Starting phenix.real_space_refine on Fri Sep 19 01:04:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mil_23855/09_2025/7mil_23855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mil_23855/09_2025/7mil_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mil_23855/09_2025/7mil_23855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mil_23855/09_2025/7mil_23855.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mil_23855/09_2025/7mil_23855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mil_23855/09_2025/7mil_23855.map" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.13, per 1000 atoms: 0.24 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 878.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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... Secondary structure from input PDB file: 128 helices and 8 sheets defined 63.0% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 114 through 130 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 131 through 146 removed outlier: 3.838A pdb=" N LEU A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) 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 153 through 163 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.844A pdb=" N LYS A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.572A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.856A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.759A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.610A pdb=" N THR A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.606A pdb=" N THR A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 removed outlier: 4.087A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.799A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 315 through 329 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 331 through 336 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.813A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.571A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 434 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) removed outlier: 3.725A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.683A pdb=" N MET A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) 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 486 through 507 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 511 through 515 removed outlier: 3.774A pdb=" N GLN A 514 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 515 " --> pdb=" O ASP A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 515' Processing helix chain 'A' and resid 521 through 542 removed outlier: 3.547A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) 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) removed outlier: 3.926A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 4.112A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 569 removed outlier: 3.558A pdb=" N TYR A 565 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 569 " --> pdb=" O THR A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 569' Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.849A pdb=" N SER A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) 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) removed outlier: 3.762A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 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) Processing helix chain 'A' and resid 624 through 638 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 650 through 666 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 686 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) removed outlier: 3.761A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 706 removed outlier: 3.668A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) 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 708 through 715 removed outlier: 3.663A pdb=" N PHE A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 751 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) removed outlier: 4.001A pdb=" N GLU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 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 131 through 146 removed outlier: 3.839A pdb=" N LEU B 135 " --> pdb=" O CYS B 131 " (cutoff:3.500A) 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 153 through 163 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.844A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.572A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.856A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.759A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.611A pdb=" N THR B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.606A pdb=" N THR B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 removed outlier: 4.087A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.800A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 315 through 329 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 331 through 336 Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.812A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.572A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 434 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) removed outlier: 3.725A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.683A pdb=" N MET B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) 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 486 through 507 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 511 through 515 removed outlier: 3.773A pdb=" N GLN B 514 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 515 " --> pdb=" O ASP B 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 515' Processing helix chain 'B' and resid 521 through 542 removed outlier: 3.546A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) 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) removed outlier: 3.926A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 4.112A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 569 removed outlier: 3.558A pdb=" N TYR B 565 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 569 " --> pdb=" O THR B 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 562 through 569' Processing helix chain 'B' and resid 572 through 584 removed outlier: 3.850A pdb=" N SER B 576 " --> pdb=" O MET B 572 " (cutoff:3.500A) 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) removed outlier: 3.762A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 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) Processing helix chain 'B' and resid 624 through 638 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 650 through 666 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 686 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) removed outlier: 3.762A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 706 removed outlier: 3.668A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) 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 708 through 715 removed outlier: 3.663A pdb=" N PHE B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 751 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) removed outlier: 4.000A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 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 131 through 146 removed outlier: 3.838A pdb=" N LEU C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) 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 153 through 163 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.844A pdb=" N LYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.572A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.857A pdb=" N ASN C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.758A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.610A pdb=" N THR C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.606A pdb=" N THR C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 removed outlier: 4.087A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.798A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) 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) Processing helix chain 'C' and resid 315 through 329 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 331 through 336 Processing helix chain 'C' and resid 345 through 352 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.813A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.572A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 434 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) removed outlier: 3.725A pdb=" N LYS C 434 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.683A pdb=" N MET C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) 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 486 through 507 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 511 through 515 removed outlier: 3.773A pdb=" N GLN C 514 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER C 515 " --> pdb=" O ASP C 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 511 through 515' Processing helix chain 'C' and resid 521 through 542 removed outlier: 3.547A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) 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) removed outlier: 3.926A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 4.112A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 569 removed outlier: 3.559A pdb=" N TYR C 565 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 569 " --> pdb=" O THR C 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 562 through 569' Processing helix chain 'C' and resid 572 through 584 removed outlier: 3.850A pdb=" N SER C 576 " --> pdb=" O MET C 572 " (cutoff:3.500A) 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) removed outlier: 3.761A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 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) Processing helix chain 'C' and resid 624 through 638 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 650 through 666 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 686 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) removed outlier: 3.761A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 706 removed outlier: 3.668A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) 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 708 through 715 removed outlier: 3.662A pdb=" N PHE C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 751 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) removed outlier: 4.001A pdb=" N GLU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 130 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 131 through 146 removed outlier: 3.839A pdb=" N LEU D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) 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 153 through 163 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.844A pdb=" N LYS D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.573A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.856A pdb=" N ASN D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.758A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.610A pdb=" N THR D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.606A pdb=" N THR D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 removed outlier: 4.087A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.800A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) 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) Processing helix chain 'D' and resid 315 through 329 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 331 through 336 Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.813A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.571A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 434 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) removed outlier: 3.725A pdb=" N LYS D 434 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.683A pdb=" N MET D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) 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 486 through 507 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 511 through 515 removed outlier: 3.774A pdb=" N GLN D 514 " --> pdb=" O SER D 511 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER D 515 " --> pdb=" O ASP D 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 511 through 515' Processing helix chain 'D' and resid 521 through 542 removed outlier: 3.547A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) 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) removed outlier: 3.926A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 4.112A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 569 removed outlier: 3.559A pdb=" N TYR D 565 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE D 569 " --> pdb=" O THR D 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 562 through 569' Processing helix chain 'D' and resid 572 through 584 removed outlier: 3.849A pdb=" N SER D 576 " --> pdb=" O MET D 572 " (cutoff:3.500A) 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) removed outlier: 3.762A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 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) Processing helix chain 'D' and resid 624 through 638 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 650 through 666 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 686 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) removed outlier: 3.762A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 706 removed outlier: 3.668A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) 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 708 through 715 removed outlier: 3.662A pdb=" N PHE D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 751 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) removed outlier: 4.000A pdb=" N GLU D 751 " --> pdb=" O SER D 747 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 3.862A pdb=" N ARG A 73 " --> pdb=" O LYS B 722 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 719 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 382 removed outlier: 5.788A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 729 through 731 removed outlier: 3.571A pdb=" N GLU A 719 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 73 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 removed outlier: 3.909A pdb=" N ARG B 73 " --> pdb=" O LYS C 722 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 722 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 719 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 376 through 382 removed outlier: 5.789A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 73 through 74 removed outlier: 3.571A pdb=" N GLU D 719 " --> pdb=" O CYS D 731 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 376 through 382 removed outlier: 5.789A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 376 through 382 removed outlier: 5.790A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 2.45 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: 0.00 - 3.89: 29579 3.89 - 7.79: 317 7.79 - 11.68: 55 11.68 - 15.57: 13 15.57 - 19.47: 4 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: 6500 2.82 - 3.34: 19100 3.34 - 3.86: 32240 3.86 - 4.38: 37863 4.38 - 4.90: 64477 Nonbonded interactions: 160180 Sorted by model distance: nonbonded pdb=" OD1 ASP A 322 " pdb=" OH TYR A 359 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASP C 322 " pdb=" OH TYR C 359 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASP D 322 " pdb=" OH TYR D 359 " model vdw 2.305 3.040 nonbonded pdb=" OD1 ASP B 322 " pdb=" OH TYR B 359 " model vdw 2.305 3.040 nonbonded pdb=" OG SER C 620 " pdb=" NE2 GLN C 646 " model vdw 2.319 3.120 ... (remaining 160175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 59 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.870 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- 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 22212 Z= 0.312 Angle : 1.169 19.467 29984 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.009 0.001 ARG B 567 TYR 0.013 0.002 TYR C 544 PHE 0.018 0.002 PHE D 316 TRP 0.011 0.002 TRP C 742 HIS 0.006 0.002 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00665 (22204) covalent geometry : angle 1.16935 (29968) SS BOND : bond 0.00430 ( 8) SS BOND : angle 0.59455 ( 16) hydrogen bonds : bond 0.34118 ( 780) hydrogen bonds : angle 9.35356 ( 2313) *********************** 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 to be fit. rotamer outliers: 16 poor density : 621 time to evaluate : 0.859 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: 0.1744 time to fit residues: 166.4044 Evaluate side-chains 342 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 336 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.1980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.0770 chunk 258 optimal weight: 5.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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** A 346 GLN A 394 ASN ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 683 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 C 180 ASN C 182 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** C 646 GLN C 683 ASN C 735 ASN D 178 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.138611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108768 restraints weight = 42362.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111925 restraints weight = 26175.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113991 restraints weight = 19403.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115366 restraints weight = 16032.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116123 restraints weight = 14176.994| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22212 Z= 0.112 Angle : 0.625 10.957 29984 Z= 0.315 Chirality : 0.039 0.136 3376 Planarity : 0.004 0.050 3708 Dihedral : 12.049 109.392 3160 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.30 % Allowed : 11.99 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.96 (0.13), residues: 2608 helix: -2.79 (0.09), residues: 1496 sheet: -3.52 (0.47), residues: 88 loop : -1.98 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 690 TYR 0.018 0.001 TYR D 208 PHE 0.024 0.001 PHE A 489 TRP 0.016 0.001 TRP D 739 HIS 0.004 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00229 (22204) covalent geometry : angle 0.62448 (29968) SS BOND : bond 0.00236 ( 8) SS BOND : angle 1.08829 ( 16) hydrogen bonds : bond 0.04645 ( 780) hydrogen bonds : angle 4.58959 ( 2313) *********************** 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 454 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 400 time to evaluate : 0.970 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: A 62 PRO cc_start: 0.6290 (Cg_endo) cc_final: 0.6065 (Cg_exo) REVERT: A 133 GLU cc_start: 0.7689 (pt0) cc_final: 0.7279 (mm-30) REVERT: A 201 ASP cc_start: 0.7410 (t70) cc_final: 0.7142 (p0) REVERT: A 399 THR cc_start: 0.8216 (p) cc_final: 0.7909 (t) REVERT: A 450 PHE cc_start: 0.7040 (t80) cc_final: 0.6528 (t80) REVERT: A 479 MET cc_start: 0.3849 (mmm) cc_final: 0.3533 (mmp) REVERT: A 484 LEU cc_start: 0.4326 (OUTLIER) cc_final: 0.3773 (mt) REVERT: A 491 LEU cc_start: 0.7601 (mt) cc_final: 0.7399 (tp) REVERT: A 493 TRP cc_start: 0.7300 (t-100) cc_final: 0.6811 (t-100) REVERT: A 542 PHE cc_start: 0.7266 (m-10) cc_final: 0.6199 (t80) REVERT: A 561 ASN cc_start: 0.8808 (m110) cc_final: 0.8418 (m110) REVERT: A 581 LYS cc_start: 0.8359 (mmmm) cc_final: 0.8014 (mmtt) REVERT: A 588 LEU cc_start: 0.9099 (mm) cc_final: 0.8675 (mt) REVERT: A 611 LYS cc_start: 0.6154 (OUTLIER) cc_final: 0.5841 (mmmt) REVERT: A 743 LYS cc_start: 0.7298 (mtpp) cc_final: 0.7041 (tmtt) REVERT: B 159 MET cc_start: 0.5800 (tpp) cc_final: 0.5506 (tpt) REVERT: B 282 MET cc_start: 0.7011 (mtp) cc_final: 0.6729 (mtp) REVERT: B 379 ASP cc_start: 0.6408 (p0) cc_final: 0.6161 (t0) REVERT: B 399 THR cc_start: 0.8243 (p) cc_final: 0.7863 (t) REVERT: B 420 LEU cc_start: 0.7625 (mt) cc_final: 0.7394 (mt) REVERT: B 450 PHE cc_start: 0.7125 (t80) cc_final: 0.6406 (t80) REVERT: B 484 LEU cc_start: 0.4321 (OUTLIER) cc_final: 0.3782 (mt) REVERT: B 493 TRP cc_start: 0.7315 (t-100) cc_final: 0.6808 (t-100) REVERT: B 542 PHE cc_start: 0.7098 (m-10) cc_final: 0.5540 (t80) REVERT: B 561 ASN cc_start: 0.8798 (m110) cc_final: 0.8362 (m110) REVERT: B 588 LEU cc_start: 0.9067 (mm) cc_final: 0.8677 (mt) REVERT: B 611 LYS cc_start: 0.6167 (OUTLIER) cc_final: 0.5842 (mmmt) REVERT: C 120 LYS cc_start: 0.7970 (mtmp) cc_final: 0.7725 (mtmt) REVERT: C 133 GLU cc_start: 0.8065 (pt0) cc_final: 0.7376 (mm-30) REVERT: C 399 THR cc_start: 0.8194 (p) cc_final: 0.7871 (t) REVERT: C 450 PHE cc_start: 0.6993 (t80) cc_final: 0.6643 (t80) REVERT: C 479 MET cc_start: 0.4074 (mmm) cc_final: 0.3772 (mmp) REVERT: C 484 LEU cc_start: 0.5470 (OUTLIER) cc_final: 0.5117 (mt) REVERT: C 561 ASN cc_start: 0.8809 (m110) cc_final: 0.8587 (m-40) REVERT: C 588 LEU cc_start: 0.9050 (mm) cc_final: 0.8617 (mt) REVERT: C 611 LYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5673 (mmmt) REVERT: C 627 ASP cc_start: 0.7392 (m-30) cc_final: 0.7118 (m-30) REVERT: C 743 LYS cc_start: 0.6990 (mtpp) cc_final: 0.6672 (tmtt) REVERT: D 147 ARG cc_start: 0.4951 (mpt-90) cc_final: 0.4312 (ttp80) REVERT: D 201 ASP cc_start: 0.7236 (t70) cc_final: 0.6788 (p0) REVERT: D 240 ASP cc_start: 0.7568 (m-30) cc_final: 0.6955 (p0) REVERT: D 379 ASP cc_start: 0.6390 (p0) cc_final: 0.5911 (t0) REVERT: D 399 THR cc_start: 0.8178 (p) cc_final: 0.7854 (t) REVERT: D 542 PHE cc_start: 0.7163 (m-10) cc_final: 0.5786 (t80) REVERT: D 561 ASN cc_start: 0.8885 (m110) cc_final: 0.8462 (m110) REVERT: D 588 LEU cc_start: 0.9082 (mm) cc_final: 0.8673 (mt) REVERT: D 611 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5939 (mmmt) REVERT: D 711 LEU cc_start: 0.7593 (tp) cc_final: 0.7303 (tt) REVERT: D 716 ARG cc_start: 0.7347 (tpp-160) cc_final: 0.7108 (tpp-160) REVERT: D 717 MET cc_start: 0.7841 (mtp) cc_final: 0.7626 (mtt) REVERT: D 743 LYS cc_start: 0.7434 (mtpp) cc_final: 0.7053 (tmtt) outliers start: 54 outliers final: 16 residues processed: 439 average time/residue: 0.1533 time to fit residues: 106.1022 Evaluate side-chains 336 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 313 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 484 LEU 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 736 GLU 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 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 481 TRP 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 177 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 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** C 585 HIS D 160 HIS D 216 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.132998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.102530 restraints weight = 42238.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105448 restraints weight = 26678.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107352 restraints weight = 20142.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108609 restraints weight = 16895.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109412 restraints weight = 15111.031| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22212 Z= 0.151 Angle : 0.648 11.368 29984 Z= 0.320 Chirality : 0.041 0.155 3376 Planarity : 0.004 0.054 3708 Dihedral : 11.920 131.879 3156 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.23 % Allowed : 13.86 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.15), residues: 2608 helix: -1.68 (0.12), residues: 1492 sheet: -2.77 (0.47), residues: 108 loop : -1.65 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.025 0.002 TYR C 451 PHE 0.024 0.001 PHE B 590 TRP 0.021 0.001 TRP D 481 HIS 0.004 0.001 HIS D 523 Details of bonding type rmsd covalent geometry : bond 0.00341 (22204) covalent geometry : angle 0.64735 (29968) SS BOND : bond 0.00292 ( 8) SS BOND : angle 0.93694 ( 16) hydrogen bonds : bond 0.04679 ( 780) hydrogen bonds : angle 4.40306 ( 2313) *********************** 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 400 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 324 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7710 (pt0) cc_final: 0.7252 (mm-30) REVERT: A 139 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5618 (tt) REVERT: A 229 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.6232 (m-30) REVERT: A 399 THR cc_start: 0.8254 (p) cc_final: 0.7946 (t) REVERT: A 450 PHE cc_start: 0.6840 (t80) cc_final: 0.6383 (t80) REVERT: A 479 MET cc_start: 0.4059 (mmm) cc_final: 0.3711 (mmp) REVERT: A 482 LEU cc_start: 0.5528 (OUTLIER) cc_final: 0.5140 (mp) REVERT: A 493 TRP cc_start: 0.7373 (t-100) cc_final: 0.6924 (t-100) REVERT: A 542 PHE cc_start: 0.7384 (m-10) cc_final: 0.6416 (t80) REVERT: A 561 ASN cc_start: 0.8772 (m110) cc_final: 0.8408 (m110) REVERT: A 588 LEU cc_start: 0.9085 (mm) cc_final: 0.8631 (mt) REVERT: A 611 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5864 (mmmt) REVERT: A 743 LYS cc_start: 0.7312 (mtpp) cc_final: 0.7052 (tmtt) REVERT: B 159 MET cc_start: 0.5786 (tpp) cc_final: 0.5528 (tpt) REVERT: B 201 ASP cc_start: 0.7299 (t70) cc_final: 0.6842 (p0) REVERT: B 399 THR cc_start: 0.8422 (p) cc_final: 0.8048 (t) REVERT: B 450 PHE cc_start: 0.6831 (t80) cc_final: 0.6288 (t80) REVERT: B 493 TRP cc_start: 0.7421 (t-100) cc_final: 0.6700 (t-100) REVERT: B 542 PHE cc_start: 0.7347 (m-10) cc_final: 0.5760 (t80) REVERT: B 561 ASN cc_start: 0.8738 (m110) cc_final: 0.8366 (m110) REVERT: B 588 LEU cc_start: 0.9040 (mm) cc_final: 0.8590 (mt) REVERT: B 611 LYS cc_start: 0.6278 (OUTLIER) cc_final: 0.5848 (mmmt) REVERT: C 120 LYS cc_start: 0.7974 (mtmp) cc_final: 0.7728 (mtmt) REVERT: C 133 GLU cc_start: 0.8083 (pt0) cc_final: 0.7328 (mm-30) REVERT: C 148 ARG cc_start: 0.5636 (mpt90) cc_final: 0.4966 (mmp80) REVERT: C 399 THR cc_start: 0.8240 (p) cc_final: 0.7910 (t) REVERT: C 450 PHE cc_start: 0.6870 (t80) cc_final: 0.6306 (t80) REVERT: C 479 MET cc_start: 0.3831 (mmm) cc_final: 0.3488 (mmp) REVERT: C 561 ASN cc_start: 0.8734 (m110) cc_final: 0.8362 (m110) REVERT: C 578 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6740 (mtt) REVERT: C 588 LEU cc_start: 0.9080 (mm) cc_final: 0.8623 (mt) REVERT: C 611 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5731 (mmmt) REVERT: C 728 PHE cc_start: 0.6777 (m-80) cc_final: 0.6511 (m-80) REVERT: C 743 LYS cc_start: 0.7209 (mtpp) cc_final: 0.6896 (tmtt) REVERT: D 147 ARG cc_start: 0.4931 (mpt-90) cc_final: 0.4260 (ttp80) REVERT: D 201 ASP cc_start: 0.7494 (t70) cc_final: 0.7120 (p0) REVERT: D 240 ASP cc_start: 0.8043 (m-30) cc_final: 0.7191 (p0) REVERT: D 254 TYR cc_start: 0.7011 (m-80) cc_final: 0.6722 (m-80) REVERT: D 399 THR cc_start: 0.8273 (p) cc_final: 0.7932 (t) REVERT: D 493 TRP cc_start: 0.7360 (t-100) cc_final: 0.6799 (t-100) REVERT: D 542 PHE cc_start: 0.7473 (m-10) cc_final: 0.6303 (t80) REVERT: D 561 ASN cc_start: 0.8826 (m110) cc_final: 0.8469 (m-40) REVERT: D 588 LEU cc_start: 0.9079 (mm) cc_final: 0.8617 (mt) REVERT: D 611 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5921 (mmmt) REVERT: D 716 ARG cc_start: 0.7305 (tpp-160) cc_final: 0.6963 (tpp80) REVERT: D 743 LYS cc_start: 0.7511 (mtpp) cc_final: 0.7135 (tmtt) outliers start: 76 outliers final: 39 residues processed: 382 average time/residue: 0.1464 time to fit residues: 89.5792 Evaluate side-chains 335 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 229 ASP 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 482 LEU 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 740 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 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 636 THR 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 396 ASP Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 663 ILE 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 312 THR 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 636 THR Chi-restraints excluded: chain D residue 673 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 252 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 24 optimal weight: 0.0010 chunk 226 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 223 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- 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** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 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 216 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100799 restraints weight = 42525.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103675 restraints weight = 27139.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105569 restraints weight = 20689.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106787 restraints weight = 17419.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107486 restraints weight = 15661.293| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22212 Z= 0.165 Angle : 0.641 11.328 29984 Z= 0.319 Chirality : 0.042 0.154 3376 Planarity : 0.004 0.063 3708 Dihedral : 11.743 130.824 3156 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.00 % Allowed : 14.24 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.15), residues: 2608 helix: -1.24 (0.12), residues: 1500 sheet: -2.62 (0.49), residues: 108 loop : -1.64 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 567 TYR 0.021 0.002 TYR C 451 PHE 0.020 0.002 PHE A 590 TRP 0.024 0.001 TRP C 481 HIS 0.005 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00378 (22204) covalent geometry : angle 0.64093 (29968) SS BOND : bond 0.00267 ( 8) SS BOND : angle 0.91594 ( 16) hydrogen bonds : bond 0.04444 ( 780) hydrogen bonds : angle 4.33474 ( 2313) *********************** 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 400 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 306 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7645 (pt0) cc_final: 0.7279 (mm-30) REVERT: A 180 ASN cc_start: 0.6383 (m-40) cc_final: 0.6070 (p0) REVERT: A 229 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6228 (m-30) REVERT: A 399 THR cc_start: 0.8337 (p) cc_final: 0.8005 (t) REVERT: A 450 PHE cc_start: 0.6852 (t80) cc_final: 0.6380 (t80) REVERT: A 479 MET cc_start: 0.4006 (mmm) cc_final: 0.3674 (mmp) REVERT: A 493 TRP cc_start: 0.7429 (t-100) cc_final: 0.6826 (t-100) REVERT: A 542 PHE cc_start: 0.7695 (m-10) cc_final: 0.6481 (t80) REVERT: A 561 ASN cc_start: 0.8696 (m110) cc_final: 0.8294 (m110) REVERT: A 588 LEU cc_start: 0.9043 (mm) cc_final: 0.8578 (mt) REVERT: A 611 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5684 (mmmt) REVERT: A 743 LYS cc_start: 0.7262 (mtpp) cc_final: 0.6901 (tmtt) REVERT: B 162 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5804 (mm) REVERT: B 163 THR cc_start: 0.7793 (p) cc_final: 0.7560 (p) REVERT: B 201 ASP cc_start: 0.7315 (t70) cc_final: 0.6996 (p0) REVERT: B 320 MET cc_start: 0.8270 (mmm) cc_final: 0.7921 (mmt) REVERT: B 399 THR cc_start: 0.8469 (p) cc_final: 0.8139 (t) REVERT: B 450 PHE cc_start: 0.6832 (t80) cc_final: 0.6402 (t80) REVERT: B 542 PHE cc_start: 0.7423 (m-10) cc_final: 0.5803 (t80) REVERT: B 561 ASN cc_start: 0.8722 (m110) cc_final: 0.8345 (m110) REVERT: B 584 LEU cc_start: 0.8221 (mp) cc_final: 0.8011 (mp) REVERT: B 588 LEU cc_start: 0.9020 (mm) cc_final: 0.8544 (mt) REVERT: B 611 LYS cc_start: 0.6177 (OUTLIER) cc_final: 0.5691 (mmmt) REVERT: C 133 GLU cc_start: 0.8068 (pt0) cc_final: 0.7402 (mm-30) REVERT: C 139 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6182 (tp) REVERT: C 148 ARG cc_start: 0.5590 (mpt90) cc_final: 0.4908 (mmp80) REVERT: C 399 THR cc_start: 0.8276 (p) cc_final: 0.7951 (t) REVERT: C 479 MET cc_start: 0.3572 (mmm) cc_final: 0.3232 (mmp) REVERT: C 484 LEU cc_start: 0.5235 (mt) cc_final: 0.4849 (mt) REVERT: C 561 ASN cc_start: 0.8736 (m110) cc_final: 0.8348 (m110) REVERT: C 588 LEU cc_start: 0.9039 (mm) cc_final: 0.8573 (mt) REVERT: C 611 LYS cc_start: 0.6162 (OUTLIER) cc_final: 0.5675 (mmmt) REVERT: C 728 PHE cc_start: 0.6974 (m-80) cc_final: 0.6750 (m-80) REVERT: C 743 LYS cc_start: 0.7320 (mtpp) cc_final: 0.6849 (tmtt) REVERT: D 201 ASP cc_start: 0.7472 (t70) cc_final: 0.7236 (p0) REVERT: D 254 TYR cc_start: 0.7006 (m-80) cc_final: 0.6794 (m-80) REVERT: D 399 THR cc_start: 0.8399 (p) cc_final: 0.8060 (t) REVERT: D 493 TRP cc_start: 0.7399 (t-100) cc_final: 0.6871 (t-100) REVERT: D 542 PHE cc_start: 0.7448 (m-10) cc_final: 0.6336 (t80) REVERT: D 561 ASN cc_start: 0.8791 (m110) cc_final: 0.8405 (m110) REVERT: D 572 MET cc_start: 0.8349 (tpp) cc_final: 0.8140 (tpp) REVERT: D 584 LEU cc_start: 0.8150 (mp) cc_final: 0.7942 (mp) REVERT: D 588 LEU cc_start: 0.9036 (mm) cc_final: 0.8546 (mt) REVERT: D 611 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5772 (mmmt) REVERT: D 743 LYS cc_start: 0.7482 (mtpp) cc_final: 0.7092 (tmtt) outliers start: 94 outliers final: 54 residues processed: 380 average time/residue: 0.1409 time to fit residues: 85.9412 Evaluate side-chains 338 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 277 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 123 ILE 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 323 MET Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 484 LEU 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 636 THR 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 162 LEU 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 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 636 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 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 221 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 323 MET 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 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 186 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 ILE 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 636 THR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 94 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 224 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- 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** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 HIS ** 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 = 0.3739 r_free = 0.3739 target = 0.133763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102902 restraints weight = 41774.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.105813 restraints weight = 26569.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107785 restraints weight = 20209.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109029 restraints weight = 16997.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.109777 restraints weight = 15234.701| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22212 Z= 0.106 Angle : 0.571 14.181 29984 Z= 0.278 Chirality : 0.039 0.134 3376 Planarity : 0.004 0.063 3708 Dihedral : 10.885 122.713 3156 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.49 % Allowed : 15.39 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.16), residues: 2608 helix: -0.67 (0.13), residues: 1500 sheet: -2.81 (0.49), residues: 108 loop : -1.55 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 371 TYR 0.019 0.001 TYR C 451 PHE 0.021 0.001 PHE C 193 TRP 0.024 0.001 TRP A 481 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00234 (22204) covalent geometry : angle 0.57064 (29968) SS BOND : bond 0.00209 ( 8) SS BOND : angle 0.90845 ( 16) hydrogen bonds : bond 0.03567 ( 780) hydrogen bonds : angle 3.93432 ( 2313) *********************** 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 378 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 296 time to evaluate : 0.872 Fit side-chains REVERT: A 133 GLU cc_start: 0.7681 (pt0) cc_final: 0.7239 (mm-30) REVERT: A 139 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5623 (tp) REVERT: A 229 ASP cc_start: 0.6428 (m-30) cc_final: 0.6127 (m-30) REVERT: A 399 THR cc_start: 0.8328 (p) cc_final: 0.8026 (t) REVERT: A 450 PHE cc_start: 0.6806 (t80) cc_final: 0.6397 (t80) REVERT: A 479 MET cc_start: 0.3827 (mmm) cc_final: 0.3434 (mmp) REVERT: A 542 PHE cc_start: 0.7723 (m-10) cc_final: 0.6505 (t80) REVERT: A 561 ASN cc_start: 0.8659 (m110) cc_final: 0.8301 (m110) REVERT: A 588 LEU cc_start: 0.9003 (mm) cc_final: 0.8548 (mt) REVERT: A 611 LYS cc_start: 0.6101 (OUTLIER) cc_final: 0.5662 (mmmt) REVERT: A 702 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: A 743 LYS cc_start: 0.7226 (mtpp) cc_final: 0.6846 (tmtt) REVERT: B 62 PRO cc_start: 0.6296 (Cg_endo) cc_final: 0.6049 (Cg_exo) REVERT: B 163 THR cc_start: 0.7823 (p) cc_final: 0.7551 (p) REVERT: B 320 MET cc_start: 0.8239 (mmm) cc_final: 0.8007 (mmt) REVERT: B 399 THR cc_start: 0.8432 (p) cc_final: 0.8147 (t) REVERT: B 450 PHE cc_start: 0.6833 (t80) cc_final: 0.6374 (t80) REVERT: B 481 TRP cc_start: 0.2045 (t60) cc_final: 0.1711 (t60) REVERT: B 542 PHE cc_start: 0.7577 (m-10) cc_final: 0.5872 (t80) REVERT: B 561 ASN cc_start: 0.8632 (m110) cc_final: 0.8265 (m110) REVERT: B 584 LEU cc_start: 0.8117 (mp) cc_final: 0.7897 (mp) REVERT: B 588 LEU cc_start: 0.8947 (mm) cc_final: 0.8504 (mt) REVERT: B 611 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5684 (mmmt) REVERT: C 122 ARG cc_start: 0.6603 (ttm110) cc_final: 0.5489 (ttp-110) REVERT: C 133 GLU cc_start: 0.7923 (pt0) cc_final: 0.7349 (mm-30) REVERT: C 139 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6221 (tt) REVERT: C 148 ARG cc_start: 0.5558 (mpt90) cc_final: 0.4965 (mmp80) REVERT: C 366 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.7125 (ptpt) REVERT: C 399 THR cc_start: 0.8267 (p) cc_final: 0.7951 (t) REVERT: C 479 MET cc_start: 0.3748 (mmm) cc_final: 0.3359 (mmp) REVERT: C 561 ASN cc_start: 0.8591 (m110) cc_final: 0.8267 (m110) REVERT: C 588 LEU cc_start: 0.9013 (mm) cc_final: 0.8606 (mt) REVERT: C 611 LYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5692 (mmmt) REVERT: C 627 ASP cc_start: 0.7286 (m-30) cc_final: 0.7060 (m-30) REVERT: C 743 LYS cc_start: 0.7172 (mtpp) cc_final: 0.6748 (tmtt) REVERT: D 196 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5598 (pm20) REVERT: D 201 ASP cc_start: 0.7447 (t70) cc_final: 0.7210 (p0) REVERT: D 254 TYR cc_start: 0.6846 (m-80) cc_final: 0.6633 (m-80) REVERT: D 361 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7390 (mm) REVERT: D 399 THR cc_start: 0.8381 (p) cc_final: 0.8057 (t) REVERT: D 450 PHE cc_start: 0.6869 (t80) cc_final: 0.6441 (t80) REVERT: D 542 PHE cc_start: 0.7477 (m-10) cc_final: 0.6324 (t80) REVERT: D 561 ASN cc_start: 0.8671 (m110) cc_final: 0.8301 (m110) REVERT: D 572 MET cc_start: 0.8305 (tpp) cc_final: 0.8055 (tpp) REVERT: D 588 LEU cc_start: 0.8960 (mm) cc_final: 0.8550 (mt) REVERT: D 611 LYS cc_start: 0.6226 (OUTLIER) cc_final: 0.5741 (mmmt) REVERT: D 672 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6647 (ttp) REVERT: D 743 LYS cc_start: 0.7336 (mtpp) cc_final: 0.7058 (tmtt) outliers start: 82 outliers final: 44 residues processed: 365 average time/residue: 0.1387 time to fit residues: 82.3424 Evaluate side-chains 325 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 484 LEU 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 636 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 144 ASP 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 636 THR 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 366 LYS Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 575 TYR 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 123 ILE Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 236 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099404 restraints weight = 42698.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102220 restraints weight = 27503.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104088 restraints weight = 21083.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105293 restraints weight = 17859.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106072 restraints weight = 16073.621| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22212 Z= 0.172 Angle : 0.645 12.743 29984 Z= 0.318 Chirality : 0.041 0.152 3376 Planarity : 0.004 0.066 3708 Dihedral : 11.397 131.966 3156 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.17 % Allowed : 15.60 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.16), residues: 2608 helix: -0.61 (0.13), residues: 1472 sheet: -2.79 (0.49), residues: 108 loop : -1.56 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 487 TYR 0.022 0.002 TYR C 451 PHE 0.028 0.002 PHE C 590 TRP 0.021 0.001 TRP A 481 HIS 0.004 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00396 (22204) covalent geometry : angle 0.64477 (29968) SS BOND : bond 0.00252 ( 8) SS BOND : angle 0.77436 ( 16) hydrogen bonds : bond 0.04413 ( 780) hydrogen bonds : angle 4.24080 ( 2313) *********************** 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 377 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 279 time to evaluate : 0.875 Fit side-chains REVERT: A 133 GLU cc_start: 0.7761 (pt0) cc_final: 0.7327 (mm-30) REVERT: A 139 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5715 (tp) REVERT: A 180 ASN cc_start: 0.6383 (m-40) cc_final: 0.6122 (p0) REVERT: A 399 THR cc_start: 0.8347 (p) cc_final: 0.8014 (t) REVERT: A 450 PHE cc_start: 0.6803 (t80) cc_final: 0.6418 (t80) REVERT: A 479 MET cc_start: 0.4008 (mmm) cc_final: 0.3734 (mmp) REVERT: A 542 PHE cc_start: 0.7647 (m-10) cc_final: 0.6344 (t80) REVERT: A 561 ASN cc_start: 0.8801 (m110) cc_final: 0.8420 (m110) REVERT: A 588 LEU cc_start: 0.9023 (mm) cc_final: 0.8513 (mt) REVERT: A 611 LYS cc_start: 0.6253 (OUTLIER) cc_final: 0.5707 (mmmt) REVERT: A 743 LYS cc_start: 0.7262 (mtpp) cc_final: 0.6848 (tmtt) REVERT: B 62 PRO cc_start: 0.6442 (Cg_endo) cc_final: 0.6218 (Cg_exo) REVERT: B 124 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6984 (t80) REVERT: B 361 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7324 (mm) REVERT: B 399 THR cc_start: 0.8391 (p) cc_final: 0.8130 (t) REVERT: B 450 PHE cc_start: 0.6810 (t80) cc_final: 0.6387 (t80) REVERT: B 542 PHE cc_start: 0.7591 (m-10) cc_final: 0.5855 (t80) REVERT: B 561 ASN cc_start: 0.8767 (m110) cc_final: 0.8382 (m110) REVERT: B 574 MET cc_start: 0.6618 (mmt) cc_final: 0.6038 (ppp) REVERT: B 588 LEU cc_start: 0.8977 (mm) cc_final: 0.8468 (mt) REVERT: B 611 LYS cc_start: 0.6156 (OUTLIER) cc_final: 0.5623 (mmmt) REVERT: C 133 GLU cc_start: 0.8003 (pt0) cc_final: 0.7412 (mm-30) REVERT: C 139 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6374 (tt) REVERT: C 148 ARG cc_start: 0.5531 (mpt90) cc_final: 0.4962 (mmp80) REVERT: C 399 THR cc_start: 0.8293 (p) cc_final: 0.7950 (t) REVERT: C 450 PHE cc_start: 0.6892 (t80) cc_final: 0.6603 (t80) REVERT: C 479 MET cc_start: 0.3840 (mmm) cc_final: 0.3472 (mmp) REVERT: C 501 GLU cc_start: 0.7499 (mp0) cc_final: 0.7259 (mp0) REVERT: C 561 ASN cc_start: 0.8713 (m110) cc_final: 0.8342 (m110) REVERT: C 588 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8589 (mt) REVERT: C 611 LYS cc_start: 0.6333 (OUTLIER) cc_final: 0.5776 (mmmt) REVERT: C 743 LYS cc_start: 0.7229 (mtpp) cc_final: 0.6775 (tmtt) REVERT: D 120 LYS cc_start: 0.6254 (tttm) cc_final: 0.5732 (mtmt) REVERT: D 139 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.5192 (tp) REVERT: D 193 PHE cc_start: 0.6928 (t80) cc_final: 0.6606 (t80) REVERT: D 196 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5498 (pm20) REVERT: D 320 MET cc_start: 0.8467 (mmm) cc_final: 0.8137 (mpp) REVERT: D 361 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7391 (mm) REVERT: D 399 THR cc_start: 0.8428 (p) cc_final: 0.8079 (t) REVERT: D 450 PHE cc_start: 0.6884 (t80) cc_final: 0.6498 (t80) REVERT: D 542 PHE cc_start: 0.7549 (m-10) cc_final: 0.6280 (t80) REVERT: D 561 ASN cc_start: 0.8762 (m110) cc_final: 0.8373 (m110) REVERT: D 572 MET cc_start: 0.8346 (tpp) cc_final: 0.8113 (tpp) REVERT: D 584 LEU cc_start: 0.8295 (mp) cc_final: 0.8077 (mp) REVERT: D 588 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8472 (mt) REVERT: D 611 LYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5649 (mmmt) REVERT: D 743 LYS cc_start: 0.7351 (mtpp) cc_final: 0.7051 (tmtt) outliers start: 98 outliers final: 65 residues processed: 357 average time/residue: 0.1420 time to fit residues: 82.4251 Evaluate side-chains 346 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 268 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 139 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 240 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 484 LEU 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 636 THR 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 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 361 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 458 VAL 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 636 THR 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 139 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 407 ILE 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 611 LYS Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 636 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 123 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 ILE 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 636 THR Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 149 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.131213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100222 restraints weight = 42219.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103090 restraints weight = 27086.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104975 restraints weight = 20651.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106194 restraints weight = 17447.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106965 restraints weight = 15678.728| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22212 Z= 0.149 Angle : 0.610 12.120 29984 Z= 0.300 Chirality : 0.040 0.148 3376 Planarity : 0.004 0.069 3708 Dihedral : 11.003 127.156 3156 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.29 % Allowed : 16.28 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.16), residues: 2608 helix: -0.47 (0.13), residues: 1492 sheet: -2.94 (0.47), residues: 108 loop : -1.49 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 371 TYR 0.020 0.002 TYR C 451 PHE 0.025 0.001 PHE C 590 TRP 0.021 0.001 TRP A 481 HIS 0.005 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00343 (22204) covalent geometry : angle 0.60961 (29968) SS BOND : bond 0.00245 ( 8) SS BOND : angle 0.86301 ( 16) hydrogen bonds : bond 0.04059 ( 780) hydrogen bonds : angle 4.10967 ( 2313) *********************** 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 393 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 292 time to evaluate : 0.880 Fit side-chains REVERT: A 133 GLU cc_start: 0.7871 (pt0) cc_final: 0.7401 (mm-30) REVERT: A 139 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.5922 (tp) REVERT: A 180 ASN cc_start: 0.6414 (m-40) cc_final: 0.6117 (p0) REVERT: A 399 THR cc_start: 0.8321 (p) cc_final: 0.8007 (t) REVERT: A 450 PHE cc_start: 0.6808 (t80) cc_final: 0.6429 (t80) REVERT: A 479 MET cc_start: 0.3965 (mmm) cc_final: 0.3583 (mmp) REVERT: A 542 PHE cc_start: 0.7663 (m-10) cc_final: 0.6318 (t80) REVERT: A 561 ASN cc_start: 0.8692 (m110) cc_final: 0.8311 (m110) REVERT: A 588 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8532 (mt) REVERT: A 611 LYS cc_start: 0.6214 (OUTLIER) cc_final: 0.5547 (mmmm) REVERT: A 688 SER cc_start: 0.7789 (p) cc_final: 0.7512 (m) REVERT: A 743 LYS cc_start: 0.7299 (mtpp) cc_final: 0.6873 (tmtt) REVERT: B 62 PRO cc_start: 0.6459 (Cg_endo) cc_final: 0.6230 (Cg_exo) REVERT: B 120 LYS cc_start: 0.6221 (tttm) cc_final: 0.5865 (mtmt) REVERT: B 124 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.7142 (t80) REVERT: B 399 THR cc_start: 0.8409 (p) cc_final: 0.8177 (t) REVERT: B 450 PHE cc_start: 0.6823 (t80) cc_final: 0.6408 (t80) REVERT: B 542 PHE cc_start: 0.7584 (m-10) cc_final: 0.6176 (t80) REVERT: B 561 ASN cc_start: 0.8702 (m110) cc_final: 0.8320 (m110) REVERT: B 588 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8555 (mt) REVERT: B 611 LYS cc_start: 0.6097 (OUTLIER) cc_final: 0.5574 (mmmt) REVERT: C 133 GLU cc_start: 0.7957 (pt0) cc_final: 0.7365 (mm-30) REVERT: C 139 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6449 (tt) REVERT: C 148 ARG cc_start: 0.5504 (mpt90) cc_final: 0.4962 (mmp80) REVERT: C 361 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7442 (mm) REVERT: C 399 THR cc_start: 0.8281 (p) cc_final: 0.7962 (t) REVERT: C 450 PHE cc_start: 0.6893 (t80) cc_final: 0.6603 (t80) REVERT: C 479 MET cc_start: 0.3708 (mmm) cc_final: 0.3316 (mmp) REVERT: C 501 GLU cc_start: 0.7442 (mp0) cc_final: 0.7215 (mp0) REVERT: C 561 ASN cc_start: 0.8616 (m110) cc_final: 0.8228 (m110) REVERT: C 588 LEU cc_start: 0.9003 (mm) cc_final: 0.8548 (mt) REVERT: C 611 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5758 (mmmt) REVERT: C 743 LYS cc_start: 0.7216 (mtpp) cc_final: 0.6786 (tmtt) REVERT: D 120 LYS cc_start: 0.6224 (tttm) cc_final: 0.5772 (mtmt) REVERT: D 139 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.5274 (tp) REVERT: D 320 MET cc_start: 0.8454 (mmm) cc_final: 0.8122 (mpp) REVERT: D 361 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7393 (mm) REVERT: D 399 THR cc_start: 0.8390 (p) cc_final: 0.8053 (t) REVERT: D 450 PHE cc_start: 0.6920 (t80) cc_final: 0.6539 (t80) REVERT: D 542 PHE cc_start: 0.7515 (m-10) cc_final: 0.6266 (t80) REVERT: D 561 ASN cc_start: 0.8689 (m110) cc_final: 0.8289 (m110) REVERT: D 588 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8518 (mt) REVERT: D 611 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5669 (mmmt) REVERT: D 743 LYS cc_start: 0.7406 (mtpp) cc_final: 0.7070 (tmtt) outliers start: 101 outliers final: 71 residues processed: 373 average time/residue: 0.1306 time to fit residues: 79.0570 Evaluate side-chains 363 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 279 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 139 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 221 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 484 LEU 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 636 THR 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 123 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 ILE 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 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 636 THR 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 139 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 636 THR 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 123 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 ILE 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 636 THR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 219 optimal weight: 0.0470 chunk 75 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- 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** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.132230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101087 restraints weight = 42231.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103968 restraints weight = 27102.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105894 restraints weight = 20709.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.107131 restraints weight = 17494.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107803 restraints weight = 15728.170| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22212 Z= 0.119 Angle : 0.574 11.743 29984 Z= 0.281 Chirality : 0.039 0.140 3376 Planarity : 0.004 0.066 3708 Dihedral : 10.569 121.972 3156 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.08 % Allowed : 16.79 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.16), residues: 2608 helix: -0.20 (0.13), residues: 1468 sheet: -3.02 (0.47), residues: 108 loop : -1.44 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 487 TYR 0.019 0.001 TYR C 451 PHE 0.024 0.001 PHE C 590 TRP 0.021 0.001 TRP A 481 HIS 0.003 0.001 HIS B 523 Details of bonding type rmsd covalent geometry : bond 0.00271 (22204) covalent geometry : angle 0.57405 (29968) SS BOND : bond 0.00214 ( 8) SS BOND : angle 0.91174 ( 16) hydrogen bonds : bond 0.03653 ( 780) hydrogen bonds : angle 3.90520 ( 2313) *********************** 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 389 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 293 time to evaluate : 0.800 Fit side-chains REVERT: A 133 GLU cc_start: 0.7884 (pt0) cc_final: 0.7398 (mm-30) REVERT: A 139 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.5972 (tp) REVERT: A 399 THR cc_start: 0.8352 (p) cc_final: 0.8063 (t) REVERT: A 450 PHE cc_start: 0.6819 (t80) cc_final: 0.6418 (t80) REVERT: A 479 MET cc_start: 0.3885 (mmm) cc_final: 0.3501 (mmp) REVERT: A 542 PHE cc_start: 0.7658 (m-10) cc_final: 0.6311 (t80) REVERT: A 561 ASN cc_start: 0.8692 (m110) cc_final: 0.8339 (m110) REVERT: A 588 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8540 (mt) REVERT: A 611 LYS cc_start: 0.6146 (OUTLIER) cc_final: 0.5563 (mmmm) REVERT: A 702 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7817 (tp30) REVERT: A 743 LYS cc_start: 0.7206 (mtpp) cc_final: 0.6843 (tmtt) REVERT: B 62 PRO cc_start: 0.6479 (Cg_endo) cc_final: 0.6277 (Cg_exo) REVERT: B 120 LYS cc_start: 0.6021 (tttm) cc_final: 0.5745 (mtmt) REVERT: B 124 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7183 (t80) REVERT: B 361 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7381 (mm) REVERT: B 399 THR cc_start: 0.8368 (p) cc_final: 0.8168 (t) REVERT: B 450 PHE cc_start: 0.6839 (t80) cc_final: 0.6401 (t80) REVERT: B 542 PHE cc_start: 0.7603 (m-10) cc_final: 0.6204 (t80) REVERT: B 561 ASN cc_start: 0.8638 (m110) cc_final: 0.8288 (m110) REVERT: B 574 MET cc_start: 0.6631 (mmt) cc_final: 0.6019 (ppp) REVERT: B 588 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8547 (mt) REVERT: B 611 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5565 (mmmm) REVERT: C 133 GLU cc_start: 0.7910 (pt0) cc_final: 0.7340 (mm-30) REVERT: C 139 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6489 (tt) REVERT: C 148 ARG cc_start: 0.5396 (mpt90) cc_final: 0.4931 (mmp80) REVERT: C 158 LEU cc_start: 0.7298 (tp) cc_final: 0.6916 (pp) REVERT: C 162 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6402 (mm) REVERT: C 361 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7381 (mm) REVERT: C 399 THR cc_start: 0.8282 (p) cc_final: 0.7982 (t) REVERT: C 450 PHE cc_start: 0.6907 (t80) cc_final: 0.6617 (t80) REVERT: C 479 MET cc_start: 0.3647 (mmm) cc_final: 0.3228 (mmp) REVERT: C 501 GLU cc_start: 0.7334 (mp0) cc_final: 0.7053 (mp0) REVERT: C 561 ASN cc_start: 0.8599 (m110) cc_final: 0.8283 (m110) REVERT: C 588 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8515 (mt) REVERT: C 611 LYS cc_start: 0.6253 (OUTLIER) cc_final: 0.5770 (mmmt) REVERT: C 627 ASP cc_start: 0.7262 (m-30) cc_final: 0.6992 (m-30) REVERT: C 743 LYS cc_start: 0.7150 (mtpp) cc_final: 0.6747 (tmtt) REVERT: D 120 LYS cc_start: 0.6184 (tttm) cc_final: 0.5768 (mtmt) REVERT: D 139 LEU cc_start: 0.5969 (OUTLIER) cc_final: 0.5413 (tp) REVERT: D 320 MET cc_start: 0.8491 (mmm) cc_final: 0.8158 (mpp) REVERT: D 361 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7461 (mm) REVERT: D 399 THR cc_start: 0.8370 (p) cc_final: 0.8043 (t) REVERT: D 450 PHE cc_start: 0.6883 (t80) cc_final: 0.6493 (t80) REVERT: D 542 PHE cc_start: 0.7596 (m-10) cc_final: 0.6322 (t80) REVERT: D 561 ASN cc_start: 0.8685 (m110) cc_final: 0.8341 (m110) REVERT: D 588 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8553 (mt) REVERT: D 611 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5580 (mmmm) REVERT: D 743 LYS cc_start: 0.7359 (mtpp) cc_final: 0.7008 (tmtt) outliers start: 96 outliers final: 59 residues processed: 369 average time/residue: 0.1440 time to fit residues: 86.1202 Evaluate side-chains 346 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 270 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 221 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 484 LEU Chi-restraints excluded: chain A residue 575 TYR 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 636 THR 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 740 THR 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 173 MET Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 458 VAL 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 636 THR 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 139 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 636 THR 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 123 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 ILE 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 636 THR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 132 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.126652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.094803 restraints weight = 43746.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.097505 restraints weight = 28433.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099293 restraints weight = 21945.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100443 restraints weight = 18706.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101063 restraints weight = 16912.343| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 22212 Z= 0.312 Angle : 0.828 12.050 29984 Z= 0.409 Chirality : 0.048 0.187 3376 Planarity : 0.006 0.074 3708 Dihedral : 12.350 138.335 3156 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.17 % Favored : 92.79 % Rotamer: Outliers : 4.38 % Allowed : 17.18 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.16), residues: 2608 helix: -0.82 (0.13), residues: 1468 sheet: -3.08 (0.45), residues: 108 loop : -1.74 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 567 TYR 0.023 0.003 TYR C 451 PHE 0.032 0.002 PHE D 193 TRP 0.028 0.002 TRP A 481 HIS 0.009 0.002 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00725 (22204) covalent geometry : angle 0.82781 (29968) SS BOND : bond 0.00336 ( 8) SS BOND : angle 0.68760 ( 16) hydrogen bonds : bond 0.05570 ( 780) hydrogen bonds : angle 4.82176 ( 2313) *********************** 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 382 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 279 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8082 (pt0) cc_final: 0.7611 (mm-30) REVERT: A 139 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6132 (tp) REVERT: A 399 THR cc_start: 0.8339 (p) cc_final: 0.7966 (t) REVERT: A 450 PHE cc_start: 0.6901 (t80) cc_final: 0.6542 (t80) REVERT: A 479 MET cc_start: 0.3943 (mmm) cc_final: 0.3619 (mmp) REVERT: A 542 PHE cc_start: 0.7696 (m-10) cc_final: 0.6115 (t80) REVERT: A 561 ASN cc_start: 0.8816 (m110) cc_final: 0.8448 (m110) REVERT: A 588 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8706 (mm) REVERT: A 611 LYS cc_start: 0.6146 (OUTLIER) cc_final: 0.5645 (mmmt) REVERT: A 743 LYS cc_start: 0.7238 (mtpp) cc_final: 0.6784 (tmtt) REVERT: B 62 PRO cc_start: 0.6602 (Cg_endo) cc_final: 0.6399 (Cg_exo) REVERT: B 124 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7249 (t80) REVERT: B 320 MET cc_start: 0.8506 (mmm) cc_final: 0.8156 (mpp) REVERT: B 361 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7215 (mm) REVERT: B 399 THR cc_start: 0.8429 (p) cc_final: 0.8161 (t) REVERT: B 450 PHE cc_start: 0.6901 (t80) cc_final: 0.6509 (t80) REVERT: B 542 PHE cc_start: 0.7598 (m-10) cc_final: 0.5858 (t80) REVERT: B 561 ASN cc_start: 0.8804 (m110) cc_final: 0.8439 (m110) REVERT: B 588 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8487 (mt) REVERT: B 611 LYS cc_start: 0.6029 (OUTLIER) cc_final: 0.5540 (mmmt) REVERT: C 133 GLU cc_start: 0.8189 (pt0) cc_final: 0.7588 (mm-30) REVERT: C 139 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6555 (tt) REVERT: C 148 ARG cc_start: 0.5284 (mpt90) cc_final: 0.4856 (mmp80) REVERT: C 361 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7376 (mm) REVERT: C 399 THR cc_start: 0.8301 (p) cc_final: 0.7920 (t) REVERT: C 450 PHE cc_start: 0.6941 (t80) cc_final: 0.6637 (t80) REVERT: C 584 LEU cc_start: 0.8420 (mp) cc_final: 0.8210 (mp) REVERT: C 588 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8507 (mt) REVERT: C 611 LYS cc_start: 0.6064 (OUTLIER) cc_final: 0.5574 (mmmt) REVERT: C 743 LYS cc_start: 0.7219 (mtpp) cc_final: 0.6717 (tmtt) REVERT: D 120 LYS cc_start: 0.6446 (tttm) cc_final: 0.5830 (mtmt) REVERT: D 139 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.5876 (tp) REVERT: D 361 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7357 (mm) REVERT: D 399 THR cc_start: 0.8377 (p) cc_final: 0.7979 (t) REVERT: D 450 PHE cc_start: 0.6958 (t80) cc_final: 0.6566 (t80) REVERT: D 542 PHE cc_start: 0.7555 (m-10) cc_final: 0.6039 (t80) REVERT: D 561 ASN cc_start: 0.8832 (m110) cc_final: 0.8462 (m110) REVERT: D 575 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.7298 (t80) REVERT: D 588 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8455 (mt) REVERT: D 611 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5657 (mmmt) REVERT: D 743 LYS cc_start: 0.7461 (mtpp) cc_final: 0.7034 (tmtt) outliers start: 103 outliers final: 68 residues processed: 361 average time/residue: 0.1435 time to fit residues: 83.0915 Evaluate side-chains 346 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 262 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 240 ASP 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 575 TYR 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 636 THR Chi-restraints excluded: chain A residue 665 THR 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 740 THR 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 165 SER Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 361 LEU 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 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 636 THR Chi-restraints excluded: chain B residue 665 THR 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 162 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 636 THR 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 123 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 240 ASP 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 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 636 THR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 177 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 167 optimal weight: 0.0370 chunk 249 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN D 180 ASN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101853 restraints weight = 42185.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104771 restraints weight = 27118.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106705 restraints weight = 20680.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107945 restraints weight = 17454.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108568 restraints weight = 15667.232| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22212 Z= 0.102 Angle : 0.580 12.699 29984 Z= 0.286 Chirality : 0.039 0.163 3376 Planarity : 0.004 0.066 3708 Dihedral : 10.564 119.191 3156 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.25 % Allowed : 19.81 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.16), residues: 2608 helix: -0.13 (0.13), residues: 1468 sheet: -3.12 (0.46), residues: 108 loop : -1.50 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 487 TYR 0.019 0.001 TYR C 451 PHE 0.027 0.001 PHE D 193 TRP 0.020 0.001 TRP A 481 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00217 (22204) covalent geometry : angle 0.57918 (29968) SS BOND : bond 0.00124 ( 8) SS BOND : angle 1.19984 ( 16) hydrogen bonds : bond 0.03314 ( 780) hydrogen bonds : angle 3.82956 ( 2313) ********************** 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 350 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 297 time to evaluate : 0.775 Fit side-chains REVERT: A 133 GLU cc_start: 0.7842 (pt0) cc_final: 0.7391 (mm-30) REVERT: A 139 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6022 (tp) REVERT: A 229 ASP cc_start: 0.6492 (m-30) cc_final: 0.6281 (m-30) REVERT: A 399 THR cc_start: 0.8346 (p) cc_final: 0.8053 (t) REVERT: A 450 PHE cc_start: 0.6826 (t80) cc_final: 0.6433 (t80) REVERT: A 479 MET cc_start: 0.4126 (mmm) cc_final: 0.3776 (mmp) REVERT: A 542 PHE cc_start: 0.7648 (m-10) cc_final: 0.6232 (t80) REVERT: A 561 ASN cc_start: 0.8611 (m110) cc_final: 0.8209 (m110) REVERT: A 588 LEU cc_start: 0.8990 (mm) cc_final: 0.8579 (mt) REVERT: A 611 LYS cc_start: 0.6181 (OUTLIER) cc_final: 0.5559 (mmmm) REVERT: A 743 LYS cc_start: 0.7053 (mtpp) cc_final: 0.6711 (tmtt) REVERT: B 120 LYS cc_start: 0.6081 (tttm) cc_final: 0.5813 (mtmt) REVERT: B 124 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7223 (t80) REVERT: B 180 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.6199 (p0) REVERT: B 320 MET cc_start: 0.8531 (mmm) cc_final: 0.8104 (mpp) REVERT: B 399 THR cc_start: 0.8436 (p) cc_final: 0.8220 (t) REVERT: B 450 PHE cc_start: 0.6847 (t80) cc_final: 0.6421 (t80) REVERT: B 561 ASN cc_start: 0.8555 (m110) cc_final: 0.8169 (m110) REVERT: B 574 MET cc_start: 0.6499 (mmt) cc_final: 0.5825 (ppp) REVERT: B 588 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8535 (mt) REVERT: B 611 LYS cc_start: 0.6165 (OUTLIER) cc_final: 0.5541 (mmmm) REVERT: C 133 GLU cc_start: 0.7936 (pt0) cc_final: 0.7330 (mm-30) REVERT: C 139 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6504 (tt) REVERT: C 158 LEU cc_start: 0.7297 (tp) cc_final: 0.6963 (pp) REVERT: C 162 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6331 (mm) REVERT: C 399 THR cc_start: 0.8271 (p) cc_final: 0.7973 (t) REVERT: C 450 PHE cc_start: 0.6868 (t80) cc_final: 0.6583 (t80) REVERT: C 561 ASN cc_start: 0.8617 (m-40) cc_final: 0.8232 (m110) REVERT: C 588 LEU cc_start: 0.8915 (mm) cc_final: 0.8533 (mt) REVERT: C 611 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5717 (mmmm) REVERT: C 743 LYS cc_start: 0.7020 (mtpp) cc_final: 0.6625 (tmtt) REVERT: D 120 LYS cc_start: 0.6256 (tttm) cc_final: 0.5822 (mtmt) REVERT: D 139 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5672 (tp) REVERT: D 371 ARG cc_start: 0.6659 (mmt90) cc_final: 0.6205 (mmm160) REVERT: D 399 THR cc_start: 0.8357 (p) cc_final: 0.8049 (t) REVERT: D 450 PHE cc_start: 0.6900 (t80) cc_final: 0.6505 (t80) REVERT: D 542 PHE cc_start: 0.7646 (m-10) cc_final: 0.6311 (t80) REVERT: D 561 ASN cc_start: 0.8608 (m110) cc_final: 0.8186 (m110) REVERT: D 574 MET cc_start: 0.6620 (mmt) cc_final: 0.6286 (ppp) REVERT: D 588 LEU cc_start: 0.8959 (mm) cc_final: 0.8566 (mt) REVERT: D 611 LYS cc_start: 0.6223 (OUTLIER) cc_final: 0.5607 (mmmm) REVERT: D 743 LYS cc_start: 0.7257 (mtpp) cc_final: 0.6935 (tmtt) outliers start: 53 outliers final: 36 residues processed: 340 average time/residue: 0.1274 time to fit residues: 69.8082 Evaluate side-chains 317 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 270 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 209 THR 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 636 THR 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 740 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 588 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 636 THR 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 162 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 636 THR 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 123 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 190 optimal weight: 2.9990 chunk 149 optimal weight: 0.0370 chunk 150 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 232 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 HIS ** 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 = 0.3739 r_free = 0.3739 target = 0.133525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102870 restraints weight = 41714.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105599 restraints weight = 27414.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107424 restraints weight = 21248.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108598 restraints weight = 18050.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109308 restraints weight = 16329.777| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22212 Z= 0.101 Angle : 0.570 12.529 29984 Z= 0.279 Chirality : 0.038 0.156 3376 Planarity : 0.004 0.077 3708 Dihedral : 10.062 111.046 3156 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.17 % Allowed : 20.37 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.16), residues: 2608 helix: 0.08 (0.13), residues: 1500 sheet: -3.14 (0.46), residues: 108 loop : -1.55 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 487 TYR 0.017 0.001 TYR C 451 PHE 0.032 0.001 PHE D 590 TRP 0.025 0.001 TRP A 481 HIS 0.007 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00215 (22204) covalent geometry : angle 0.56967 (29968) SS BOND : bond 0.00151 ( 8) SS BOND : angle 1.06247 ( 16) hydrogen bonds : bond 0.03209 ( 780) hydrogen bonds : angle 3.64082 ( 2313) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3614.90 seconds wall clock time: 63 minutes 12.35 seconds (3792.35 seconds total)