 % Allowed : 13.73 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.14), residues: 2608 helix: -1.74 (0.12), residues: 1472 sheet: -3.38 (0.45), residues: 88 loop : -1.80 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 481 HIS 0.003 0.001 HIS A 523 PHE 0.030 0.001 PHE A 590 TYR 0.009 0.001 TYR D 451 ARG 0.005 0.000 ARG C 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 343 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7798 (pt0) cc_final: 0.7333 (mm-30) REVERT: A 201 ASP cc_start: 0.7750 (t70) cc_final: 0.7398 (p0) REVERT: A 399 THR cc_start: 0.8247 (p) cc_final: 0.7950 (t) REVERT: A 450 PHE cc_start: 0.6884 (t80) cc_final: 0.6493 (t80) REVERT: A 479 MET cc_start: 0.3835 (mmm) cc_final: 0.3437 (mmp) REVERT: A 493 TRP cc_start: 0.7430 (t-100) cc_final: 0.6943 (t-100) REVERT: A 542 PHE cc_start: 0.7486 (m-10) cc_final: 0.6252 (t80) REVERT: A 561 ASN cc_start: 0.8727 (m110) cc_final: 0.8369 (m110) REVERT: A 588 LEU cc_start: 0.9065 (mm) cc_final: 0.8630 (mt) REVERT: A 611 LYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5725 (mmmt) REVERT: A 743 LYS cc_start: 0.7300 (mtpp) cc_final: 0.7013 (tmtt) REVERT: B 159 MET cc_start: 0.5837 (tpp) cc_final: 0.5564 (tpt) REVERT: B 282 MET cc_start: 0.7021 (mtp) cc_final: 0.6636 (mtp) REVERT: B 358 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7255 (mtpp) REVERT: B 379 ASP cc_start: 0.6155 (p0) cc_final: 0.5774 (t0) REVERT: B 399 THR cc_start: 0.8384 (p) cc_final: 0.8025 (t) REVERT: B 450 PHE cc_start: 0.6878 (t80) cc_final: 0.6437 (t80) REVERT: B 493 TRP cc_start: 0.7469 (t-100) cc_final: 0.7025 (t-100) REVERT: B 542 PHE cc_start: 0.7308 (m-10) cc_final: 0.5692 (t80) REVERT: B 561 ASN cc_start: 0.8768 (m110) cc_final: 0.8384 (m110) REVERT: B 588 LEU cc_start: 0.9073 (mm) cc_final: 0.8636 (mt) REVERT: B 611 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5736 (mmmt) REVERT: B 743 LYS cc_start: 0.7468 (mtpp) cc_final: 0.7254 (tmtt) REVERT: C 133 GLU cc_start: 0.8094 (pt0) cc_final: 0.7374 (mm-30) REVERT: C 135 LEU cc_start: 0.7557 (mm) cc_final: 0.7147 (tt) REVERT: C 137 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6874 (mm-30) REVERT: C 399 THR cc_start: 0.8224 (p) cc_final: 0.7907 (t) REVERT: C 450 PHE cc_start: 0.6801 (t80) cc_final: 0.6515 (t80) REVERT: C 561 ASN cc_start: 0.8681 (m110) cc_final: 0.8329 (m110) REVERT: C 565 TYR cc_start: 0.8817 (m-80) cc_final: 0.8612 (m-80) REVERT: C 588 LEU cc_start: 0.9102 (mm) cc_final: 0.8637 (mt) REVERT: C 611 LYS cc_start: 0.6148 (OUTLIER) cc_final: 0.5679 (mmmt) REVERT: C 627 ASP cc_start: 0.7373 (m-30) cc_final: 0.7083 (m-30) REVERT: C 728 PHE cc_start: 0.6837 (m-80) cc_final: 0.6507 (m-80) REVERT: C 743 LYS cc_start: 0.7088 (mtpp) cc_final: 0.6775 (tmtt) REVERT: D 201 ASP cc_start: 0.7542 (t70) cc_final: 0.7087 (p0) REVERT: D 240 ASP cc_start: 0.7588 (m-30) cc_final: 0.7030 (p0) REVERT: D 254 TYR cc_start: 0.6902 (m-80) cc_final: 0.6659 (m-80) REVERT: D 320 MET cc_start: 0.8581 (mmm) cc_final: 0.8273 (mmt) REVERT: D 358 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7385 (mtpp) REVERT: D 399 THR cc_start: 0.8236 (p) cc_final: 0.7910 (t) REVERT: D 450 PHE cc_start: 0.6935 (t80) cc_final: 0.6499 (t80) REVERT: D 542 PHE cc_start: 0.7513 (m-10) cc_final: 0.6344 (t80) REVERT: D 561 ASN cc_start: 0.8812 (m110) cc_final: 0.8453 (m110) REVERT: D 588 LEU cc_start: 0.9073 (mm) cc_final: 0.8625 (mt) REVERT: D 611 LYS cc_start: 0.6175 (OUTLIER) cc_final: 0.5786 (mmmt) REVERT: D 711 LEU cc_start: 0.7625 (tp) cc_final: 0.7394 (tt) REVERT: D 716 ARG cc_start: 0.7323 (tpp-160) cc_final: 0.7027 (tpp-160) REVERT: D 738 LYS cc_start: 0.8264 (mtpp) cc_final: 0.7922 (mtpt) REVERT: D 743 LYS cc_start: 0.7372 (mtpp) cc_final: 0.6887 (tmtt) outliers start: 68 outliers final: 43 residues processed: 392 average time/residue: 0.3082 time to fit residues: 191.4368 Evaluate side-chains 343 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 296 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 216 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 394 ASN B 178 ASN B 216 GLN B 256 HIS ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 346 GLN B 394 ASN B 401 ASN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 394 ASN ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN D 216 GLN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22204 Z= 0.304 Angle : 0.698 11.400 29968 Z= 0.349 Chirality : 0.044 0.169 3376 Planarity : 0.005 0.062 3708 Dihedral : 12.262 139.385 3158 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.89 % Allowed : 13.39 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.15), residues: 2608 helix: -1.48 (0.12), residues: 1436 sheet: -3.49 (0.47), residues: 88 loop : -1.78 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 481 HIS 0.006 0.002 HIS C 426 PHE 0.024 0.002 PHE C 590 TYR 0.027 0.002 TYR C 451 ARG 0.007 0.001 ARG D 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 294 time to evaluate : 2.323 Fit side-chains REVERT: A 133 GLU cc_start: 0.7667 (pt0) cc_final: 0.7305 (mm-30) REVERT: A 139 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.5773 (tp) REVERT: A 201 ASP cc_start: 0.7744 (t70) cc_final: 0.7432 (p0) REVERT: A 399 THR cc_start: 0.8399 (p) cc_final: 0.8061 (t) REVERT: A 450 PHE cc_start: 0.6821 (t80) cc_final: 0.6382 (t80) REVERT: A 479 MET cc_start: 0.3739 (mmm) cc_final: 0.3379 (mmp) REVERT: A 493 TRP cc_start: 0.7381 (t-100) cc_final: 0.6995 (t-100) REVERT: A 542 PHE cc_start: 0.7671 (m-10) cc_final: 0.6393 (t80) REVERT: A 561 ASN cc_start: 0.8748 (m110) cc_final: 0.8477 (m-40) REVERT: A 588 LEU cc_start: 0.9093 (mm) cc_final: 0.8578 (mt) REVERT: A 611 LYS cc_start: 0.6213 (OUTLIER) cc_final: 0.5766 (mmmt) REVERT: A 702 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.8019 (tp30) REVERT: A 743 LYS cc_start: 0.7348 (mtpp) cc_final: 0.6885 (tmtt) REVERT: B 124 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6898 (t80) REVERT: B 159 MET cc_start: 0.6206 (tpp) cc_final: 0.5960 (tpt) REVERT: B 163 THR cc_start: 0.7920 (p) cc_final: 0.7660 (p) REVERT: B 201 ASP cc_start: 0.7506 (t70) cc_final: 0.7140 (p0) REVERT: B 399 THR cc_start: 0.8415 (p) cc_final: 0.8061 (t) REVERT: B 450 PHE cc_start: 0.6786 (t80) cc_final: 0.6279 (t80) REVERT: B 493 TRP cc_start: 0.7438 (t-100) cc_final: 0.6932 (t-100) REVERT: B 561 ASN cc_start: 0.8787 (m110) cc_final: 0.8533 (m-40) REVERT: B 588 LEU cc_start: 0.9051 (mm) cc_final: 0.8541 (mt) REVERT: B 611 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5760 (mmmt) REVERT: B 702 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8071 (tp30) REVERT: B 743 LYS cc_start: 0.7493 (mtpp) cc_final: 0.7162 (tmtt) REVERT: C 133 GLU cc_start: 0.8199 (pt0) cc_final: 0.7457 (mm-30) REVERT: C 135 LEU cc_start: 0.7586 (mm) cc_final: 0.7301 (tt) REVERT: C 139 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6108 (tp) REVERT: C 366 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7051 (ptpt) REVERT: C 399 THR cc_start: 0.8310 (p) cc_final: 0.7964 (t) REVERT: C 479 MET cc_start: 0.3158 (mmm) cc_final: 0.2738 (mmp) REVERT: C 561 ASN cc_start: 0.8705 (m110) cc_final: 0.8459 (m-40) REVERT: C 574 MET cc_start: 0.7112 (pp-130) cc_final: 0.6865 (mmt) REVERT: C 584 LEU cc_start: 0.8202 (mp) cc_final: 0.7996 (mp) REVERT: C 588 LEU cc_start: 0.9104 (mm) cc_final: 0.8602 (mt) REVERT: C 611 LYS cc_start: 0.6240 (OUTLIER) cc_final: 0.5702 (mmmt) REVERT: C 711 LEU cc_start: 0.8023 (tp) cc_final: 0.7821 (tt) REVERT: C 728 PHE cc_start: 0.7078 (m-80) cc_final: 0.6723 (m-80) REVERT: C 743 LYS cc_start: 0.7319 (mtpp) cc_final: 0.6800 (tmtt) REVERT: D 62 PRO cc_start: 0.6429 (Cg_endo) cc_final: 0.6206 (Cg_exo) REVERT: D 124 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.7000 (t80) REVERT: D 201 ASP cc_start: 0.7682 (t70) cc_final: 0.7308 (p0) REVERT: D 399 THR cc_start: 0.8451 (p) cc_final: 0.8097 (t) REVERT: D 450 PHE cc_start: 0.6948 (t80) cc_final: 0.6460 (t80) REVERT: D 481 TRP cc_start: 0.2378 (t60) cc_final: 0.2062 (t60) REVERT: D 493 TRP cc_start: 0.7410 (t-100) cc_final: 0.6993 (t-100) REVERT: D 542 PHE cc_start: 0.7538 (m-10) cc_final: 0.6358 (t80) REVERT: D 561 ASN cc_start: 0.8833 (m110) cc_final: 0.8552 (m-40) REVERT: D 572 MET cc_start: 0.8328 (tpp) cc_final: 0.8103 (tpp) REVERT: D 588 LEU cc_start: 0.9079 (mm) cc_final: 0.8557 (mt) REVERT: D 611 LYS cc_start: 0.6153 (OUTLIER) cc_final: 0.5773 (mmmt) REVERT: D 702 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7979 (tp30) REVERT: D 743 LYS cc_start: 0.7528 (mtpp) cc_final: 0.7020 (tmtt) outliers start: 115 outliers final: 72 residues processed: 386 average time/residue: 0.2980 time to fit residues: 184.4139 Evaluate side-chains 347 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 263 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 736 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 214 optimal weight: 0.3980 chunk 173 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 225 optimal weight: 0.0870 chunk 63 optimal weight: 6.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN B 292 GLN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN D 394 ASN ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22204 Z= 0.132 Angle : 0.549 14.947 29968 Z= 0.266 Chirality : 0.038 0.132 3376 Planarity : 0.003 0.062 3708 Dihedral : 10.810 123.121 3158 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.57 % Allowed : 15.52 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.15), residues: 2608 helix: -0.84 (0.13), residues: 1464 sheet: -3.21 (0.50), residues: 88 loop : -1.71 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 481 HIS 0.003 0.001 HIS B 523 PHE 0.022 0.001 PHE D 590 TYR 0.018 0.001 TYR C 451 ARG 0.003 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 307 time to evaluate : 2.580 Fit side-chains REVERT: A 133 GLU cc_start: 0.7710 (pt0) cc_final: 0.7298 (mm-30) REVERT: A 139 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5718 (tp) REVERT: A 162 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6260 (mm) REVERT: A 180 ASN cc_start: 0.6298 (m-40) cc_final: 0.6062 (p0) REVERT: A 201 ASP cc_start: 0.7732 (t70) cc_final: 0.7469 (p0) REVERT: A 399 THR cc_start: 0.8360 (p) cc_final: 0.8030 (t) REVERT: A 443 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 450 PHE cc_start: 0.6726 (t80) cc_final: 0.6349 (t80) REVERT: A 479 MET cc_start: 0.3783 (mmm) cc_final: 0.3402 (mmp) REVERT: A 542 PHE cc_start: 0.7667 (m-10) cc_final: 0.6449 (t80) REVERT: A 561 ASN cc_start: 0.8643 (m110) cc_final: 0.8280 (m110) REVERT: A 588 LEU cc_start: 0.9079 (mm) cc_final: 0.8601 (mt) REVERT: A 611 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5748 (mmmt) REVERT: A 743 LYS cc_start: 0.7266 (mtpp) cc_final: 0.6870 (tmtt) REVERT: B 120 LYS cc_start: 0.5951 (tttt) cc_final: 0.5511 (pttt) REVERT: B 124 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6996 (t80) REVERT: B 159 MET cc_start: 0.6167 (tpp) cc_final: 0.5942 (tpt) REVERT: B 163 THR cc_start: 0.7795 (p) cc_final: 0.7423 (p) REVERT: B 201 ASP cc_start: 0.7373 (t70) cc_final: 0.7032 (p0) REVERT: B 320 MET cc_start: 0.8369 (mmm) cc_final: 0.8134 (mpp) REVERT: B 399 THR cc_start: 0.8468 (p) cc_final: 0.8169 (t) REVERT: B 443 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8480 (mp) REVERT: B 450 PHE cc_start: 0.6771 (t80) cc_final: 0.6370 (t80) REVERT: B 561 ASN cc_start: 0.8646 (m110) cc_final: 0.8276 (m110) REVERT: B 588 LEU cc_start: 0.9031 (mm) cc_final: 0.8595 (mt) REVERT: B 611 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5730 (mmmt) REVERT: B 743 LYS cc_start: 0.7390 (mtpp) cc_final: 0.7125 (tmtt) REVERT: C 133 GLU cc_start: 0.7981 (pt0) cc_final: 0.7365 (mm-30) REVERT: C 135 LEU cc_start: 0.7496 (mm) cc_final: 0.7213 (tt) REVERT: C 139 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6269 (tt) REVERT: C 148 ARG cc_start: 0.5451 (mpt90) cc_final: 0.4900 (mmp80) REVERT: C 399 THR cc_start: 0.8276 (p) cc_final: 0.7966 (t) REVERT: C 443 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8458 (mp) REVERT: C 450 PHE cc_start: 0.6847 (t80) cc_final: 0.6464 (t80) REVERT: C 479 MET cc_start: 0.3174 (mmm) cc_final: 0.2857 (mmp) REVERT: C 561 ASN cc_start: 0.8663 (m110) cc_final: 0.8326 (m110) REVERT: C 588 LEU cc_start: 0.9068 (mm) cc_final: 0.8666 (mt) REVERT: C 611 LYS cc_start: 0.6295 (OUTLIER) cc_final: 0.5750 (mmmt) REVERT: C 728 PHE cc_start: 0.7065 (m-80) cc_final: 0.6850 (m-80) REVERT: C 736 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6976 (mt-10) REVERT: C 743 LYS cc_start: 0.7119 (mtpp) cc_final: 0.6664 (tmtt) REVERT: D 74 GLN cc_start: 0.6400 (mm-40) cc_final: 0.5425 (mp10) REVERT: D 124 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6999 (t80) REVERT: D 201 ASP cc_start: 0.7592 (t70) cc_final: 0.7295 (p0) REVERT: D 399 THR cc_start: 0.8391 (p) cc_final: 0.8061 (t) REVERT: D 450 PHE cc_start: 0.6813 (t80) cc_final: 0.6430 (t80) REVERT: D 481 TRP cc_start: 0.2234 (t60) cc_final: 0.2001 (t60) REVERT: D 542 PHE cc_start: 0.7526 (m-10) cc_final: 0.6324 (t80) REVERT: D 561 ASN cc_start: 0.8702 (m110) cc_final: 0.8327 (m110) REVERT: D 572 MET cc_start: 0.8301 (tpp) cc_final: 0.8060 (tpp) REVERT: D 588 LEU cc_start: 0.9056 (mm) cc_final: 0.8579 (mt) REVERT: D 611 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5709 (mmmt) REVERT: D 743 LYS cc_start: 0.7414 (mtpp) cc_final: 0.6987 (tmtt) outliers start: 84 outliers final: 44 residues processed: 377 average time/residue: 0.2992 time to fit residues: 180.3889 Evaluate side-chains 336 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 280 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 251 optimal weight: 0.9980 chunk 208 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 216 GLN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 394 ASN ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22204 Z= 0.232 Angle : 0.613 13.742 29968 Z= 0.301 Chirality : 0.041 0.152 3376 Planarity : 0.004 0.071 3708 Dihedral : 11.224 130.405 3156 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.42 % Allowed : 15.73 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2608 helix: -0.74 (0.13), residues: 1460 sheet: -3.19 (0.52), residues: 88 loop : -1.71 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 481 HIS 0.004 0.001 HIS D 471 PHE 0.023 0.002 PHE D 590 TYR 0.023 0.002 TYR C 451 ARG 0.004 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 277 time to evaluate : 2.434 Fit side-chains REVERT: A 124 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.7000 (t80) REVERT: A 133 GLU cc_start: 0.7742 (pt0) cc_final: 0.7307 (mm-30) REVERT: A 139 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.5757 (tp) REVERT: A 162 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6325 (mm) REVERT: A 201 ASP cc_start: 0.7803 (t70) cc_final: 0.7502 (p0) REVERT: A 399 THR cc_start: 0.8330 (p) cc_final: 0.8013 (t) REVERT: A 450 PHE cc_start: 0.6720 (t80) cc_final: 0.6319 (t80) REVERT: A 479 MET cc_start: 0.3876 (mmm) cc_final: 0.3469 (mmp) REVERT: A 542 PHE cc_start: 0.7705 (m-10) cc_final: 0.6314 (t80) REVERT: A 561 ASN cc_start: 0.8753 (m110) cc_final: 0.8489 (m-40) REVERT: A 588 LEU cc_start: 0.9096 (mm) cc_final: 0.8606 (mt) REVERT: A 611 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5709 (mmmt) REVERT: A 743 LYS cc_start: 0.7288 (mtpp) cc_final: 0.6817 (tmtt) REVERT: B 62 PRO cc_start: 0.6483 (Cg_endo) cc_final: 0.6231 (Cg_exo) REVERT: B 124 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.7009 (t80) REVERT: B 159 MET cc_start: 0.6417 (tpp) cc_final: 0.6209 (tpt) REVERT: B 163 THR cc_start: 0.7855 (p) cc_final: 0.7537 (p) REVERT: B 201 ASP cc_start: 0.7426 (t70) cc_final: 0.7141 (p0) REVERT: B 320 MET cc_start: 0.8284 (mmm) cc_final: 0.8038 (mpp) REVERT: B 399 THR cc_start: 0.8398 (p) cc_final: 0.8091 (t) REVERT: B 450 PHE cc_start: 0.6746 (t80) cc_final: 0.6326 (t80) REVERT: B 561 ASN cc_start: 0.8776 (m110) cc_final: 0.8464 (m110) REVERT: B 588 LEU cc_start: 0.9040 (mm) cc_final: 0.8585 (mt) REVERT: B 611 LYS cc_start: 0.6161 (OUTLIER) cc_final: 0.5690 (mmmt) REVERT: B 743 LYS cc_start: 0.7382 (mtpp) cc_final: 0.7094 (tmtt) REVERT: C 133 GLU cc_start: 0.8091 (pt0) cc_final: 0.7441 (mm-30) REVERT: C 135 LEU cc_start: 0.7608 (mm) cc_final: 0.7337 (tt) REVERT: C 139 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6319 (tt) REVERT: C 148 ARG cc_start: 0.5500 (mpt90) cc_final: 0.4951 (mmp80) REVERT: C 169 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7547 (ttmt) REVERT: C 399 THR cc_start: 0.8304 (p) cc_final: 0.7948 (t) REVERT: C 450 PHE cc_start: 0.6849 (t80) cc_final: 0.6463 (t80) REVERT: C 479 MET cc_start: 0.3101 (mmm) cc_final: 0.2796 (mmp) REVERT: C 481 TRP cc_start: 0.2652 (t60) cc_final: 0.2398 (t60) REVERT: C 561 ASN cc_start: 0.8699 (m110) cc_final: 0.8440 (m-40) REVERT: C 584 LEU cc_start: 0.8222 (mp) cc_final: 0.7983 (mp) REVERT: C 588 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8577 (mt) REVERT: C 611 LYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5676 (mmmt) REVERT: C 728 PHE cc_start: 0.7036 (m-80) cc_final: 0.6766 (m-80) REVERT: C 736 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7067 (mt-10) REVERT: C 743 LYS cc_start: 0.7209 (mtpp) cc_final: 0.6687 (tmtt) REVERT: D 74 GLN cc_start: 0.6528 (mm-40) cc_final: 0.5554 (mp10) REVERT: D 124 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.7094 (t80) REVERT: D 201 ASP cc_start: 0.7731 (t70) cc_final: 0.7433 (p0) REVERT: D 399 THR cc_start: 0.8426 (p) cc_final: 0.8070 (t) REVERT: D 450 PHE cc_start: 0.6835 (t80) cc_final: 0.6476 (t80) REVERT: D 542 PHE cc_start: 0.7538 (m-10) cc_final: 0.6243 (t80) REVERT: D 561 ASN cc_start: 0.8778 (m110) cc_final: 0.8496 (m-40) REVERT: D 572 MET cc_start: 0.8303 (tpp) cc_final: 0.8088 (tpp) REVERT: D 588 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8566 (mt) REVERT: D 611 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5648 (mmmt) REVERT: D 672 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6685 (ttp) REVERT: D 743 LYS cc_start: 0.7447 (mtpp) cc_final: 0.7009 (tmtt) outliers start: 104 outliers final: 66 residues processed: 352 average time/residue: 0.3028 time to fit residues: 170.7566 Evaluate side-chains 348 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 268 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 736 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 140 optimal weight: 0.0970 chunk 250 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 216 GLN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 394 ASN ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22204 Z= 0.123 Angle : 0.518 14.537 29968 Z= 0.252 Chirality : 0.037 0.133 3376 Planarity : 0.003 0.069 3708 Dihedral : 10.209 118.373 3156 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.53 % Allowed : 16.88 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.16), residues: 2608 helix: -0.29 (0.14), residues: 1440 sheet: -2.94 (0.54), residues: 88 loop : -1.66 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 481 HIS 0.003 0.001 HIS D 523 PHE 0.020 0.001 PHE C 590 TYR 0.018 0.001 TYR C 451 ARG 0.003 0.000 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 294 time to evaluate : 2.410 Fit side-chains REVERT: A 124 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7045 (t80) REVERT: A 133 GLU cc_start: 0.7804 (pt0) cc_final: 0.7293 (mm-30) REVERT: A 139 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.5999 (tt) REVERT: A 162 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6264 (mm) REVERT: A 180 ASN cc_start: 0.6405 (m-40) cc_final: 0.6140 (p0) REVERT: A 201 ASP cc_start: 0.7751 (t70) cc_final: 0.7502 (p0) REVERT: A 254 TYR cc_start: 0.6861 (m-80) cc_final: 0.6561 (m-80) REVERT: A 399 THR cc_start: 0.8334 (p) cc_final: 0.8055 (t) REVERT: A 450 PHE cc_start: 0.6700 (t80) cc_final: 0.6313 (t80) REVERT: A 542 PHE cc_start: 0.7690 (m-10) cc_final: 0.6294 (t80) REVERT: A 561 ASN cc_start: 0.8711 (m110) cc_final: 0.8359 (m110) REVERT: A 588 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8634 (mt) REVERT: A 611 LYS cc_start: 0.6234 (OUTLIER) cc_final: 0.5735 (mmmt) REVERT: A 743 LYS cc_start: 0.7212 (mtpp) cc_final: 0.6794 (tmtt) REVERT: B 62 PRO cc_start: 0.6433 (Cg_endo) cc_final: 0.6209 (Cg_exo) REVERT: B 124 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.7042 (t80) REVERT: B 201 ASP cc_start: 0.7407 (t70) cc_final: 0.7130 (p0) REVERT: B 399 THR cc_start: 0.8373 (p) cc_final: 0.8099 (t) REVERT: B 450 PHE cc_start: 0.6708 (t80) cc_final: 0.6310 (t80) REVERT: B 561 ASN cc_start: 0.8685 (m110) cc_final: 0.8323 (m110) REVERT: B 574 MET cc_start: 0.6315 (mmt) cc_final: 0.5791 (ppp) REVERT: B 588 LEU cc_start: 0.8993 (mm) cc_final: 0.8517 (mt) REVERT: B 611 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5737 (mmmt) REVERT: B 743 LYS cc_start: 0.7336 (mtpp) cc_final: 0.7070 (tmtt) REVERT: C 74 GLN cc_start: 0.5815 (mm110) cc_final: 0.5450 (mp10) REVERT: C 133 GLU cc_start: 0.7985 (pt0) cc_final: 0.7364 (mm-30) REVERT: C 135 LEU cc_start: 0.7656 (mm) cc_final: 0.7276 (tt) REVERT: C 139 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6500 (tt) REVERT: C 148 ARG cc_start: 0.5356 (mpt90) cc_final: 0.4907 (mmp80) REVERT: C 399 THR cc_start: 0.8288 (p) cc_final: 0.7971 (t) REVERT: C 450 PHE cc_start: 0.6809 (t80) cc_final: 0.6178 (t80) REVERT: C 479 MET cc_start: 0.3131 (mmm) cc_final: 0.2803 (mmp) REVERT: C 561 ASN cc_start: 0.8628 (m110) cc_final: 0.8283 (m110) REVERT: C 588 LEU cc_start: 0.9060 (mm) cc_final: 0.8648 (mt) REVERT: C 611 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5778 (mmmt) REVERT: C 728 PHE cc_start: 0.7003 (m-80) cc_final: 0.6798 (m-80) REVERT: C 736 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6997 (mt-10) REVERT: C 743 LYS cc_start: 0.7202 (mtpp) cc_final: 0.6782 (tmtt) REVERT: D 74 GLN cc_start: 0.6516 (mm-40) cc_final: 0.5651 (mp10) REVERT: D 124 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.7087 (t80) REVERT: D 201 ASP cc_start: 0.7725 (t70) cc_final: 0.7424 (p0) REVERT: D 399 THR cc_start: 0.8429 (p) cc_final: 0.8101 (t) REVERT: D 450 PHE cc_start: 0.6784 (t80) cc_final: 0.6407 (t80) REVERT: D 481 TRP cc_start: 0.1742 (t60) cc_final: 0.1536 (t60) REVERT: D 484 LEU cc_start: 0.5069 (OUTLIER) cc_final: 0.4173 (pt) REVERT: D 542 PHE cc_start: 0.7619 (m-10) cc_final: 0.6295 (t80) REVERT: D 561 ASN cc_start: 0.8728 (m110) cc_final: 0.8356 (m110) REVERT: D 588 LEU cc_start: 0.8996 (mm) cc_final: 0.8510 (mt) REVERT: D 611 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.5729 (mmmt) REVERT: D 743 LYS cc_start: 0.7386 (mtpp) cc_final: 0.6963 (tmtt) outliers start: 83 outliers final: 52 residues processed: 360 average time/residue: 0.3044 time to fit residues: 174.4237 Evaluate side-chains 348 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 284 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 736 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 180 ASN B 216 GLN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22204 Z= 0.280 Angle : 0.642 14.152 29968 Z= 0.316 Chirality : 0.042 0.157 3376 Planarity : 0.004 0.070 3708 Dihedral : 11.370 132.774 3156 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.25 % Allowed : 16.84 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.16), residues: 2608 helix: -0.59 (0.13), residues: 1484 sheet: -3.09 (0.53), residues: 88 loop : -1.85 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 481 HIS 0.006 0.001 HIS B 160 PHE 0.030 0.002 PHE A 590 TYR 0.022 0.002 TYR C 451 ARG 0.005 0.001 ARG D 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 285 time to evaluate : 2.317 Fit side-chains REVERT: A 133 GLU cc_start: 0.7888 (pt0) cc_final: 0.7460 (mm-30) REVERT: A 139 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6129 (tt) REVERT: A 162 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6225 (mm) REVERT: A 201 ASP cc_start: 0.7835 (t70) cc_final: 0.7521 (p0) REVERT: A 399 THR cc_start: 0.8339 (p) cc_final: 0.8011 (t) REVERT: A 450 PHE cc_start: 0.6704 (t80) cc_final: 0.6343 (t80) REVERT: A 542 PHE cc_start: 0.7690 (m-10) cc_final: 0.6278 (t80) REVERT: A 561 ASN cc_start: 0.8781 (m110) cc_final: 0.8506 (m-40) REVERT: A 588 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8556 (mt) REVERT: A 611 LYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5664 (mmmt) REVERT: A 743 LYS cc_start: 0.7291 (mtpp) cc_final: 0.6818 (tmtt) REVERT: B 62 PRO cc_start: 0.6547 (Cg_endo) cc_final: 0.6332 (Cg_exo) REVERT: B 124 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.7139 (t80) REVERT: B 193 PHE cc_start: 0.6686 (t80) cc_final: 0.6458 (t80) REVERT: B 201 ASP cc_start: 0.7427 (t70) cc_final: 0.7188 (p0) REVERT: B 399 THR cc_start: 0.8414 (p) cc_final: 0.8079 (t) REVERT: B 450 PHE cc_start: 0.6721 (t80) cc_final: 0.6318 (t80) REVERT: B 561 ASN cc_start: 0.8772 (m110) cc_final: 0.8501 (m-40) REVERT: B 574 MET cc_start: 0.6574 (mmt) cc_final: 0.5963 (ppp) REVERT: B 588 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8531 (mt) REVERT: B 611 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5647 (mmmt) REVERT: B 743 LYS cc_start: 0.7413 (mtpp) cc_final: 0.7041 (tmtt) REVERT: C 133 GLU cc_start: 0.8078 (pt0) cc_final: 0.7491 (mm-30) REVERT: C 135 LEU cc_start: 0.7582 (mm) cc_final: 0.7240 (tt) REVERT: C 139 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6526 (tt) REVERT: C 148 ARG cc_start: 0.5342 (mpt90) cc_final: 0.4903 (mmp80) REVERT: C 399 THR cc_start: 0.8370 (p) cc_final: 0.8010 (t) REVERT: C 450 PHE cc_start: 0.6731 (t80) cc_final: 0.6310 (t80) REVERT: C 479 MET cc_start: 0.3208 (mmm) cc_final: 0.2921 (mmp) REVERT: C 561 ASN cc_start: 0.8678 (m110) cc_final: 0.8389 (m-40) REVERT: C 584 LEU cc_start: 0.8309 (mp) cc_final: 0.8095 (mp) REVERT: C 588 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8561 (mt) REVERT: C 611 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5709 (mmmt) REVERT: C 711 LEU cc_start: 0.8023 (tp) cc_final: 0.7811 (tt) REVERT: C 728 PHE cc_start: 0.7235 (m-80) cc_final: 0.6890 (m-80) REVERT: C 734 ILE cc_start: 0.7448 (mp) cc_final: 0.7048 (tp) REVERT: C 743 LYS cc_start: 0.7166 (mtpp) cc_final: 0.6676 (tmtt) REVERT: D 74 GLN cc_start: 0.6559 (mm-40) cc_final: 0.5701 (mp10) REVERT: D 124 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.7151 (t80) REVERT: D 201 ASP cc_start: 0.7780 (t70) cc_final: 0.7459 (p0) REVERT: D 361 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7692 (mm) REVERT: D 399 THR cc_start: 0.8434 (p) cc_final: 0.8065 (t) REVERT: D 450 PHE cc_start: 0.6853 (t80) cc_final: 0.6506 (t80) REVERT: D 542 PHE cc_start: 0.7569 (m-10) cc_final: 0.6271 (t80) REVERT: D 561 ASN cc_start: 0.8796 (m110) cc_final: 0.8495 (m-40) REVERT: D 588 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8534 (mt) REVERT: D 611 LYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5653 (mmmt) REVERT: D 743 LYS cc_start: 0.7382 (mtpp) cc_final: 0.6921 (tmtt) outliers start: 100 outliers final: 71 residues processed: 361 average time/residue: 0.3019 time to fit residues: 173.7515 Evaluate side-chains 355 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 270 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 736 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 233 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 232 optimal weight: 0.0270 overall best weight: 2.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22204 Z= 0.188 Angle : 0.570 13.757 29968 Z= 0.280 Chirality : 0.039 0.145 3376 Planarity : 0.004 0.068 3708 Dihedral : 10.840 126.898 3156 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.87 % Allowed : 17.94 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2608 helix: -0.39 (0.14), residues: 1460 sheet: -2.88 (0.54), residues: 88 loop : -1.75 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 481 HIS 0.003 0.001 HIS B 523 PHE 0.027 0.001 PHE A 590 TYR 0.020 0.001 TYR C 451 ARG 0.003 0.000 ARG D 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 285 time to evaluate : 2.562 Fit side-chains REVERT: A 133 GLU cc_start: 0.7908 (pt0) cc_final: 0.7437 (mm-30) REVERT: A 139 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6232 (tt) REVERT: A 162 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6241 (mm) REVERT: A 180 ASN cc_start: 0.6443 (m-40) cc_final: 0.6222 (p0) REVERT: A 201 ASP cc_start: 0.7827 (t70) cc_final: 0.7528 (p0) REVERT: A 399 THR cc_start: 0.8269 (p) cc_final: 0.7956 (t) REVERT: A 450 PHE cc_start: 0.6722 (t80) cc_final: 0.6347 (t80) REVERT: A 542 PHE cc_start: 0.7662 (m-10) cc_final: 0.6241 (t80) REVERT: A 561 ASN cc_start: 0.8745 (m110) cc_final: 0.8419 (m110) REVERT: A 588 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8552 (mt) REVERT: A 611 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5717 (mmmt) REVERT: A 743 LYS cc_start: 0.7151 (mtpp) cc_final: 0.6735 (tmtt) REVERT: B 62 PRO cc_start: 0.6559 (Cg_endo) cc_final: 0.6354 (Cg_exo) REVERT: B 124 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7244 (t80) REVERT: B 193 PHE cc_start: 0.6733 (t80) cc_final: 0.6530 (t80) REVERT: B 201 ASP cc_start: 0.7453 (t70) cc_final: 0.7208 (p0) REVERT: B 399 THR cc_start: 0.8382 (p) cc_final: 0.8060 (t) REVERT: B 450 PHE cc_start: 0.6723 (t80) cc_final: 0.6314 (t80) REVERT: B 561 ASN cc_start: 0.8715 (m110) cc_final: 0.8382 (m110) REVERT: B 574 MET cc_start: 0.6486 (mmt) cc_final: 0.5804 (ppp) REVERT: B 588 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8516 (mt) REVERT: B 611 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5683 (mmmt) REVERT: B 743 LYS cc_start: 0.7320 (mtpp) cc_final: 0.7019 (tmtt) REVERT: C 133 GLU cc_start: 0.8022 (pt0) cc_final: 0.7421 (mm-30) REVERT: C 135 LEU cc_start: 0.7576 (mm) cc_final: 0.7248 (tt) REVERT: C 139 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6525 (tt) REVERT: C 148 ARG cc_start: 0.5269 (mpt90) cc_final: 0.4840 (mmp80) REVERT: C 399 THR cc_start: 0.8368 (p) cc_final: 0.8021 (t) REVERT: C 450 PHE cc_start: 0.6691 (t80) cc_final: 0.6265 (t80) REVERT: C 479 MET cc_start: 0.3468 (mmm) cc_final: 0.3153 (mmp) REVERT: C 561 ASN cc_start: 0.8630 (m110) cc_final: 0.8296 (m110) REVERT: C 574 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6270 (ppp) REVERT: C 588 LEU cc_start: 0.9014 (mm) cc_final: 0.8595 (mt) REVERT: C 611 LYS cc_start: 0.6301 (OUTLIER) cc_final: 0.5719 (mmmt) REVERT: C 711 LEU cc_start: 0.7968 (tp) cc_final: 0.7761 (tt) REVERT: C 728 PHE cc_start: 0.7205 (m-80) cc_final: 0.6862 (m-80) REVERT: C 734 ILE cc_start: 0.7604 (mp) cc_final: 0.7073 (tp) REVERT: C 743 LYS cc_start: 0.7189 (mtpp) cc_final: 0.6712 (tmtt) REVERT: D 74 GLN cc_start: 0.6506 (mm-40) cc_final: 0.5636 (mp10) REVERT: D 124 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7166 (t80) REVERT: D 163 THR cc_start: 0.7444 (p) cc_final: 0.7221 (p) REVERT: D 201 ASP cc_start: 0.7773 (t70) cc_final: 0.7451 (p0) REVERT: D 361 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7641 (mm) REVERT: D 399 THR cc_start: 0.8424 (p) cc_final: 0.8074 (t) REVERT: D 450 PHE cc_start: 0.6840 (t80) cc_final: 0.6497 (t80) REVERT: D 542 PHE cc_start: 0.7614 (m-10) cc_final: 0.6295 (t80) REVERT: D 561 ASN cc_start: 0.8724 (m110) cc_final: 0.8387 (m110) REVERT: D 588 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8515 (mt) REVERT: D 611 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5674 (mmmt) REVERT: D 743 LYS cc_start: 0.7290 (mtpp) cc_final: 0.6832 (tmtt) outliers start: 91 outliers final: 66 residues processed: 351 average time/residue: 0.3004 time to fit residues: 168.4901 Evaluate side-chains 357 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 277 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 736 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 171 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22204 Z= 0.194 Angle : 0.572 13.417 29968 Z= 0.281 Chirality : 0.039 0.146 3376 Planarity : 0.004 0.066 3708 Dihedral : 10.803 126.370 3156 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.61 % Allowed : 18.15 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2608 helix: -0.30 (0.14), residues: 1460 sheet: -2.93 (0.54), residues: 88 loop : -1.78 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 481 HIS 0.003 0.001 HIS C 471 PHE 0.028 0.001 PHE A 590 TYR 0.020 0.001 TYR C 451 ARG 0.004 0.000 ARG D 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 286 time to evaluate : 2.688 Fit side-chains REVERT: A 133 GLU cc_start: 0.7839 (pt0) cc_final: 0.7351 (mm-30) REVERT: A 139 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6270 (tt) REVERT: A 162 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6260 (mm) REVERT: A 201 ASP cc_start: 0.7835 (t70) cc_final: 0.7537 (p0) REVERT: A 399 THR cc_start: 0.8299 (p) cc_final: 0.7994 (t) REVERT: A 450 PHE cc_start: 0.6705 (t80) cc_final: 0.6323 (t80) REVERT: A 542 PHE cc_start: 0.7689 (m-10) cc_final: 0.6271 (t80) REVERT: A 561 ASN cc_start: 0.8727 (m110) cc_final: 0.8390 (m110) REVERT: A 588 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8558 (mt) REVERT: A 611 LYS cc_start: 0.6215 (OUTLIER) cc_final: 0.5737 (mmmt) REVERT: A 743 LYS cc_start: 0.7170 (mtpp) cc_final: 0.6729 (tmtt) REVERT: B 201 ASP cc_start: 0.7492 (t70) cc_final: 0.7248 (p0) REVERT: B 399 THR cc_start: 0.8316 (p) cc_final: 0.8003 (t) REVERT: B 450 PHE cc_start: 0.6699 (t80) cc_final: 0.6288 (t80) REVERT: B 561 ASN cc_start: 0.8701 (m110) cc_final: 0.8375 (m110) REVERT: B 574 MET cc_start: 0.6551 (mmt) cc_final: 0.5783 (ppp) REVERT: B 588 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8530 (mt) REVERT: B 611 LYS cc_start: 0.6218 (OUTLIER) cc_final: 0.5714 (mmmt) REVERT: B 743 LYS cc_start: 0.7268 (mtpp) cc_final: 0.6972 (tmtt) REVERT: C 133 GLU cc_start: 0.8009 (pt0) cc_final: 0.7383 (mm-30) REVERT: C 135 LEU cc_start: 0.7587 (mm) cc_final: 0.7104 (tt) REVERT: C 148 ARG cc_start: 0.5252 (mpt90) cc_final: 0.4848 (mmp80) REVERT: C 399 THR cc_start: 0.8369 (p) cc_final: 0.8019 (t) REVERT: C 450 PHE cc_start: 0.6678 (t80) cc_final: 0.6260 (t80) REVERT: C 479 MET cc_start: 0.3290 (mmm) cc_final: 0.2910 (mmp) REVERT: C 561 ASN cc_start: 0.8677 (m110) cc_final: 0.8354 (m110) REVERT: C 578 MET cc_start: 0.7362 (mtt) cc_final: 0.6970 (mtt) REVERT: C 588 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8597 (mt) REVERT: C 611 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5696 (mmmt) REVERT: C 728 PHE cc_start: 0.7199 (m-80) cc_final: 0.6833 (m-80) REVERT: C 734 ILE cc_start: 0.7288 (mp) cc_final: 0.7074 (tp) REVERT: C 743 LYS cc_start: 0.7159 (mtpp) cc_final: 0.6679 (tmtt) REVERT: D 74 GLN cc_start: 0.6451 (mm-40) cc_final: 0.5588 (mp10) REVERT: D 124 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7170 (t80) REVERT: D 201 ASP cc_start: 0.7792 (t70) cc_final: 0.7482 (p0) REVERT: D 361 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7645 (mm) REVERT: D 399 THR cc_start: 0.8427 (p) cc_final: 0.8085 (t) REVERT: D 450 PHE cc_start: 0.6827 (t80) cc_final: 0.6492 (t80) REVERT: D 542 PHE cc_start: 0.7616 (m-10) cc_final: 0.6296 (t80) REVERT: D 561 ASN cc_start: 0.8737 (m110) cc_final: 0.8394 (m110) REVERT: D 575 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6971 (t80) REVERT: D 588 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8527 (mt) REVERT: D 611 LYS cc_start: 0.6220 (OUTLIER) cc_final: 0.5751 (mmmt) REVERT: D 743 LYS cc_start: 0.7358 (mtpp) cc_final: 0.6825 (tmtt) outliers start: 85 outliers final: 67 residues processed: 350 average time/residue: 0.3063 time to fit residues: 170.9316 Evaluate side-chains 359 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 279 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 736 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 206 optimal weight: 0.0010 chunk 86 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.130125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.098699 restraints weight = 43446.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101511 restraints weight = 28084.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103402 restraints weight = 21541.870| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22204 Z= 0.195 Angle : 0.568 13.249 29968 Z= 0.280 Chirality : 0.039 0.144 3376 Planarity : 0.004 0.084 3708 Dihedral : 10.792 126.497 3156 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.83 % Allowed : 18.20 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.47 (0.16), residues: 2608 helix: -0.25 (0.14), residues: 1456 sheet: -2.88 (0.54), residues: 88 loop : -1.75 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 481 HIS 0.003 0.001 HIS A 160 PHE 0.027 0.001 PHE A 590 TYR 0.020 0.001 TYR C 451 ARG 0.003 0.000 ARG D 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4345.86 seconds wall clock time: 80 minutes 3.07 seconds (4803.07 seconds total)