Starting phenix.real_space_refine on Thu Aug 8 06:47:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6o_42998/08_2024/8v6o_42998.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6o_42998/08_2024/8v6o_42998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6o_42998/08_2024/8v6o_42998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6o_42998/08_2024/8v6o_42998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6o_42998/08_2024/8v6o_42998.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6o_42998/08_2024/8v6o_42998.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.050 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: 7 Type Number sf(0) Gaussians P 32 5.49 5 S 128 5.16 5 Na 3 4.78 5 B 8 2.79 5 C 15000 2.51 5 N 3496 2.21 5 O 4016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 295": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B ARG 295": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C ARG 295": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 698": "NH1" <-> "NH2" Residue "C ARG 712": "NH1" <-> "NH2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 698": "NH1" <-> "NH2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D ARG 729": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 22683 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5209 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "B" Number of atoms: 5209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5209 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "C" Number of atoms: 5209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5209 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "D" Number of atoms: 5209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5209 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "A" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 504 Unusual residues: {' NA': 2, 'FZ4': 2, 'POV': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 450 Unusual residues: {'FZ4': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 398 Unusual residues: {'FZ4': 2, 'POV': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 451 Unusual residues: {' NA': 1, 'FZ4': 2, 'POV': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 12.01, per 1000 atoms: 0.53 Number of scatterers: 22683 At special positions: 0 Unit cell: (156.8, 156, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 128 16.00 P 32 15.00 Na 3 11.00 O 4016 8.00 N 3496 7.00 C 15000 6.00 B 8 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.02 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.02 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.02 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.64 Conformation dependent library (CDL) restraints added in 4.4 seconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 64.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.586A pdb=" N LYS A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 removed outlier: 3.613A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.975A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.524A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 removed outlier: 3.748A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.691A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.599A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.612A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.586A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.644A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.548A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.658A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.519A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.529A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.580A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 458 removed outlier: 3.526A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 505 removed outlier: 3.503A pdb=" N GLY A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.836A pdb=" N ASP A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 542 removed outlier: 4.057A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.593A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.578A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 606 removed outlier: 3.732A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.721A pdb=" N LYS A 614 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP A 615 " --> pdb=" O CYS A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 611 through 615' Processing helix chain 'A' and resid 623 through 638 removed outlier: 3.593A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 650 through 677 removed outlier: 3.725A pdb=" N LEU A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 removed outlier: 3.952A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.703A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.523A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.613A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.976A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.524A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 197 removed outlier: 3.747A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.692A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.600A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.613A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.587A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.644A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.548A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.658A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.519A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.529A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.580A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 458 removed outlier: 3.527A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 505 removed outlier: 3.502A pdb=" N GLY B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 removed outlier: 3.836A pdb=" N ASP B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 542 removed outlier: 4.057A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.593A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.578A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 606 removed outlier: 3.732A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.721A pdb=" N LYS B 614 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 615 " --> pdb=" O CYS B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 611 through 615' Processing helix chain 'B' and resid 623 through 638 removed outlier: 3.592A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 647 Processing helix chain 'B' and resid 650 through 677 removed outlier: 3.725A pdb=" N LEU B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 707 removed outlier: 3.952A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.703A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 removed outlier: 3.523A pdb=" N ARG C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.613A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.975A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 163 " --> pdb=" O MET C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.524A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.747A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.691A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.599A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.613A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.587A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.644A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.500A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.658A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.518A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.529A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.580A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 458 removed outlier: 3.527A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 505 removed outlier: 3.503A pdb=" N GLY C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 removed outlier: 3.836A pdb=" N ASP C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 542 removed outlier: 4.056A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.594A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.579A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 606 removed outlier: 3.732A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 615 removed outlier: 3.721A pdb=" N LYS C 614 " --> pdb=" O LYS C 611 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP C 615 " --> pdb=" O CYS C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 611 through 615' Processing helix chain 'C' and resid 623 through 638 removed outlier: 3.592A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 632 " --> pdb=" O ALA C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 650 through 677 removed outlier: 3.725A pdb=" N LEU C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 707 removed outlier: 3.952A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.704A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.524A pdb=" N ARG D 122 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 145 removed outlier: 3.614A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.976A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D 163 " --> pdb=" O MET D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.525A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 197 removed outlier: 3.748A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.691A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.599A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.613A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.588A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.645A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.500A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.658A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.518A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.529A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.580A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 458 removed outlier: 3.527A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 456 " --> pdb=" O ASN D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 505 removed outlier: 3.502A pdb=" N GLY D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 520 removed outlier: 3.836A pdb=" N ASP D 519 " --> pdb=" O SER D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 removed outlier: 4.056A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.594A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.579A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 606 removed outlier: 3.732A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 removed outlier: 3.721A pdb=" N LYS D 614 " --> pdb=" O LYS D 611 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP D 615 " --> pdb=" O CYS D 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 611 through 615' Processing helix chain 'D' and resid 623 through 638 removed outlier: 3.593A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU D 631 " --> pdb=" O ASP D 627 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 647 Processing helix chain 'D' and resid 650 through 677 removed outlier: 3.725A pdb=" N LEU D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 707 removed outlier: 3.951A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 692 " --> pdb=" O SER D 688 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.704A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 7.112A pdb=" N LYS A 376 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP A 391 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 7.111A pdb=" N LYS B 376 " --> pdb=" O ASP B 391 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP B 391 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 7.112A pdb=" N LYS C 376 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP C 391 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 7.112A pdb=" N LYS D 376 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP D 391 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2778 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.23 Time building geometry restraints manager: 9.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3416 1.31 - 1.44: 6092 1.44 - 1.56: 13276 1.56 - 1.69: 80 1.69 - 1.81: 212 Bond restraints: 23076 Sorted by residual: bond pdb=" C21 POV D 904 " pdb=" O21 POV D 904 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C21 POV A 902 " pdb=" O21 POV A 902 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C21 POV A 911 " pdb=" O21 POV A 911 " ideal model delta sigma weight residual 1.330 1.429 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C21 POV C 901 " pdb=" O21 POV C 901 " ideal model delta sigma weight residual 1.330 1.429 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C21 POV A 905 " pdb=" O21 POV A 905 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.31e+01 ... (remaining 23071 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.34: 494 106.34 - 113.27: 12730 113.27 - 120.19: 8146 120.19 - 127.12: 9302 127.12 - 134.04: 216 Bond angle restraints: 30888 Sorted by residual: angle pdb=" C LYS A 611 " pdb=" N CYS A 612 " pdb=" CA CYS A 612 " ideal model delta sigma weight residual 120.58 127.05 -6.47 1.32e+00 5.74e-01 2.41e+01 angle pdb=" C LYS C 611 " pdb=" N CYS C 612 " pdb=" CA CYS C 612 " ideal model delta sigma weight residual 120.58 127.02 -6.44 1.32e+00 5.74e-01 2.38e+01 angle pdb=" C LYS D 611 " pdb=" N CYS D 612 " pdb=" CA CYS D 612 " ideal model delta sigma weight residual 120.58 127.02 -6.44 1.32e+00 5.74e-01 2.38e+01 angle pdb=" C LYS B 611 " pdb=" N CYS B 612 " pdb=" CA CYS B 612 " ideal model delta sigma weight residual 120.58 127.00 -6.42 1.32e+00 5.74e-01 2.37e+01 angle pdb=" O11 POV D 908 " pdb=" P POV D 908 " pdb=" O12 POV D 908 " ideal model delta sigma weight residual 97.67 111.86 -14.19 3.00e+00 1.11e-01 2.24e+01 ... (remaining 30883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 13434 35.31 - 70.62: 594 70.62 - 105.94: 72 105.94 - 141.25: 47 141.25 - 176.56: 9 Dihedral angle restraints: 14156 sinusoidal: 6612 harmonic: 7544 Sorted by residual: dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual 93.00 152.10 -59.10 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual 93.00 152.08 -59.08 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual 93.00 152.07 -59.07 1 1.00e+01 1.00e-02 4.67e+01 ... (remaining 14153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2155 0.035 - 0.069: 763 0.069 - 0.104: 305 0.104 - 0.139: 59 0.139 - 0.173: 26 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CA PRO D 613 " pdb=" N PRO D 613 " pdb=" C PRO D 613 " pdb=" CB PRO D 613 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C2 POV C 901 " pdb=" C1 POV C 901 " pdb=" C3 POV C 901 " pdb=" O21 POV C 901 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA PRO A 613 " pdb=" N PRO A 613 " pdb=" C PRO A 613 " pdb=" CB PRO A 613 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 3305 not shown) Planarity restraints: 3716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 462 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 463 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 462 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO C 463 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 462 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO D 463 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 463 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 463 " -0.033 5.00e-02 4.00e+02 ... (remaining 3713 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6217 2.81 - 3.33: 18557 3.33 - 3.86: 35233 3.86 - 4.38: 43074 4.38 - 4.90: 73203 Nonbonded interactions: 176284 Sorted by model distance: nonbonded pdb=" O PRO C 753 " pdb=" OH TYR D 213 " model vdw 2.290 3.040 nonbonded pdb=" O HIS B 417 " pdb=" OG1 THR B 421 " model vdw 2.294 3.040 nonbonded pdb=" O HIS C 417 " pdb=" OG1 THR C 421 " model vdw 2.295 3.040 nonbonded pdb=" O HIS A 417 " pdb=" OG1 THR A 421 " model vdw 2.295 3.040 nonbonded pdb=" O HIS D 417 " pdb=" OG1 THR D 421 " model vdw 2.295 3.040 ... (remaining 176279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 117 through 756 or resid 901 through 905)) selection = (chain 'B' and (resid 117 through 756 or resid 901 through 905)) selection = (chain 'C' and (resid 117 through 756 or resid 901 through 905)) selection = (chain 'D' and (resid 117 through 756 or resid 901 through 905)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 56.220 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 : 0.009 0.100 23076 Z= 0.544 Angle : 1.361 14.190 30888 Z= 0.640 Chirality : 0.043 0.173 3308 Planarity : 0.006 0.060 3716 Dihedral : 20.284 176.559 9248 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.35 % Allowed : 3.17 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.54 (0.09), residues: 2552 helix: -4.73 (0.04), residues: 1576 sheet: -1.03 (0.41), residues: 112 loop : -3.55 (0.15), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 692 HIS 0.008 0.002 HIS C 471 PHE 0.023 0.002 PHE A 633 TYR 0.012 0.001 TYR A 461 ARG 0.009 0.001 ARG D 693 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 574 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6981 (tmmt) REVERT: B 478 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7170 (tmmt) REVERT: B 716 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7288 (tpp-160) REVERT: C 121 LYS cc_start: 0.7596 (mptt) cc_final: 0.7122 (pttm) REVERT: C 367 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7441 (pt0) REVERT: C 478 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7090 (tmmt) REVERT: C 716 ARG cc_start: 0.8008 (ttp-170) cc_final: 0.7378 (tpm170) REVERT: D 156 ASP cc_start: 0.7795 (t0) cc_final: 0.7356 (t0) REVERT: D 431 MET cc_start: 0.7045 (mtp) cc_final: 0.6665 (mmt) REVERT: D 478 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7083 (tmmt) REVERT: D 592 PHE cc_start: 0.6920 (m-10) cc_final: 0.6696 (m-10) REVERT: D 595 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7135 (mm) REVERT: D 716 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7289 (tpp-160) outliers start: 8 outliers final: 0 residues processed: 582 average time/residue: 1.3150 time to fit residues: 870.3238 Evaluate side-chains 344 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 339 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 232 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 286 GLN A 314 ASN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 HIS A 671 ASN B 286 GLN B 314 ASN B 671 ASN C 160 HIS C 286 GLN C 314 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 251 ASN D 279 GLN D 286 GLN D 314 ASN D 580 GLN D 643 ASN D 671 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23076 Z= 0.328 Angle : 0.723 7.295 30888 Z= 0.360 Chirality : 0.043 0.180 3308 Planarity : 0.006 0.055 3716 Dihedral : 24.078 155.962 4226 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.44 % Rotamer: Outliers : 3.79 % Allowed : 12.21 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.13), residues: 2552 helix: -1.84 (0.10), residues: 1588 sheet: -1.12 (0.41), residues: 112 loop : -2.76 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 692 HIS 0.010 0.002 HIS A 471 PHE 0.028 0.002 PHE B 633 TYR 0.020 0.002 TYR D 451 ARG 0.005 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 377 time to evaluate : 2.292 Fit side-chains REVERT: A 220 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8108 (m-40) REVERT: A 431 MET cc_start: 0.6794 (mtp) cc_final: 0.6394 (mmt) REVERT: A 478 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7089 (tmmt) REVERT: A 631 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: A 690 ARG cc_start: 0.7592 (mtt90) cc_final: 0.7030 (mtm110) REVERT: A 712 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7519 (mtt90) REVERT: B 159 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6541 (mmp) REVERT: B 202 ARG cc_start: 0.7896 (ptm160) cc_final: 0.7488 (ptm160) REVERT: B 478 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7183 (tmmt) REVERT: B 631 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: B 690 ARG cc_start: 0.7527 (mtt90) cc_final: 0.7044 (mtm110) REVERT: B 716 ARG cc_start: 0.7925 (ttp-170) cc_final: 0.7311 (tpp-160) REVERT: C 327 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.6961 (mmm-85) REVERT: C 367 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7317 (pt0) REVERT: C 478 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7128 (tmmt) REVERT: C 631 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: C 712 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7659 (mtm110) REVERT: C 716 ARG cc_start: 0.8004 (ttp-170) cc_final: 0.7355 (tpm170) REVERT: D 156 ASP cc_start: 0.7587 (t0) cc_final: 0.7046 (p0) REVERT: D 320 MET cc_start: 0.9048 (mmm) cc_final: 0.8753 (tpp) REVERT: D 368 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8121 (ttmp) REVERT: D 421 THR cc_start: 0.9049 (m) cc_final: 0.8844 (p) REVERT: D 478 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7106 (tmmt) REVERT: D 553 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7573 (mt) REVERT: D 581 LYS cc_start: 0.7158 (tppt) cc_final: 0.6720 (mmpt) REVERT: D 672 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7067 (mmt) REVERT: D 716 ARG cc_start: 0.7944 (ttp-170) cc_final: 0.7333 (tpm170) outliers start: 86 outliers final: 15 residues processed: 429 average time/residue: 1.3639 time to fit residues: 665.3845 Evaluate side-chains 339 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 310 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 691 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 193 optimal weight: 0.0270 chunk 158 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 232 optimal weight: 10.0000 chunk 251 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 643 ASN A 645 GLN B 274 GLN B 286 GLN B 643 ASN C 286 GLN C 643 ASN D 330 ASN D 643 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23076 Z= 0.128 Angle : 0.529 5.914 30888 Z= 0.270 Chirality : 0.037 0.133 3308 Planarity : 0.004 0.056 3716 Dihedral : 22.308 144.625 4224 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.40 % Allowed : 14.77 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2552 helix: -0.21 (0.12), residues: 1604 sheet: -0.70 (0.43), residues: 112 loop : -2.61 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 692 HIS 0.006 0.001 HIS D 471 PHE 0.015 0.001 PHE B 522 TYR 0.021 0.001 TYR A 461 ARG 0.008 0.000 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 329 time to evaluate : 2.444 Fit side-chains REVERT: A 156 ASP cc_start: 0.7661 (t0) cc_final: 0.7193 (p0) REVERT: A 431 MET cc_start: 0.6666 (mtp) cc_final: 0.6245 (mmt) REVERT: A 478 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6975 (tmmt) REVERT: A 631 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: A 690 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7081 (mtm110) REVERT: A 691 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7705 (pt) REVERT: B 156 ASP cc_start: 0.7654 (t0) cc_final: 0.6979 (p0) REVERT: B 159 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6534 (mmp) REVERT: B 202 ARG cc_start: 0.7873 (ptm160) cc_final: 0.7618 (ptm160) REVERT: B 431 MET cc_start: 0.6736 (mtm) cc_final: 0.6534 (mtp) REVERT: B 478 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7167 (tmmt) REVERT: B 631 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: B 690 ARG cc_start: 0.7483 (mtt90) cc_final: 0.7078 (mtm110) REVERT: B 691 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7716 (pt) REVERT: C 286 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7709 (mp-120) REVERT: C 327 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.6776 (mmm-85) REVERT: C 368 LYS cc_start: 0.7970 (mmmm) cc_final: 0.7715 (mptt) REVERT: C 478 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7048 (tmmt) REVERT: C 631 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: C 687 GLU cc_start: 0.7208 (tp30) cc_final: 0.6880 (mm-30) REVERT: C 691 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7672 (pt) REVERT: C 716 ARG cc_start: 0.8002 (ttp-170) cc_final: 0.7299 (tpp-160) REVERT: D 283 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: D 368 LYS cc_start: 0.8365 (mmmm) cc_final: 0.8075 (ttmp) REVERT: D 431 MET cc_start: 0.6474 (mtp) cc_final: 0.6103 (mmt) REVERT: D 478 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7001 (tmmt) REVERT: D 581 LYS cc_start: 0.7192 (tppt) cc_final: 0.6811 (mmpt) REVERT: D 631 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: D 690 ARG cc_start: 0.7680 (ptp-110) cc_final: 0.7165 (mtm110) REVERT: D 716 ARG cc_start: 0.7991 (ttp-170) cc_final: 0.7320 (tpp-160) outliers start: 77 outliers final: 6 residues processed: 376 average time/residue: 1.3239 time to fit residues: 567.6229 Evaluate side-chains 313 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 292 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 631 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 122 optimal weight: 0.1980 chunk 221 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 643 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23076 Z= 0.139 Angle : 0.523 8.368 30888 Z= 0.264 Chirality : 0.037 0.139 3308 Planarity : 0.004 0.055 3716 Dihedral : 21.487 145.744 4224 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.70 % Allowed : 14.90 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2552 helix: 0.53 (0.13), residues: 1628 sheet: -0.27 (0.44), residues: 112 loop : -2.41 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.005 0.001 HIS B 160 PHE 0.012 0.001 PHE B 522 TYR 0.020 0.001 TYR A 461 ARG 0.008 0.000 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 318 time to evaluate : 2.325 Fit side-chains REVERT: A 156 ASP cc_start: 0.7581 (t0) cc_final: 0.7009 (p0) REVERT: A 431 MET cc_start: 0.6607 (mtp) cc_final: 0.6181 (mmt) REVERT: A 478 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7032 (tmmt) REVERT: A 631 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6632 (mp0) REVERT: A 690 ARG cc_start: 0.7548 (mtt90) cc_final: 0.7097 (mtm110) REVERT: A 712 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7525 (mtt90) REVERT: A 716 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7366 (tpp-160) REVERT: B 156 ASP cc_start: 0.7487 (t0) cc_final: 0.7023 (p0) REVERT: B 478 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7079 (tmmt) REVERT: B 553 LEU cc_start: 0.8016 (tp) cc_final: 0.7787 (mt) REVERT: B 631 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: B 690 ARG cc_start: 0.7477 (mtt90) cc_final: 0.7125 (mtm110) REVERT: B 716 ARG cc_start: 0.7979 (ttp-170) cc_final: 0.7332 (tpm170) REVERT: C 156 ASP cc_start: 0.7579 (t0) cc_final: 0.7163 (p0) REVERT: C 167 THR cc_start: 0.8226 (p) cc_final: 0.7893 (t) REVERT: C 327 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.6926 (mmm-85) REVERT: C 431 MET cc_start: 0.6511 (mtm) cc_final: 0.6028 (mmp) REVERT: C 478 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6988 (tmmt) REVERT: C 631 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: C 687 GLU cc_start: 0.7175 (tp30) cc_final: 0.6849 (mm-30) REVERT: C 712 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7671 (mtm110) REVERT: C 716 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.7271 (tpp-160) REVERT: C 736 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6603 (pt0) REVERT: D 291 SER cc_start: 0.8690 (m) cc_final: 0.8360 (p) REVERT: D 368 LYS cc_start: 0.8405 (mmmm) cc_final: 0.8082 (ttmp) REVERT: D 431 MET cc_start: 0.6482 (mtp) cc_final: 0.6085 (mmt) REVERT: D 478 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6963 (tmmt) REVERT: D 581 LYS cc_start: 0.7184 (tppt) cc_final: 0.6800 (mmpt) REVERT: D 690 ARG cc_start: 0.7732 (ptp-110) cc_final: 0.7149 (mtm110) REVERT: D 691 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7867 (mt) REVERT: D 716 ARG cc_start: 0.7949 (ttp-170) cc_final: 0.7279 (tpp-160) outliers start: 84 outliers final: 18 residues processed: 374 average time/residue: 1.3042 time to fit residues: 561.0833 Evaluate side-chains 328 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 298 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 691 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 222 optimal weight: 0.9980 chunk 62 optimal weight: 0.0980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 160 HIS B 274 GLN B 643 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 330 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23076 Z= 0.248 Angle : 0.596 6.551 30888 Z= 0.298 Chirality : 0.040 0.152 3308 Planarity : 0.004 0.056 3716 Dihedral : 21.345 153.663 4224 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.31 % Allowed : 16.40 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2552 helix: 0.88 (0.13), residues: 1600 sheet: -0.22 (0.45), residues: 112 loop : -2.11 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 692 HIS 0.006 0.001 HIS B 160 PHE 0.014 0.001 PHE D 316 TYR 0.020 0.002 TYR A 390 ARG 0.011 0.000 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 331 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.7839 (ttmp) cc_final: 0.7564 (mmtt) REVERT: A 431 MET cc_start: 0.6662 (mtp) cc_final: 0.6264 (mmp) REVERT: A 478 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6936 (tmmt) REVERT: A 631 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: A 690 ARG cc_start: 0.7477 (mtt90) cc_final: 0.7102 (mtm110) REVERT: A 712 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7468 (mtt90) REVERT: A 716 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7283 (tpp-160) REVERT: B 156 ASP cc_start: 0.7419 (t0) cc_final: 0.7147 (p0) REVERT: B 253 LYS cc_start: 0.7835 (ttmp) cc_final: 0.7493 (mmtt) REVERT: B 478 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7015 (tmmt) REVERT: B 592 PHE cc_start: 0.7275 (m-10) cc_final: 0.7006 (m-10) REVERT: B 631 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: B 690 ARG cc_start: 0.7447 (mtt90) cc_final: 0.7208 (mtm110) REVERT: B 716 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.7308 (tpp-160) REVERT: C 129 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: C 156 ASP cc_start: 0.7442 (t0) cc_final: 0.7000 (p0) REVERT: C 253 LYS cc_start: 0.7873 (ttmp) cc_final: 0.7539 (mmtt) REVERT: C 327 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7006 (mmm-85) REVERT: C 368 LYS cc_start: 0.8299 (mmmm) cc_final: 0.7757 (mmtt) REVERT: C 431 MET cc_start: 0.6598 (mtm) cc_final: 0.6285 (mmp) REVERT: C 434 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7677 (tttt) REVERT: C 478 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6837 (tmmt) REVERT: C 592 PHE cc_start: 0.7227 (m-10) cc_final: 0.6892 (m-10) REVERT: C 631 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: C 687 GLU cc_start: 0.7226 (tp30) cc_final: 0.6885 (mm-30) REVERT: C 712 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7591 (mtm110) REVERT: C 716 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7265 (tpm170) REVERT: C 736 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6834 (pt0) REVERT: D 202 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7786 (ptm160) REVERT: D 291 SER cc_start: 0.8655 (m) cc_final: 0.8362 (p) REVERT: D 368 LYS cc_start: 0.8418 (mmmm) cc_final: 0.8137 (ttmp) REVERT: D 431 MET cc_start: 0.6569 (mtp) cc_final: 0.6105 (mmt) REVERT: D 478 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6825 (tmmt) REVERT: D 581 LYS cc_start: 0.7139 (tppt) cc_final: 0.6888 (mmtm) REVERT: D 631 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6189 (mp0) REVERT: D 690 ARG cc_start: 0.7735 (ptp-110) cc_final: 0.7205 (mtm110) REVERT: D 691 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8158 (mt) REVERT: D 716 ARG cc_start: 0.8023 (ttp-170) cc_final: 0.7280 (tpp-160) outliers start: 75 outliers final: 25 residues processed: 384 average time/residue: 1.3260 time to fit residues: 580.8300 Evaluate side-chains 349 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 310 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 691 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 247 optimal weight: 0.8980 chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 0.0770 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 0.0170 chunk 130 optimal weight: 6.9990 overall best weight: 1.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 330 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23076 Z= 0.160 Angle : 0.536 6.714 30888 Z= 0.271 Chirality : 0.038 0.157 3308 Planarity : 0.004 0.056 3716 Dihedral : 20.630 148.945 4224 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.62 % Allowed : 16.53 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2552 helix: 1.10 (0.13), residues: 1632 sheet: -0.16 (0.44), residues: 112 loop : -2.21 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 481 HIS 0.007 0.001 HIS A 160 PHE 0.012 0.001 PHE C 316 TYR 0.021 0.001 TYR D 461 ARG 0.009 0.000 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 324 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6948 (mp) REVERT: A 148 ARG cc_start: 0.5485 (OUTLIER) cc_final: 0.5249 (mpt180) REVERT: A 253 LYS cc_start: 0.7848 (ttmp) cc_final: 0.7564 (mmtt) REVERT: A 431 MET cc_start: 0.6540 (mtp) cc_final: 0.6221 (mmt) REVERT: A 478 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.6956 (tmmt) REVERT: A 631 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: A 690 ARG cc_start: 0.7414 (mtt90) cc_final: 0.7148 (mtm110) REVERT: A 712 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7430 (mtt90) REVERT: A 716 ARG cc_start: 0.7931 (ttp-170) cc_final: 0.7267 (tpp-160) REVERT: B 253 LYS cc_start: 0.7839 (ttmp) cc_final: 0.7481 (mmtt) REVERT: B 327 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.6565 (mmm-85) REVERT: B 431 MET cc_start: 0.6696 (mtp) cc_final: 0.6489 (mtp) REVERT: B 478 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6989 (tmmt) REVERT: B 592 PHE cc_start: 0.7241 (m-10) cc_final: 0.6992 (m-10) REVERT: B 631 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: B 641 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7804 (p0) REVERT: B 690 ARG cc_start: 0.7401 (mtt90) cc_final: 0.7158 (mtm110) REVERT: B 716 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7266 (tpp-160) REVERT: C 145 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6837 (mp) REVERT: C 156 ASP cc_start: 0.7330 (t0) cc_final: 0.7061 (p0) REVERT: C 167 THR cc_start: 0.8172 (p) cc_final: 0.7841 (t) REVERT: C 253 LYS cc_start: 0.7869 (ttmp) cc_final: 0.7499 (mmtt) REVERT: C 327 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.6963 (mmm-85) REVERT: C 368 LYS cc_start: 0.8328 (mmmm) cc_final: 0.7775 (mmtt) REVERT: C 431 MET cc_start: 0.6546 (mtm) cc_final: 0.6284 (mmp) REVERT: C 434 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7716 (tttt) REVERT: C 478 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6869 (tmmt) REVERT: C 592 PHE cc_start: 0.7169 (m-10) cc_final: 0.6841 (m-10) REVERT: C 631 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: C 687 GLU cc_start: 0.7243 (tp30) cc_final: 0.6788 (mm-30) REVERT: C 712 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7560 (mtm110) REVERT: C 716 ARG cc_start: 0.8010 (ttp-170) cc_final: 0.7233 (tpp-160) REVERT: C 736 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6772 (pt0) REVERT: D 202 ARG cc_start: 0.8006 (ptm160) cc_final: 0.7711 (ptm160) REVERT: D 279 GLN cc_start: 0.8270 (mt0) cc_final: 0.8047 (mt0) REVERT: D 283 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: D 291 SER cc_start: 0.8641 (m) cc_final: 0.8366 (p) REVERT: D 368 LYS cc_start: 0.8419 (mmmm) cc_final: 0.8102 (ttmp) REVERT: D 431 MET cc_start: 0.6482 (mtp) cc_final: 0.6098 (mmp) REVERT: D 478 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6863 (tmmt) REVERT: D 482 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6869 (pt) REVERT: D 581 LYS cc_start: 0.7191 (tppt) cc_final: 0.6967 (mmtm) REVERT: D 631 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6194 (mp0) REVERT: D 690 ARG cc_start: 0.7736 (ptp-110) cc_final: 0.7197 (mtm110) REVERT: D 691 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8041 (mt) REVERT: D 716 ARG cc_start: 0.8026 (ttp-170) cc_final: 0.7279 (tpp-160) outliers start: 82 outliers final: 27 residues processed: 381 average time/residue: 1.3133 time to fit residues: 570.8129 Evaluate side-chains 353 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 306 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 180 optimal weight: 0.5980 chunk 140 optimal weight: 10.0000 chunk 208 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 643 ASN C 160 HIS C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 330 ASN D 643 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23076 Z= 0.137 Angle : 0.518 12.822 30888 Z= 0.261 Chirality : 0.038 0.154 3308 Planarity : 0.004 0.056 3716 Dihedral : 19.885 145.513 4224 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.87 % Allowed : 17.42 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.17), residues: 2552 helix: 1.36 (0.13), residues: 1636 sheet: -0.09 (0.45), residues: 112 loop : -2.15 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 521 HIS 0.007 0.001 HIS C 160 PHE 0.012 0.001 PHE D 316 TYR 0.018 0.001 TYR B 540 ARG 0.010 0.000 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 328 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6922 (mp) REVERT: A 148 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.5296 (mpt180) REVERT: A 199 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.7115 (pp) REVERT: A 253 LYS cc_start: 0.7857 (ttmp) cc_final: 0.7579 (mmtt) REVERT: A 431 MET cc_start: 0.6533 (mtp) cc_final: 0.6198 (mmt) REVERT: A 478 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.6881 (tmmt) REVERT: A 690 ARG cc_start: 0.7352 (mtt90) cc_final: 0.7118 (mtm110) REVERT: A 702 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 712 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7403 (mtt90) REVERT: A 716 ARG cc_start: 0.7966 (ttp-170) cc_final: 0.7278 (tpp-160) REVERT: B 202 ARG cc_start: 0.8102 (ptm160) cc_final: 0.7886 (ptm160) REVERT: B 253 LYS cc_start: 0.7868 (ttmp) cc_final: 0.7502 (mmtt) REVERT: B 431 MET cc_start: 0.6533 (mtp) cc_final: 0.6293 (mtp) REVERT: B 478 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7003 (tmmt) REVERT: B 592 PHE cc_start: 0.7136 (m-10) cc_final: 0.6909 (m-10) REVERT: B 690 ARG cc_start: 0.7371 (mtt90) cc_final: 0.7140 (mtm110) REVERT: B 702 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 716 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7283 (tpp-160) REVERT: C 167 THR cc_start: 0.8131 (p) cc_final: 0.7780 (t) REVERT: C 202 ARG cc_start: 0.7955 (ptm160) cc_final: 0.7553 (ptm160) REVERT: C 253 LYS cc_start: 0.7891 (ttmp) cc_final: 0.7510 (mmtt) REVERT: C 368 LYS cc_start: 0.8343 (mmmm) cc_final: 0.7979 (ttmt) REVERT: C 431 MET cc_start: 0.6465 (mtm) cc_final: 0.6190 (mmp) REVERT: C 478 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6806 (tmmt) REVERT: C 592 PHE cc_start: 0.7081 (m-10) cc_final: 0.6780 (m-10) REVERT: C 631 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: C 687 GLU cc_start: 0.7191 (tp30) cc_final: 0.6780 (mm-30) REVERT: C 712 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7515 (mtm110) REVERT: C 716 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7265 (tpm170) REVERT: D 202 ARG cc_start: 0.8034 (ptm160) cc_final: 0.7725 (ptm160) REVERT: D 291 SER cc_start: 0.8646 (m) cc_final: 0.8383 (p) REVERT: D 368 LYS cc_start: 0.8395 (mmmm) cc_final: 0.8068 (ttmp) REVERT: D 431 MET cc_start: 0.6476 (mtp) cc_final: 0.6088 (mmt) REVERT: D 478 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6814 (tmmt) REVERT: D 482 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6884 (pt) REVERT: D 581 LYS cc_start: 0.7171 (tppt) cc_final: 0.6939 (mmtm) REVERT: D 631 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: D 690 ARG cc_start: 0.7773 (ptp-110) cc_final: 0.7230 (mtm110) REVERT: D 691 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7888 (mt) REVERT: D 702 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7620 (mm-30) REVERT: D 716 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7278 (tpp-160) outliers start: 65 outliers final: 20 residues processed: 368 average time/residue: 1.3486 time to fit residues: 565.2464 Evaluate side-chains 343 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 310 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 691 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.0000 chunk 98 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 193 optimal weight: 9.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 279 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 643 ASN C 430 HIS C 643 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23076 Z= 0.137 Angle : 0.522 8.981 30888 Z= 0.263 Chirality : 0.038 0.145 3308 Planarity : 0.004 0.056 3716 Dihedral : 19.356 144.256 4224 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.16 % Allowed : 18.65 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2552 helix: 1.51 (0.13), residues: 1640 sheet: -0.01 (0.45), residues: 112 loop : -2.19 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 692 HIS 0.005 0.001 HIS C 256 PHE 0.012 0.001 PHE B 316 TYR 0.015 0.001 TYR D 461 ARG 0.014 0.000 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 303 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6876 (mp) REVERT: A 253 LYS cc_start: 0.7866 (ttmp) cc_final: 0.7596 (mmtt) REVERT: A 431 MET cc_start: 0.6552 (mtp) cc_final: 0.6192 (mmt) REVERT: A 478 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6852 (tmmt) REVERT: A 702 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 716 ARG cc_start: 0.7976 (ttp-170) cc_final: 0.7298 (tpp-160) REVERT: B 253 LYS cc_start: 0.7872 (ttmp) cc_final: 0.7527 (mmtt) REVERT: B 431 MET cc_start: 0.6502 (mtp) cc_final: 0.6270 (mtp) REVERT: B 478 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6961 (tmmt) REVERT: B 592 PHE cc_start: 0.7075 (m-10) cc_final: 0.6854 (m-10) REVERT: B 690 ARG cc_start: 0.7343 (mtt90) cc_final: 0.7120 (mtm110) REVERT: B 702 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7593 (mm-30) REVERT: B 716 ARG cc_start: 0.7898 (ttp-170) cc_final: 0.7265 (tpm170) REVERT: C 167 THR cc_start: 0.8126 (p) cc_final: 0.7846 (t) REVERT: C 253 LYS cc_start: 0.7906 (ttmp) cc_final: 0.7521 (mmtt) REVERT: C 431 MET cc_start: 0.6491 (mtm) cc_final: 0.6179 (mmp) REVERT: C 434 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7732 (tttt) REVERT: C 478 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6801 (tmmt) REVERT: C 592 PHE cc_start: 0.7020 (m-10) cc_final: 0.6721 (m-10) REVERT: C 631 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: C 641 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7573 (p0) REVERT: C 687 GLU cc_start: 0.7182 (tp30) cc_final: 0.6713 (mm-30) REVERT: C 702 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7739 (mm-30) REVERT: C 712 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7509 (mtm110) REVERT: C 716 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7224 (tpp-160) REVERT: C 736 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6710 (pt0) REVERT: D 202 ARG cc_start: 0.8012 (ptm160) cc_final: 0.7712 (ptm160) REVERT: D 291 SER cc_start: 0.8636 (m) cc_final: 0.8391 (p) REVERT: D 368 LYS cc_start: 0.8367 (mmmm) cc_final: 0.8033 (ttmp) REVERT: D 431 MET cc_start: 0.6486 (mtp) cc_final: 0.6078 (mmt) REVERT: D 478 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6743 (tmmt) REVERT: D 482 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6882 (pt) REVERT: D 581 LYS cc_start: 0.7181 (tppt) cc_final: 0.6946 (mmtm) REVERT: D 641 ASP cc_start: 0.8202 (p0) cc_final: 0.7994 (p0) REVERT: D 690 ARG cc_start: 0.7782 (ptp-110) cc_final: 0.7200 (mtm110) REVERT: D 691 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7888 (mt) REVERT: D 702 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7614 (mm-30) REVERT: D 716 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7248 (tpp-160) REVERT: D 741 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6794 (mp0) outliers start: 49 outliers final: 19 residues processed: 337 average time/residue: 1.3272 time to fit residues: 510.4464 Evaluate side-chains 331 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 300 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 10.0000 chunk 236 optimal weight: 0.5980 chunk 215 optimal weight: 0.7980 chunk 229 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 100 optimal weight: 0.0770 chunk 180 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 217 optimal weight: 0.0030 chunk 150 optimal weight: 0.6980 overall best weight: 0.4348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN B 160 HIS B 643 ASN C 643 ASN D 643 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23076 Z= 0.118 Angle : 0.509 9.426 30888 Z= 0.256 Chirality : 0.037 0.161 3308 Planarity : 0.004 0.077 3716 Dihedral : 18.649 139.193 4224 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.90 % Allowed : 19.09 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.17), residues: 2552 helix: 1.73 (0.13), residues: 1636 sheet: 0.17 (0.47), residues: 112 loop : -2.16 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 739 HIS 0.007 0.001 HIS B 160 PHE 0.011 0.001 PHE B 316 TYR 0.013 0.001 TYR D 461 ARG 0.019 0.000 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 321 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.7807 (ttmp) cc_final: 0.7563 (mmtt) REVERT: A 431 MET cc_start: 0.6564 (mtp) cc_final: 0.6198 (mmt) REVERT: A 461 TYR cc_start: 0.6266 (t80) cc_final: 0.6029 (t80) REVERT: A 478 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6866 (tmmt) REVERT: A 687 GLU cc_start: 0.7199 (tp30) cc_final: 0.6554 (mm-30) REVERT: A 690 ARG cc_start: 0.7184 (mtm110) cc_final: 0.6972 (mtm110) REVERT: A 716 ARG cc_start: 0.7952 (ttp-170) cc_final: 0.7289 (tpp-160) REVERT: B 202 ARG cc_start: 0.7977 (ttp-110) cc_final: 0.7600 (ptm160) REVERT: B 253 LYS cc_start: 0.7874 (ttmp) cc_final: 0.7573 (mmtt) REVERT: B 431 MET cc_start: 0.6469 (mtp) cc_final: 0.6248 (mtp) REVERT: B 478 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6941 (tmmt) REVERT: B 592 PHE cc_start: 0.6969 (m-10) cc_final: 0.6759 (m-10) REVERT: B 690 ARG cc_start: 0.7297 (mtt90) cc_final: 0.7075 (mtm110) REVERT: B 716 ARG cc_start: 0.7795 (ttp-170) cc_final: 0.7174 (tpp-160) REVERT: C 167 THR cc_start: 0.8116 (p) cc_final: 0.7809 (t) REVERT: C 202 ARG cc_start: 0.7912 (ptm160) cc_final: 0.7677 (ptm160) REVERT: C 253 LYS cc_start: 0.7896 (ttmp) cc_final: 0.7606 (mmtt) REVERT: C 368 LYS cc_start: 0.8275 (mmmm) cc_final: 0.7868 (ttmt) REVERT: C 431 MET cc_start: 0.6448 (mtm) cc_final: 0.6181 (mmp) REVERT: C 434 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7704 (tttt) REVERT: C 478 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6796 (tmmt) REVERT: C 482 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6880 (pt) REVERT: C 631 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: C 687 GLU cc_start: 0.7148 (tp30) cc_final: 0.6547 (mm-30) REVERT: C 690 ARG cc_start: 0.7077 (mtm110) cc_final: 0.6714 (mtm110) REVERT: C 702 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7741 (mm-30) REVERT: C 712 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7474 (mtm110) REVERT: C 716 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7198 (tpm170) REVERT: D 291 SER cc_start: 0.8659 (m) cc_final: 0.8451 (p) REVERT: D 368 LYS cc_start: 0.8378 (mmmm) cc_final: 0.7830 (mmtt) REVERT: D 431 MET cc_start: 0.6458 (mtp) cc_final: 0.6082 (mmt) REVERT: D 478 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6744 (tmmt) REVERT: D 482 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6894 (pt) REVERT: D 581 LYS cc_start: 0.7139 (tppt) cc_final: 0.6938 (mmtm) REVERT: D 690 ARG cc_start: 0.7772 (ptp-110) cc_final: 0.7168 (mtm110) REVERT: D 702 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7606 (mm-30) REVERT: D 716 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.7242 (tpp-160) REVERT: D 741 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6803 (mp0) outliers start: 43 outliers final: 16 residues processed: 354 average time/residue: 1.3531 time to fit residues: 549.7833 Evaluate side-chains 331 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 306 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 643 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23076 Z= 0.162 Angle : 0.545 9.850 30888 Z= 0.273 Chirality : 0.038 0.149 3308 Planarity : 0.004 0.080 3716 Dihedral : 18.539 143.774 4224 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.46 % Allowed : 19.80 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.17), residues: 2552 helix: 1.71 (0.13), residues: 1636 sheet: 0.11 (0.48), residues: 112 loop : -2.14 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 710 HIS 0.006 0.001 HIS C 417 PHE 0.010 0.001 PHE A 316 TYR 0.016 0.001 TYR D 461 ARG 0.020 0.001 ARG D 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 301 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 ARG cc_start: 0.8084 (ttp-110) cc_final: 0.7659 (tmm-80) REVERT: A 253 LYS cc_start: 0.7901 (ttmp) cc_final: 0.7608 (mmtt) REVERT: A 431 MET cc_start: 0.6713 (mtp) cc_final: 0.6268 (mmt) REVERT: A 461 TYR cc_start: 0.6397 (t80) cc_final: 0.6133 (t80) REVERT: A 478 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6795 (tmmt) REVERT: A 690 ARG cc_start: 0.7306 (mtm110) cc_final: 0.7101 (mtm110) REVERT: A 716 ARG cc_start: 0.7953 (ttp-170) cc_final: 0.7264 (tpp-160) REVERT: B 253 LYS cc_start: 0.7894 (ttmp) cc_final: 0.7535 (mmtt) REVERT: B 431 MET cc_start: 0.6547 (mtp) cc_final: 0.6266 (mtp) REVERT: B 478 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6929 (tmmt) REVERT: B 716 ARG cc_start: 0.7821 (ttp-170) cc_final: 0.7228 (tpp-160) REVERT: C 167 THR cc_start: 0.8150 (p) cc_final: 0.7897 (t) REVERT: C 253 LYS cc_start: 0.7937 (ttmp) cc_final: 0.7613 (mmtt) REVERT: C 368 LYS cc_start: 0.8271 (mmmm) cc_final: 0.7835 (ttmt) REVERT: C 431 MET cc_start: 0.6568 (mtm) cc_final: 0.6241 (mmp) REVERT: C 434 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7719 (tttt) REVERT: C 478 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6754 (tmmt) REVERT: C 482 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6935 (pt) REVERT: C 631 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: C 687 GLU cc_start: 0.7198 (tp30) cc_final: 0.6753 (mm-30) REVERT: C 712 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7441 (mtm110) REVERT: C 716 ARG cc_start: 0.7942 (ttp-170) cc_final: 0.7186 (tpp-160) REVERT: C 736 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6696 (pt0) REVERT: D 291 SER cc_start: 0.8653 (m) cc_final: 0.8431 (p) REVERT: D 368 LYS cc_start: 0.8357 (mmmm) cc_final: 0.7794 (mmtt) REVERT: D 431 MET cc_start: 0.6544 (mtp) cc_final: 0.6101 (mmt) REVERT: D 478 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6715 (tmmt) REVERT: D 482 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6898 (pt) REVERT: D 690 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7236 (mtm110) REVERT: D 691 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7980 (mt) REVERT: D 702 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7617 (mm-30) REVERT: D 716 ARG cc_start: 0.8004 (ttp-170) cc_final: 0.7256 (tpp-160) REVERT: D 741 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6778 (mp0) outliers start: 33 outliers final: 15 residues processed: 325 average time/residue: 1.3109 time to fit residues: 487.0899 Evaluate side-chains 328 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 301 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 643 ASN C 643 ASN D 643 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.174014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121768 restraints weight = 26555.852| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.30 r_work: 0.3219 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23076 Z= 0.145 Angle : 0.534 9.583 30888 Z= 0.268 Chirality : 0.038 0.152 3308 Planarity : 0.004 0.081 3716 Dihedral : 18.203 142.953 4224 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.41 % Allowed : 19.93 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2552 helix: 1.87 (0.13), residues: 1604 sheet: 0.21 (0.49), residues: 112 loop : -1.95 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 710 HIS 0.005 0.001 HIS C 256 PHE 0.011 0.001 PHE B 316 TYR 0.014 0.001 TYR D 461 ARG 0.020 0.001 ARG D 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8960.00 seconds wall clock time: 157 minutes 50.99 seconds (9470.99 seconds total)