Starting phenix.real_space_refine on Sun May 12 18:32:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6o_42998/05_2024/8v6o_42998_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6o_42998/05_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_42998/05_2024/8v6o_42998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6o_42998/05_2024/8v6o_42998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6o_42998/05_2024/8v6o_42998_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6o_42998/05_2024/8v6o_42998_updated.pdb" } 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 11.92, 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: 7.73 Conformation dependent library (CDL) restraints added in 3.8 seconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 4 sheets defined 56.4% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 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) Processing helix chain 'A' and resid 132 through 146 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) removed outlier: 4.083A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 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) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.606A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.624A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.612A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 283 removed outlier: 3.586A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 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 316 through 328 removed outlier: 3.548A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 removed outlier: 3.658A 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 354 through 361 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.529A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 435 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 437 through 457 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 481 through 504 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 516 through 519 No H-bonds generated for 'chain 'A' and resid 516 through 519' Processing helix chain 'A' and resid 521 through 541 removed outlier: 3.661A pdb=" N PHE A 524 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 525 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE A 526 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 528 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN A 529 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 532 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 533 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 535 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 536 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 539 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 541 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 568 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) removed outlier: 4.027A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARG A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY A 568 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 587 through 607 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) removed outlier: 4.190A pdb=" N SER A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 624 through 637 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 643 through 646 No H-bonds generated for 'chain 'A' and resid 643 through 646' Processing helix chain 'A' and resid 651 through 676 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 706 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) Processing helix chain 'A' and resid 709 through 712 No H-bonds generated for 'chain 'A' and resid 709 through 712' Processing helix chain 'B' and resid 118 through 129 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) Processing helix chain 'B' and resid 132 through 146 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) removed outlier: 4.082A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 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) Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 185 through 196 removed outlier: 3.607A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.625A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 removed outlier: 3.613A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 283 removed outlier: 3.587A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 305 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 316 through 328 removed outlier: 3.548A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.658A 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 354 through 361 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.529A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 435 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 437 through 457 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 481 through 504 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 516 through 519 No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 521 through 541 removed outlier: 3.662A pdb=" N PHE B 524 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE B 526 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 528 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN B 529 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 532 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 533 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 535 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 536 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 539 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 541 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 568 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) removed outlier: 4.028A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ARG B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLY B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 587 through 607 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) removed outlier: 4.190A pdb=" N SER B 607 " --> pdb=" O VAL B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 624 through 637 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 643 through 646 No H-bonds generated for 'chain 'B' and resid 643 through 646' Processing helix chain 'B' and resid 651 through 676 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 706 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) Processing helix chain 'B' and resid 709 through 712 No H-bonds generated for 'chain 'B' and resid 709 through 712' Processing helix chain 'C' and resid 118 through 129 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) Processing helix chain 'C' and resid 132 through 146 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) removed outlier: 4.082A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 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) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 185 through 196 removed outlier: 3.608A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 removed outlier: 3.624A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.613A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.587A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 305 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 316 through 328 removed outlier: 3.547A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 351 removed outlier: 3.658A 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 354 through 361 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.529A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 435 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 437 through 457 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 481 through 504 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 516 through 519 No H-bonds generated for 'chain 'C' and resid 516 through 519' Processing helix chain 'C' and resid 521 through 541 removed outlier: 3.662A pdb=" N PHE C 524 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 525 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE C 526 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE C 528 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN C 529 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 532 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 533 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 535 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 536 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 539 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 541 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 568 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) removed outlier: 4.028A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARG C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLY C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 Processing helix chain 'C' and resid 587 through 607 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) removed outlier: 4.191A pdb=" N SER C 607 " --> pdb=" O VAL C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 614 No H-bonds generated for 'chain 'C' and resid 612 through 614' Processing helix chain 'C' and resid 624 through 637 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 643 through 646 No H-bonds generated for 'chain 'C' and resid 643 through 646' Processing helix chain 'C' and resid 651 through 676 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 706 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) Processing helix chain 'C' and resid 709 through 712 No H-bonds generated for 'chain 'C' and resid 709 through 712' Processing helix chain 'D' and resid 118 through 129 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) Processing helix chain 'D' and resid 132 through 146 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) removed outlier: 4.083A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 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) Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 185 through 196 removed outlier: 3.608A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.624A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.613A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 283 removed outlier: 3.588A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 305 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 316 through 328 removed outlier: 3.547A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 351 removed outlier: 3.658A 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 354 through 361 Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.529A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 435 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 437 through 457 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 481 through 504 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 516 through 519 No H-bonds generated for 'chain 'D' and resid 516 through 519' Processing helix chain 'D' and resid 521 through 541 removed outlier: 3.661A pdb=" N PHE D 524 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 525 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE D 526 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 528 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN D 529 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 532 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 533 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU D 535 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 536 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 539 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 541 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 568 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) removed outlier: 4.027A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARG D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLY D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 585 Processing helix chain 'D' and resid 587 through 607 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) removed outlier: 4.191A pdb=" N SER D 607 " --> pdb=" O VAL D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 614 No H-bonds generated for 'chain 'D' and resid 612 through 614' Processing helix chain 'D' and resid 624 through 637 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 643 through 646 No H-bonds generated for 'chain 'D' and resid 643 through 646' Processing helix chain 'D' and resid 651 through 676 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 706 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) Processing helix chain 'D' and resid 709 through 712 No H-bonds generated for 'chain 'D' and resid 709 through 712' Processing sheet with id= A, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.945A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 727 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 724 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ARG A 729 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS A 722 " --> pdb=" O ARG A 729 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS A 731 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU A 720 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.945A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 727 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 724 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ARG B 729 " --> pdb=" O LYS B 722 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS B 722 " --> pdb=" O ARG B 729 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS B 731 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU B 720 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.945A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP C 727 " --> pdb=" O ALA C 724 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C 724 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG C 729 " --> pdb=" O LYS C 722 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS C 722 " --> pdb=" O ARG C 729 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS C 731 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU C 720 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.945A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP D 727 " --> pdb=" O ALA D 724 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA D 724 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG D 729 " --> pdb=" O LYS D 722 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS D 722 " --> pdb=" O ARG D 729 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS D 731 " --> pdb=" O LEU D 720 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU D 720 " --> pdb=" O CYS D 731 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.75 Time building geometry restraints manager: 8.54 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: 6233 2.81 - 3.33: 18685 3.33 - 3.86: 35375 3.86 - 4.38: 43540 4.38 - 4.90: 73307 Nonbonded interactions: 177140 Sorted by model distance: nonbonded pdb=" O PRO C 753 " pdb=" OH TYR D 213 " model vdw 2.290 2.440 nonbonded pdb=" O HIS B 417 " pdb=" OG1 THR B 421 " model vdw 2.294 2.440 nonbonded pdb=" O HIS C 417 " pdb=" OG1 THR C 421 " model vdw 2.295 2.440 nonbonded pdb=" O HIS A 417 " pdb=" OG1 THR A 421 " model vdw 2.295 2.440 nonbonded pdb=" O HIS D 417 " pdb=" OG1 THR D 421 " model vdw 2.295 2.440 ... (remaining 177135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.350 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 56.130 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.150 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.790 ------------------------------------------------------------------------------- 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= 0.545 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 : 2.201 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: 1.4131 time to fit residues: 932.7327 Evaluate side-chains 344 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 339 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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: 0.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 HIS A 671 ASN B 314 ASN B 671 ASN 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23076 Z= 0.311 Angle : 0.694 7.396 30888 Z= 0.342 Chirality : 0.042 0.196 3308 Planarity : 0.006 0.052 3716 Dihedral : 24.117 157.072 4226 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.94 % Favored : 94.91 % Rotamer: Outliers : 4.01 % Allowed : 12.04 % Favored : 83.95 % 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: -3.64 (0.13), residues: 2552 helix: -2.18 (0.10), residues: 1556 sheet: -0.86 (0.42), residues: 112 loop : -2.78 (0.17), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 692 HIS 0.009 0.002 HIS B 471 PHE 0.026 0.002 PHE C 633 TYR 0.020 0.002 TYR D 451 ARG 0.006 0.001 ARG C 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: 91 poor density : 372 time to evaluate : 2.479 Fit side-chains REVERT: A 220 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8051 (m-40) REVERT: A 309 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: A 478 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7065 (tmmt) REVERT: A 690 ARG cc_start: 0.7483 (mtt90) cc_final: 0.6960 (mtm110) REVERT: B 129 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7202 (pm20) REVERT: B 159 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6789 (mmp) REVERT: B 309 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: B 478 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7134 (tmmt) REVERT: B 690 ARG cc_start: 0.7460 (mtt90) cc_final: 0.7066 (mtm110) REVERT: B 702 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7667 (mm-30) REVERT: C 210 GLU cc_start: 0.7268 (tp30) cc_final: 0.6935 (tp30) REVERT: C 327 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.6845 (mmm-85) REVERT: C 367 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7300 (pt0) REVERT: C 478 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7109 (tmmt) REVERT: C 631 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: C 716 ARG cc_start: 0.8006 (ttp-170) cc_final: 0.7337 (tpm170) REVERT: D 202 ARG cc_start: 0.8153 (ptm160) cc_final: 0.7847 (ptm160) REVERT: D 368 LYS cc_start: 0.8380 (mmmm) cc_final: 0.8067 (ttmp) REVERT: D 371 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7946 (ttp80) REVERT: D 478 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7079 (tmmt) REVERT: D 581 LYS cc_start: 0.7229 (tppt) cc_final: 0.6892 (mmpt) REVERT: D 716 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7282 (tpp-160) outliers start: 91 outliers final: 25 residues processed: 431 average time/residue: 1.4364 time to fit residues: 703.3405 Evaluate side-chains 356 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 320 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 309 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 322 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 536 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 211 GLU 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 536 SER Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain D residue 229 ASP 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 536 SER 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: 8.9990 chunk 72 optimal weight: 0.6980 chunk 193 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 286 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 645 GLN B 279 GLN B 286 GLN C 286 GLN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 279 GLN D 286 GLN D 330 ASN D 643 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23076 Z= 0.247 Angle : 0.606 9.333 30888 Z= 0.299 Chirality : 0.039 0.151 3308 Planarity : 0.004 0.049 3716 Dihedral : 22.710 152.449 4224 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.03 % Allowed : 13.14 % 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: -2.05 (0.15), residues: 2552 helix: -0.76 (0.12), residues: 1596 sheet: -0.68 (0.43), residues: 112 loop : -2.45 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 692 HIS 0.008 0.001 HIS C 301 PHE 0.015 0.001 PHE A 316 TYR 0.031 0.002 TYR A 390 ARG 0.007 0.001 ARG A 487 *********************** 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 455 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 341 time to evaluate : 2.550 Fit side-chains REVERT: A 156 ASP cc_start: 0.7788 (t0) cc_final: 0.7225 (p0) REVERT: A 253 LYS cc_start: 0.7820 (ttmp) cc_final: 0.7499 (mmtt) REVERT: A 309 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: A 355 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: A 431 MET cc_start: 0.6816 (mtm) cc_final: 0.6555 (mtp) REVERT: A 478 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.6989 (tmmt) REVERT: A 690 ARG cc_start: 0.7495 (mtt90) cc_final: 0.7078 (mtm110) REVERT: A 691 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8042 (pt) REVERT: A 716 ARG cc_start: 0.7950 (ttp-170) cc_final: 0.7238 (tpp-160) REVERT: B 156 ASP cc_start: 0.7674 (t0) cc_final: 0.7012 (p0) REVERT: B 159 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6598 (mmp) REVERT: B 202 ARG cc_start: 0.8126 (ptm160) cc_final: 0.7674 (ptm160) REVERT: B 253 LYS cc_start: 0.7824 (ttmp) cc_final: 0.7514 (mmtt) REVERT: B 309 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: B 355 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.6143 (mp0) REVERT: B 431 MET cc_start: 0.6811 (mtm) cc_final: 0.6589 (mtp) REVERT: B 478 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7051 (tmmt) REVERT: B 631 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: B 690 ARG cc_start: 0.7531 (mtt90) cc_final: 0.7151 (mtm110) REVERT: B 691 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.8010 (pt) REVERT: B 716 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7265 (tpp-160) REVERT: C 156 ASP cc_start: 0.7653 (t0) cc_final: 0.7167 (p0) REVERT: C 309 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: C 330 ASN cc_start: 0.8208 (m110) cc_final: 0.7980 (m-40) REVERT: C 355 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6191 (mp0) REVERT: C 367 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7252 (pt0) REVERT: C 431 MET cc_start: 0.6663 (mtm) cc_final: 0.6110 (mmp) REVERT: C 478 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6885 (tmmt) REVERT: C 631 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: C 690 ARG cc_start: 0.7241 (mtm110) cc_final: 0.6916 (mtm110) REVERT: C 691 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7995 (pt) REVERT: C 712 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7677 (mtm110) REVERT: C 716 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7265 (tpm170) REVERT: C 736 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6525 (pt0) REVERT: D 202 ARG cc_start: 0.8063 (ptm160) cc_final: 0.7752 (ptm160) REVERT: D 279 GLN cc_start: 0.8389 (mt0) cc_final: 0.8064 (mt0) REVERT: D 283 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: D 291 SER cc_start: 0.8655 (m) cc_final: 0.8335 (p) REVERT: D 309 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: D 368 LYS cc_start: 0.8480 (mmmm) cc_final: 0.8197 (ttmp) REVERT: D 431 MET cc_start: 0.6548 (mtp) cc_final: 0.6150 (mmt) REVERT: D 472 PRO cc_start: 0.8429 (Cg_exo) cc_final: 0.8219 (Cg_endo) REVERT: D 478 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6829 (tmmt) REVERT: D 581 LYS cc_start: 0.7174 (tppt) cc_final: 0.6918 (mmtt) REVERT: D 687 GLU cc_start: 0.7378 (tp30) cc_final: 0.7139 (tp30) REVERT: D 690 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7188 (mtm110) REVERT: D 691 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8126 (mt) REVERT: D 716 ARG cc_start: 0.8029 (ttp-170) cc_final: 0.7256 (tpp-160) outliers start: 114 outliers final: 20 residues processed: 413 average time/residue: 1.4500 time to fit residues: 678.4823 Evaluate side-chains 348 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 306 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 691 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 0.0670 chunk 111 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 221 optimal weight: 0.4980 chunk 66 optimal weight: 7.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 286 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 279 GLN B 286 GLN B 643 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4334 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= 0.125 Angle : 0.500 6.376 30888 Z= 0.250 Chirality : 0.037 0.137 3308 Planarity : 0.003 0.047 3716 Dihedral : 21.508 146.774 4224 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.01 % Allowed : 15.70 % 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: -1.13 (0.16), residues: 2552 helix: 0.04 (0.13), residues: 1616 sheet: -0.36 (0.44), residues: 112 loop : -2.32 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 692 HIS 0.005 0.001 HIS B 160 PHE 0.013 0.001 PHE B 316 TYR 0.024 0.001 TYR D 461 ARG 0.006 0.000 ARG B 371 *********************** 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 417 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 326 time to evaluate : 2.372 Fit side-chains revert: symmetry clash REVERT: A 156 ASP cc_start: 0.7658 (t0) cc_final: 0.7201 (p0) REVERT: A 202 ARG cc_start: 0.8048 (ptp-170) cc_final: 0.7823 (ptm160) REVERT: A 253 LYS cc_start: 0.7777 (ttmp) cc_final: 0.7500 (mmtt) REVERT: A 327 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.6774 (mmm160) REVERT: A 431 MET cc_start: 0.6708 (mtm) cc_final: 0.6441 (mtp) REVERT: A 478 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.6907 (tmmt) REVERT: A 641 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.8061 (p0) REVERT: A 690 ARG cc_start: 0.7501 (mtt90) cc_final: 0.7108 (mtm110) REVERT: A 716 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.7239 (tpp-160) REVERT: B 156 ASP cc_start: 0.7461 (t0) cc_final: 0.7007 (p0) REVERT: B 159 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6461 (mmp) REVERT: B 202 ARG cc_start: 0.8076 (ptm160) cc_final: 0.7576 (ptm160) REVERT: B 253 LYS cc_start: 0.7779 (ttmp) cc_final: 0.7466 (mmtt) REVERT: B 309 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: B 478 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7075 (tmmt) REVERT: B 487 ARG cc_start: 0.7341 (mpt-90) cc_final: 0.7138 (mtt-85) REVERT: B 581 LYS cc_start: 0.7912 (tmtt) cc_final: 0.6624 (mmtm) REVERT: B 631 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: B 641 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7957 (p0) REVERT: B 716 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7302 (tpm170) REVERT: C 156 ASP cc_start: 0.7551 (t0) cc_final: 0.7108 (p0) REVERT: C 367 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7352 (pt0) REVERT: C 431 MET cc_start: 0.6526 (mtm) cc_final: 0.6212 (mmt) REVERT: C 478 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6935 (tmmt) REVERT: C 631 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: C 712 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7628 (mtm110) REVERT: C 716 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7254 (tpp-160) REVERT: D 202 ARG cc_start: 0.8056 (ptm160) cc_final: 0.7734 (ptm160) REVERT: D 286 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: D 291 SER cc_start: 0.8667 (m) cc_final: 0.8377 (p) REVERT: D 368 LYS cc_start: 0.8387 (mmmm) cc_final: 0.8067 (ttmp) REVERT: D 431 MET cc_start: 0.6538 (mtp) cc_final: 0.6235 (mmt) REVERT: D 478 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6828 (tmmt) REVERT: D 581 LYS cc_start: 0.7130 (tppt) cc_final: 0.6929 (mmtm) REVERT: D 641 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8161 (p0) REVERT: D 691 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7848 (mt) REVERT: D 716 ARG cc_start: 0.8001 (ttp-170) cc_final: 0.7311 (tpm170) outliers start: 91 outliers final: 21 residues processed: 387 average time/residue: 1.4979 time to fit residues: 658.1123 Evaluate side-chains 348 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 312 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 309 ASP 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 548 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 286 GLN 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 641 ASP 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: 5.9990 chunk 140 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 0.0770 chunk 222 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 overall best weight: 1.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN B 643 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 279 GLN D 330 ASN D 643 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23076 Z= 0.169 Angle : 0.523 6.422 30888 Z= 0.259 Chirality : 0.038 0.145 3308 Planarity : 0.003 0.046 3716 Dihedral : 20.986 144.662 4224 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.01 % Allowed : 15.87 % Favored : 80.11 % 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: -0.61 (0.17), residues: 2552 helix: 0.53 (0.13), residues: 1592 sheet: -0.28 (0.45), residues: 112 loop : -2.20 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 692 HIS 0.006 0.001 HIS B 160 PHE 0.013 0.001 PHE D 316 TYR 0.027 0.002 TYR C 461 ARG 0.006 0.000 ARG B 371 *********************** 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 412 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 321 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.7535 (t0) cc_final: 0.7244 (p0) REVERT: A 202 ARG cc_start: 0.8030 (ptp-170) cc_final: 0.7766 (ptm160) REVERT: A 220 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.7922 (m-40) REVERT: A 253 LYS cc_start: 0.7806 (ttmp) cc_final: 0.7510 (mmtt) REVERT: A 327 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.6729 (mmm160) REVERT: A 478 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6858 (tmmt) REVERT: A 495 MET cc_start: 0.7533 (mtt) cc_final: 0.7316 (mtt) REVERT: A 581 LYS cc_start: 0.7912 (tmtt) cc_final: 0.6560 (mmtm) REVERT: A 690 ARG cc_start: 0.7445 (mtt90) cc_final: 0.7137 (mtm110) REVERT: A 716 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.7254 (tpp-160) REVERT: B 156 ASP cc_start: 0.7457 (t0) cc_final: 0.7012 (p0) REVERT: B 253 LYS cc_start: 0.7878 (ttmp) cc_final: 0.7516 (mmtt) REVERT: B 309 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7488 (m-30) REVERT: B 478 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.6974 (tmmt) REVERT: B 581 LYS cc_start: 0.7883 (tmtt) cc_final: 0.6563 (mmtm) REVERT: B 641 ASP cc_start: 0.8248 (p0) cc_final: 0.8047 (p0) REVERT: B 716 ARG cc_start: 0.7994 (ttp-170) cc_final: 0.7249 (tpp-160) REVERT: C 156 ASP cc_start: 0.7563 (t0) cc_final: 0.7218 (p0) REVERT: C 253 LYS cc_start: 0.7849 (ttmp) cc_final: 0.7464 (mmtt) REVERT: C 367 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7378 (pt0) REVERT: C 431 MET cc_start: 0.6578 (mtm) cc_final: 0.6270 (mmp) REVERT: C 478 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6855 (tmmt) REVERT: C 631 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: C 712 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7557 (mtm110) REVERT: C 716 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7185 (tpp-160) REVERT: C 736 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6617 (pt0) REVERT: D 148 ARG cc_start: 0.6113 (OUTLIER) cc_final: 0.5878 (mpt180) REVERT: D 291 SER cc_start: 0.8654 (m) cc_final: 0.8369 (p) REVERT: D 368 LYS cc_start: 0.8373 (mmmm) cc_final: 0.8028 (ttmp) REVERT: D 431 MET cc_start: 0.6565 (mtp) cc_final: 0.6233 (mmt) REVERT: D 478 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6775 (tmmt) REVERT: D 482 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6870 (pt) REVERT: D 581 LYS cc_start: 0.7168 (tppt) cc_final: 0.6957 (mmtm) REVERT: D 641 ASP cc_start: 0.8402 (p0) cc_final: 0.8183 (p0) REVERT: D 691 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8040 (mt) REVERT: D 716 ARG cc_start: 0.8033 (ttp-170) cc_final: 0.7269 (tpm170) REVERT: D 741 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6711 (mp0) outliers start: 91 outliers final: 27 residues processed: 383 average time/residue: 1.4554 time to fit residues: 631.7262 Evaluate side-chains 347 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 306 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL 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 327 ARG Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 327 ARG 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 536 SER Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 309 ASP 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 484 LEU Chi-restraints excluded: chain C residue 536 SER 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 148 ARG 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 482 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 286 GLN B 643 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 330 ASN D 643 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23076 Z= 0.125 Angle : 0.484 8.328 30888 Z= 0.242 Chirality : 0.037 0.139 3308 Planarity : 0.003 0.046 3716 Dihedral : 20.024 135.897 4224 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.22 % Allowed : 16.89 % Favored : 79.89 % 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: -0.25 (0.17), residues: 2552 helix: 0.77 (0.13), residues: 1616 sheet: -0.03 (0.47), residues: 112 loop : -2.07 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 739 HIS 0.006 0.001 HIS B 160 PHE 0.012 0.001 PHE B 316 TYR 0.019 0.001 TYR C 461 ARG 0.007 0.000 ARG B 371 *********************** 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 398 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 325 time to evaluate : 2.607 Fit side-chains revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5530 (OUTLIER) cc_final: 0.5248 (mpt180) REVERT: A 202 ARG cc_start: 0.7994 (ptp-170) cc_final: 0.7653 (ptm160) REVERT: A 253 LYS cc_start: 0.7811 (ttmp) cc_final: 0.7530 (mmtt) REVERT: A 327 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.6658 (mmm160) REVERT: A 431 MET cc_start: 0.6719 (mtp) cc_final: 0.6432 (mtp) REVERT: A 478 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6794 (tmmt) REVERT: A 581 LYS cc_start: 0.7911 (tmtt) cc_final: 0.6580 (mmtm) REVERT: A 690 ARG cc_start: 0.7449 (mtt90) cc_final: 0.7169 (mtm110) REVERT: A 716 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.7206 (tpp-160) REVERT: B 156 ASP cc_start: 0.7509 (t0) cc_final: 0.7024 (p0) REVERT: B 253 LYS cc_start: 0.7826 (ttmp) cc_final: 0.7501 (mmtt) REVERT: B 478 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6947 (tmmt) REVERT: B 581 LYS cc_start: 0.7873 (tmtt) cc_final: 0.6585 (mmtm) REVERT: B 690 ARG cc_start: 0.7505 (mtt90) cc_final: 0.7126 (mtm110) REVERT: B 716 ARG cc_start: 0.7943 (ttp-170) cc_final: 0.7231 (tpp-160) REVERT: B 750 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.8010 (m-40) REVERT: C 253 LYS cc_start: 0.7881 (ttmp) cc_final: 0.7482 (mmtt) REVERT: C 367 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7397 (pt0) REVERT: C 431 MET cc_start: 0.6558 (mtm) cc_final: 0.6243 (mmp) REVERT: C 478 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6851 (tmmt) REVERT: C 553 LEU cc_start: 0.7859 (mp) cc_final: 0.7618 (tp) REVERT: C 581 LYS cc_start: 0.7879 (tmtt) cc_final: 0.6567 (mmtm) REVERT: C 631 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: C 712 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7505 (mtm110) REVERT: C 716 ARG cc_start: 0.8002 (ttp-170) cc_final: 0.7198 (tpp-160) REVERT: D 145 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6950 (mt) REVERT: D 148 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5919 (mpt90) REVERT: D 202 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7683 (ptm160) REVERT: D 283 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: D 291 SER cc_start: 0.8650 (m) cc_final: 0.8400 (p) REVERT: D 368 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7888 (ttmp) REVERT: D 431 MET cc_start: 0.6548 (mtp) cc_final: 0.6168 (mmp) REVERT: D 478 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6841 (tmmt) REVERT: D 482 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6797 (pt) REVERT: D 581 LYS cc_start: 0.7168 (tppt) cc_final: 0.6962 (mmtm) REVERT: D 641 ASP cc_start: 0.8386 (p0) cc_final: 0.8164 (p0) REVERT: D 691 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7859 (mt) REVERT: D 716 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7205 (tpp-160) REVERT: D 741 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6794 (mp0) outliers start: 73 outliers final: 22 residues processed: 375 average time/residue: 1.4837 time to fit residues: 629.6614 Evaluate side-chains 347 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 310 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 536 SER 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 572 MET Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 309 ASP 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 548 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 283 GLU 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 482 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 141 optimal weight: 0.4980 chunk 180 optimal weight: 7.9990 chunk 140 optimal weight: 0.0570 chunk 208 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 246 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 286 GLN B 643 ASN C 274 GLN C 286 GLN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 274 GLN D 279 GLN D 330 ASN D 643 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23076 Z= 0.137 Angle : 0.500 9.247 30888 Z= 0.248 Chirality : 0.037 0.145 3308 Planarity : 0.003 0.053 3716 Dihedral : 19.612 128.583 4224 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.70 % Allowed : 16.49 % Favored : 79.81 % 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: 0.05 (0.17), residues: 2552 helix: 1.08 (0.13), residues: 1588 sheet: -0.03 (0.47), residues: 112 loop : -1.99 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 692 HIS 0.007 0.001 HIS B 160 PHE 0.012 0.001 PHE C 316 TYR 0.017 0.001 TYR D 461 ARG 0.016 0.000 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 315 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5445 (OUTLIER) cc_final: 0.5241 (mpt180) REVERT: A 253 LYS cc_start: 0.7800 (ttmp) cc_final: 0.7531 (mmtt) REVERT: A 327 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.6662 (mmm160) REVERT: A 431 MET cc_start: 0.6702 (mtp) cc_final: 0.6415 (mtp) REVERT: A 478 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6793 (ttpt) REVERT: A 495 MET cc_start: 0.7538 (mtt) cc_final: 0.7322 (mtt) REVERT: A 581 LYS cc_start: 0.7914 (tmtt) cc_final: 0.6577 (mmtm) REVERT: A 690 ARG cc_start: 0.7453 (mtt90) cc_final: 0.7162 (mtm110) REVERT: A 716 ARG cc_start: 0.7940 (ttp-170) cc_final: 0.7216 (tpp-160) REVERT: B 253 LYS cc_start: 0.7894 (ttmp) cc_final: 0.7533 (mmtt) REVERT: B 478 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6964 (tmmt) REVERT: B 488 MET cc_start: 0.8017 (mmp) cc_final: 0.7744 (tpt) REVERT: B 581 LYS cc_start: 0.7870 (tmtt) cc_final: 0.6587 (mmtm) REVERT: B 690 ARG cc_start: 0.7505 (mtt90) cc_final: 0.7107 (mtm110) REVERT: B 716 ARG cc_start: 0.7940 (ttp-170) cc_final: 0.7225 (tpp-160) REVERT: C 167 THR cc_start: 0.8087 (p) cc_final: 0.7705 (t) REVERT: C 253 LYS cc_start: 0.7880 (ttmp) cc_final: 0.7452 (mmtt) REVERT: C 367 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7378 (pt0) REVERT: C 431 MET cc_start: 0.6566 (mtm) cc_final: 0.6234 (mmp) REVERT: C 478 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6747 (tmmt) REVERT: C 553 LEU cc_start: 0.7841 (mp) cc_final: 0.7608 (tp) REVERT: C 581 LYS cc_start: 0.7898 (tmtt) cc_final: 0.6577 (mmtm) REVERT: C 631 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: C 712 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7527 (mtm110) REVERT: C 716 ARG cc_start: 0.7998 (ttp-170) cc_final: 0.7180 (tpp-160) REVERT: C 736 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6689 (pt0) REVERT: D 145 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7002 (mt) REVERT: D 148 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.5986 (mpt90) REVERT: D 202 ARG cc_start: 0.8115 (ptm160) cc_final: 0.7638 (ptm160) REVERT: D 291 SER cc_start: 0.8650 (m) cc_final: 0.8408 (p) REVERT: D 368 LYS cc_start: 0.8252 (mmmm) cc_final: 0.7854 (ttmp) REVERT: D 431 MET cc_start: 0.6548 (mtp) cc_final: 0.6216 (mmt) REVERT: D 478 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6784 (tmmt) REVERT: D 482 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6816 (pt) REVERT: D 691 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7937 (mt) REVERT: D 716 ARG cc_start: 0.8029 (ttp-170) cc_final: 0.7265 (tpm170) REVERT: D 738 LYS cc_start: 0.8883 (tttp) cc_final: 0.8620 (tttp) REVERT: D 741 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6792 (mp0) outliers start: 84 outliers final: 25 residues processed: 374 average time/residue: 1.4168 time to fit residues: 603.3757 Evaluate side-chains 346 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 307 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 327 ARG 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 129 GLU 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 572 MET Chi-restraints excluded: chain B residue 732 LEU 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 309 ASP Chi-restraints excluded: chain C residue 323 MET 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 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 145 LEU Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain D residue 229 ASP 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 482 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 147 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 160 HIS B 286 GLN B 643 ASN C 286 GLN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 643 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23076 Z= 0.128 Angle : 0.489 9.076 30888 Z= 0.244 Chirality : 0.037 0.150 3308 Planarity : 0.003 0.075 3716 Dihedral : 19.141 118.631 4224 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.47 % Allowed : 17.86 % Favored : 79.67 % 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: 0.24 (0.17), residues: 2552 helix: 1.23 (0.13), residues: 1588 sheet: 0.09 (0.47), residues: 112 loop : -1.94 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 710 HIS 0.006 0.001 HIS B 160 PHE 0.012 0.001 PHE C 316 TYR 0.015 0.001 TYR C 461 ARG 0.017 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 375 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 319 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5549 (OUTLIER) cc_final: 0.5324 (mpt180) REVERT: A 253 LYS cc_start: 0.7894 (ttmp) cc_final: 0.7607 (mmtt) REVERT: A 327 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.6693 (mmm160) REVERT: A 431 MET cc_start: 0.6643 (mtp) cc_final: 0.6387 (mtp) REVERT: A 478 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6730 (ttpt) REVERT: A 495 MET cc_start: 0.7497 (mtt) cc_final: 0.7280 (mtt) REVERT: A 581 LYS cc_start: 0.7918 (tmtt) cc_final: 0.6577 (mmpt) REVERT: A 690 ARG cc_start: 0.7464 (mtt90) cc_final: 0.7128 (mtm110) REVERT: A 716 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7210 (tpp-160) REVERT: B 202 ARG cc_start: 0.8137 (ptm160) cc_final: 0.7903 (ptm160) REVERT: B 253 LYS cc_start: 0.7900 (ttmp) cc_final: 0.7537 (mmtt) REVERT: B 478 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6930 (tmmt) REVERT: B 581 LYS cc_start: 0.7865 (tmtt) cc_final: 0.6598 (mmtt) REVERT: B 690 ARG cc_start: 0.7452 (mtt90) cc_final: 0.7103 (mtm110) REVERT: B 716 ARG cc_start: 0.7923 (ttp-170) cc_final: 0.7212 (tpp-160) REVERT: C 167 THR cc_start: 0.8142 (p) cc_final: 0.7744 (t) REVERT: C 202 ARG cc_start: 0.8002 (ptm160) cc_final: 0.7671 (ptm160) REVERT: C 253 LYS cc_start: 0.7892 (ttmp) cc_final: 0.7469 (mmtt) REVERT: C 367 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7385 (pt0) REVERT: C 431 MET cc_start: 0.6562 (mtm) cc_final: 0.6226 (mmp) REVERT: C 478 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6723 (tmmt) REVERT: C 488 MET cc_start: 0.7853 (mmp) cc_final: 0.7521 (tpt) REVERT: C 553 LEU cc_start: 0.7821 (mp) cc_final: 0.7595 (tp) REVERT: C 581 LYS cc_start: 0.7904 (tmtt) cc_final: 0.6572 (mmpt) REVERT: C 631 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: C 712 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7506 (mtm110) REVERT: C 716 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7163 (tpp-160) REVERT: C 736 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6678 (pt0) REVERT: D 145 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7015 (mt) REVERT: D 148 ARG cc_start: 0.6200 (OUTLIER) cc_final: 0.5985 (mpt90) REVERT: D 291 SER cc_start: 0.8651 (m) cc_final: 0.8432 (p) REVERT: D 368 LYS cc_start: 0.8301 (mmmm) cc_final: 0.7897 (ttmp) REVERT: D 431 MET cc_start: 0.6554 (mtp) cc_final: 0.6226 (mmt) REVERT: D 478 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6694 (tmmt) REVERT: D 482 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6820 (pt) REVERT: D 691 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7883 (mt) REVERT: D 716 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7220 (tpp-160) REVERT: D 738 LYS cc_start: 0.8875 (tttp) cc_final: 0.8596 (tttp) REVERT: D 741 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6796 (mp0) outliers start: 56 outliers final: 20 residues processed: 357 average time/residue: 1.4560 time to fit residues: 589.5728 Evaluate side-chains 345 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 311 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 327 ARG 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 229 ASP 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 572 MET Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 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 C residue 740 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain D residue 229 ASP 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 548 LEU Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 732 LEU 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: 8.9990 chunk 236 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 chunk 180 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 207 optimal weight: 0.0770 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 160 HIS B 286 GLN B 643 ASN C 286 GLN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 643 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4979 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= 0.122 Angle : 0.490 10.031 30888 Z= 0.243 Chirality : 0.037 0.149 3308 Planarity : 0.003 0.077 3716 Dihedral : 18.588 109.404 4224 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.16 % Allowed : 18.61 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2552 helix: 1.36 (0.13), residues: 1584 sheet: 0.19 (0.48), residues: 112 loop : -1.88 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 710 HIS 0.006 0.001 HIS B 160 PHE 0.011 0.001 PHE C 316 TYR 0.015 0.001 TYR D 461 ARG 0.018 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 358 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 309 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5602 (OUTLIER) cc_final: 0.5359 (mpt180) REVERT: A 202 ARG cc_start: 0.7875 (ptm160) cc_final: 0.7597 (ptm160) REVERT: A 253 LYS cc_start: 0.7895 (ttmp) cc_final: 0.7555 (mmtt) REVERT: A 327 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.6695 (mmm160) REVERT: A 431 MET cc_start: 0.6639 (mtp) cc_final: 0.6376 (mtp) REVERT: A 478 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6821 (ttpt) REVERT: A 495 MET cc_start: 0.7478 (mtt) cc_final: 0.7226 (mtt) REVERT: A 581 LYS cc_start: 0.7910 (tmtt) cc_final: 0.6587 (mmtm) REVERT: A 690 ARG cc_start: 0.7464 (mtt90) cc_final: 0.7115 (mtm110) REVERT: A 716 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7200 (tpp-160) REVERT: B 253 LYS cc_start: 0.7938 (ttmp) cc_final: 0.7574 (mmtt) REVERT: B 478 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6928 (tmmt) REVERT: B 488 MET cc_start: 0.7903 (mmp) cc_final: 0.7606 (tpt) REVERT: B 581 LYS cc_start: 0.7921 (tmtt) cc_final: 0.6603 (mmpt) REVERT: B 716 ARG cc_start: 0.7944 (ttp-170) cc_final: 0.7237 (tpp-160) REVERT: C 167 THR cc_start: 0.8140 (p) cc_final: 0.7782 (t) REVERT: C 202 ARG cc_start: 0.7993 (ptm160) cc_final: 0.7663 (ptm160) REVERT: C 253 LYS cc_start: 0.7939 (ttmp) cc_final: 0.7524 (mmtt) REVERT: C 367 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7388 (pt0) REVERT: C 431 MET cc_start: 0.6536 (mtm) cc_final: 0.6205 (mmt) REVERT: C 478 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6737 (tmmt) REVERT: C 553 LEU cc_start: 0.7798 (mp) cc_final: 0.7583 (tp) REVERT: C 581 LYS cc_start: 0.7904 (tmtt) cc_final: 0.6569 (mmpt) REVERT: C 631 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: C 716 ARG cc_start: 0.7997 (ttp-170) cc_final: 0.7152 (tpp-160) REVERT: C 736 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6672 (pt0) REVERT: D 145 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7060 (mt) REVERT: D 202 ARG cc_start: 0.8094 (ptm160) cc_final: 0.7589 (ptm160) REVERT: D 291 SER cc_start: 0.8655 (m) cc_final: 0.8449 (p) REVERT: D 431 MET cc_start: 0.6562 (mtp) cc_final: 0.6222 (mmt) REVERT: D 478 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6628 (tmmt) REVERT: D 482 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6836 (pt) REVERT: D 691 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7855 (mt) REVERT: D 716 ARG cc_start: 0.8026 (ttp-170) cc_final: 0.7202 (tpp-160) REVERT: D 738 LYS cc_start: 0.8884 (tttp) cc_final: 0.8656 (tttp) REVERT: D 741 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6787 (mp0) outliers start: 49 outliers final: 16 residues processed: 340 average time/residue: 1.4325 time to fit residues: 554.9700 Evaluate side-chains 332 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 304 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 327 ARG 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 229 ASP Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 145 LEU 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 691 ILE Chi-restraints excluded: chain D residue 732 LEU 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: 0.8980 chunk 148 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 255 optimal weight: 0.0870 chunk 234 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 156 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 160 HIS B 286 GLN B 643 ASN C 286 GLN C 643 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5059 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 : 0.485 9.026 30888 Z= 0.242 Chirality : 0.036 0.147 3308 Planarity : 0.003 0.080 3716 Dihedral : 18.020 106.103 4224 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.68 % Allowed : 19.00 % Favored : 79.32 % 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: 1.47 (0.13), residues: 1576 sheet: 0.31 (0.49), residues: 112 loop : -1.88 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 710 HIS 0.007 0.001 HIS B 160 PHE 0.011 0.001 PHE A 316 TYR 0.015 0.001 TYR D 461 ARG 0.019 0.000 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 355 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 317 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5716 (OUTLIER) cc_final: 0.5444 (mpt180) REVERT: A 202 ARG cc_start: 0.7888 (ptm160) cc_final: 0.7654 (ptm160) REVERT: A 253 LYS cc_start: 0.7902 (ttmp) cc_final: 0.7560 (mmtt) REVERT: A 327 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.6944 (mmm160) REVERT: A 431 MET cc_start: 0.6641 (mtp) cc_final: 0.6377 (mtp) REVERT: A 478 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6746 (ttpt) REVERT: A 495 MET cc_start: 0.7449 (mtt) cc_final: 0.7195 (mtt) REVERT: A 581 LYS cc_start: 0.7910 (tmtt) cc_final: 0.6592 (mmtm) REVERT: A 690 ARG cc_start: 0.7429 (mtt90) cc_final: 0.7083 (mtm110) REVERT: A 716 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7243 (tpp-160) REVERT: B 202 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7940 (ptm160) REVERT: B 253 LYS cc_start: 0.7901 (ttmp) cc_final: 0.7576 (mmtt) REVERT: B 461 TYR cc_start: 0.6349 (t80) cc_final: 0.6082 (t80) REVERT: B 478 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6900 (tmmt) REVERT: B 581 LYS cc_start: 0.7853 (tmtt) cc_final: 0.6575 (mmtt) REVERT: B 690 ARG cc_start: 0.7451 (mtt90) cc_final: 0.7090 (mtm110) REVERT: B 716 ARG cc_start: 0.7896 (ttp-170) cc_final: 0.7281 (tpp-160) REVERT: C 167 THR cc_start: 0.8123 (p) cc_final: 0.7740 (t) REVERT: C 202 ARG cc_start: 0.7987 (ptm160) cc_final: 0.7660 (ptm160) REVERT: C 253 LYS cc_start: 0.7966 (ttmp) cc_final: 0.7537 (mmtt) REVERT: C 320 MET cc_start: 0.8954 (mmt) cc_final: 0.8707 (mmt) REVERT: C 367 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7387 (pt0) REVERT: C 431 MET cc_start: 0.6498 (mtm) cc_final: 0.6185 (mmt) REVERT: C 478 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6770 (tmmt) REVERT: C 482 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6869 (pt) REVERT: C 553 LEU cc_start: 0.7792 (mp) cc_final: 0.7591 (tp) REVERT: C 581 LYS cc_start: 0.7887 (tmtt) cc_final: 0.6561 (mmpt) REVERT: C 631 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: C 716 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.7159 (tpp-160) REVERT: C 736 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6679 (pt0) REVERT: D 121 LYS cc_start: 0.8263 (mmtm) cc_final: 0.8029 (mmmm) REVERT: D 202 ARG cc_start: 0.8101 (ptm160) cc_final: 0.7595 (ptm160) REVERT: D 368 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7841 (ttmp) REVERT: D 431 MET cc_start: 0.6559 (mtp) cc_final: 0.6210 (mmt) REVERT: D 478 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6659 (tmmt) REVERT: D 482 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6839 (pt) REVERT: D 691 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7806 (mt) REVERT: D 716 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.7230 (tpp-160) REVERT: D 738 LYS cc_start: 0.8876 (tttp) cc_final: 0.8638 (tttp) REVERT: D 741 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6807 (mp0) outliers start: 38 outliers final: 13 residues processed: 343 average time/residue: 1.4745 time to fit residues: 572.5978 Evaluate side-chains 329 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 304 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 327 ARG 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 732 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 631 GLU 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 536 SER Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 732 LEU 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: 0.9990 chunk 62 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 203 optimal weight: 0.0020 chunk 85 optimal weight: 10.0000 chunk 208 optimal weight: 0.0270 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN B 643 ASN C 286 GLN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 274 GLN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118232 restraints weight = 25716.299| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.40 r_work: 0.3170 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5126 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= 0.156 Angle : 0.516 9.314 30888 Z= 0.256 Chirality : 0.038 0.163 3308 Planarity : 0.003 0.079 3716 Dihedral : 17.999 106.128 4224 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.85 % Allowed : 18.92 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2552 helix: 1.41 (0.13), residues: 1588 sheet: 0.27 (0.49), residues: 112 loop : -1.96 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 710 HIS 0.005 0.001 HIS C 301 PHE 0.010 0.001 PHE A 316 TYR 0.015 0.001 TYR D 461 ARG 0.019 0.000 ARG D 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9517.95 seconds wall clock time: 170 minutes 51.08 seconds (10251.08 seconds total)