Starting phenix.real_space_refine on Thu Mar 5 13:53:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mio_23858/03_2026/7mio_23858.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mio_23858/03_2026/7mio_23858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mio_23858/03_2026/7mio_23858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mio_23858/03_2026/7mio_23858.map" model { file = "/net/cci-nas-00/data/ceres_data/7mio_23858/03_2026/7mio_23858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mio_23858/03_2026/7mio_23858.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 28 5.49 5 S 132 5.16 5 Na 1 4.78 5 C 15124 2.51 5 N 3588 2.21 5 O 4072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22945 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5372 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 18, 'TRANS': 640} Chain breaks: 1 Chain: "B" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5372 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 18, 'TRANS': 640} Chain breaks: 1 Chain: "C" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5372 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 18, 'TRANS': 640} Chain breaks: 1 Chain: "D" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5372 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 18, 'TRANS': 640} Chain breaks: 1 Chain: "A" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 365 Unusual residues: {' NA': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 5.52, per 1000 atoms: 0.24 Number of scatterers: 22945 At special positions: 0 Unit cell: (141.944, 141.944, 128.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 28 15.00 Na 1 11.00 O 4072 8.00 N 3588 7.00 C 15124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5064 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 62.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.706A pdb=" N LEU A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.681A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 161 removed outlier: 3.717A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.787A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.728A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.584A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.787A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 removed outlier: 3.778A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.552A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.606A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.812A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.534A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.762A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 374' Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.733A pdb=" N ILE A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 3.577A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.708A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.554A pdb=" N MET A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 507 removed outlier: 4.115A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 497 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.681A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 4.028A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.736A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 575 removed outlier: 4.185A pdb=" N MET A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.714A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 4.445A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.689A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 removed outlier: 3.535A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 687 removed outlier: 3.653A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 704 removed outlier: 3.592A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'A' and resid 738 through 748 removed outlier: 3.670A pdb=" N THR A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 removed outlier: 3.706A pdb=" N LEU B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 148 removed outlier: 3.680A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.717A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.787A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.728A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.585A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.788A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 removed outlier: 3.777A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.552A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.607A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.811A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.534A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.762A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 374' Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.733A pdb=" N ILE B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.577A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.709A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.554A pdb=" N MET B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 507 removed outlier: 4.115A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.681A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 561 removed outlier: 4.028A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.735A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 575 removed outlier: 4.184A pdb=" N MET B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.714A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 4.445A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 3.690A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 removed outlier: 3.535A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 687 removed outlier: 3.653A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 704 removed outlier: 3.592A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'B' and resid 738 through 748 removed outlier: 3.670A pdb=" N THR B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 removed outlier: 3.706A pdb=" N LEU C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.681A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.717A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.788A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.728A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.584A pdb=" N ASN C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.787A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 236 removed outlier: 3.777A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 271 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.552A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.606A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.812A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.534A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.761A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 374' Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.733A pdb=" N ILE C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 removed outlier: 3.577A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.708A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.553A pdb=" N MET C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 507 removed outlier: 4.115A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 497 " --> pdb=" O TRP C 493 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.681A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 561 removed outlier: 4.028A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.736A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 575 removed outlier: 4.184A pdb=" N MET C 574 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.714A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 583 " --> pdb=" O ILE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 4.445A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.689A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 removed outlier: 3.535A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 687 removed outlier: 3.654A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 704 removed outlier: 3.592A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 697 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 704 " --> pdb=" O ILE C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 738 through 748 removed outlier: 3.670A pdb=" N THR C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 130 removed outlier: 3.706A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 122 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 148 removed outlier: 3.680A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 161 removed outlier: 3.717A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS D 161 " --> pdb=" O PHE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.788A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.728A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.584A pdb=" N ASN D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.788A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 236 removed outlier: 3.777A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 271 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.551A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.606A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.812A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.534A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.761A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 374 " --> pdb=" O ARG D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 374' Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.734A pdb=" N ILE D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 421 removed outlier: 3.577A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.708A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.553A pdb=" N MET D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 507 removed outlier: 4.115A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 497 " --> pdb=" O TRP D 493 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.682A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 561 removed outlier: 4.028A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.736A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 575 removed outlier: 4.184A pdb=" N MET D 574 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.714A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 4.446A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 3.690A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 removed outlier: 3.534A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 687 removed outlier: 3.654A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 704 removed outlier: 3.591A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 704 " --> pdb=" O ILE D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing helix chain 'D' and resid 738 through 748 removed outlier: 3.670A pdb=" N THR D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 5.597A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 385 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 732 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 723 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 5.598A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 385 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 732 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 723 " --> pdb=" O ASP B 727 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 5.598A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 385 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 732 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 723 " --> pdb=" O ASP C 727 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 5.597A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 385 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 732 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL D 723 " --> pdb=" O ASP D 727 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3523 1.31 - 1.44: 6077 1.44 - 1.57: 13504 1.57 - 1.70: 56 1.70 - 1.82: 216 Bond restraints: 23376 Sorted by residual: bond pdb=" C21 POV B 903 " pdb=" O21 POV B 903 " ideal model delta sigma weight residual 1.330 1.427 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C21 POV D 905 " pdb=" O21 POV D 905 " ideal model delta sigma weight residual 1.330 1.427 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C21 POV C 903 " pdb=" O21 POV C 903 " ideal model delta sigma weight residual 1.330 1.427 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C21 POV A 907 " pdb=" O21 POV A 907 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C21 POV A 903 " pdb=" O21 POV A 903 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 23371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 30090 2.60 - 5.20: 817 5.20 - 7.81: 249 7.81 - 10.41: 92 10.41 - 13.01: 84 Bond angle restraints: 31332 Sorted by residual: angle pdb=" C THR B 411 " pdb=" N ASN B 412 " pdb=" CA ASN B 412 " ideal model delta sigma weight residual 125.66 135.12 -9.46 1.85e+00 2.92e-01 2.61e+01 angle pdb=" C THR A 411 " pdb=" N ASN A 412 " pdb=" CA ASN A 412 " ideal model delta sigma weight residual 125.66 135.08 -9.42 1.85e+00 2.92e-01 2.59e+01 angle pdb=" C THR D 411 " pdb=" N ASN D 412 " pdb=" CA ASN D 412 " ideal model delta sigma weight residual 125.66 135.06 -9.40 1.85e+00 2.92e-01 2.58e+01 angle pdb=" C THR C 411 " pdb=" N ASN C 412 " pdb=" CA ASN C 412 " ideal model delta sigma weight residual 125.66 135.05 -9.39 1.85e+00 2.92e-01 2.58e+01 angle pdb=" C12 POV D 904 " pdb=" N POV D 904 " pdb=" C14 POV D 904 " ideal model delta sigma weight residual 107.13 120.14 -13.01 3.00e+00 1.11e-01 1.88e+01 ... (remaining 31327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 13668 31.42 - 62.84: 631 62.84 - 94.26: 57 94.26 - 125.67: 20 125.67 - 157.09: 20 Dihedral angle restraints: 14396 sinusoidal: 6608 harmonic: 7788 Sorted by residual: dihedral pdb=" CA THR A 411 " pdb=" C THR A 411 " pdb=" N ASN A 412 " pdb=" CA ASN A 412 " ideal model delta harmonic sigma weight residual -180.00 -154.14 -25.86 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA THR B 411 " pdb=" C THR B 411 " pdb=" N ASN B 412 " pdb=" CA ASN B 412 " ideal model delta harmonic sigma weight residual -180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA THR C 411 " pdb=" C THR C 411 " pdb=" N ASN C 412 " pdb=" CA ASN C 412 " ideal model delta harmonic sigma weight residual -180.00 -154.20 -25.80 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 14393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2389 0.053 - 0.105: 873 0.105 - 0.158: 110 0.158 - 0.211: 32 0.211 - 0.264: 8 Chirality restraints: 3412 Sorted by residual: chirality pdb=" CB VAL C 154 " pdb=" CA VAL C 154 " pdb=" CG1 VAL C 154 " pdb=" CG2 VAL C 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB VAL A 154 " pdb=" CA VAL A 154 " pdb=" CG1 VAL A 154 " pdb=" CG2 VAL A 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB VAL D 154 " pdb=" CA VAL D 154 " pdb=" CG1 VAL D 154 " pdb=" CG2 VAL D 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 3409 not shown) Planarity restraints: 3788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 343 " -0.039 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO D 344 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 344 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 344 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 343 " 0.039 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO B 344 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 344 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 344 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 343 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO A 344 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.033 5.00e-02 4.00e+02 ... (remaining 3785 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7425 2.87 - 3.38: 19661 3.38 - 3.89: 32810 3.89 - 4.39: 39585 4.39 - 4.90: 68323 Nonbonded interactions: 167804 Sorted by model distance: nonbonded pdb=" OG SER B 444 " pdb=" O14 POV B 904 " model vdw 2.363 3.040 nonbonded pdb=" OG SER C 444 " pdb=" O14 POV C 904 " model vdw 2.365 3.040 nonbonded pdb=" OG SER D 444 " pdb=" O14 POV D 906 " model vdw 2.368 3.040 nonbonded pdb=" OG SER A 444 " pdb=" O14 POV A 901 " model vdw 2.372 3.040 nonbonded pdb=" OD1 ASN A 298 " pdb=" ND1 HIS A 301 " model vdw 2.374 3.120 ... (remaining 167799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 58 through 907) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.020 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.011 0.097 23380 Z= 0.484 Angle : 1.323 13.009 31340 Z= 0.578 Chirality : 0.054 0.264 3412 Planarity : 0.006 0.059 3788 Dihedral : 18.150 157.093 9320 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.34 % Allowed : 5.08 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.90 (0.11), residues: 2620 helix: -4.50 (0.05), residues: 1580 sheet: 0.67 (0.64), residues: 56 loop : -2.79 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 375 TYR 0.019 0.003 TYR C 451 PHE 0.025 0.003 PHE C 703 TRP 0.030 0.003 TRP D 481 HIS 0.011 0.003 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.01054 (23376) covalent geometry : angle 1.32280 (31332) SS BOND : bond 0.00025 ( 4) SS BOND : angle 0.49762 ( 8) hydrogen bonds : bond 0.36214 ( 838) hydrogen bonds : angle 9.19867 ( 2478) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 489 time to evaluate : 0.811 Fit side-chains REVERT: A 254 TYR cc_start: 0.8370 (m-10) cc_final: 0.8008 (m-80) REVERT: A 282 MET cc_start: 0.8122 (mtm) cc_final: 0.7796 (mtp) REVERT: A 330 ASN cc_start: 0.8536 (m-40) cc_final: 0.8206 (m110) REVERT: A 371 ARG cc_start: 0.8150 (tpt170) cc_final: 0.7827 (tpt170) REVERT: A 487 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7467 (ttm170) REVERT: A 518 SER cc_start: 0.8948 (t) cc_final: 0.8672 (p) REVERT: A 525 VAL cc_start: 0.9204 (t) cc_final: 0.8948 (m) REVERT: A 690 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.7254 (mtm110) REVERT: B 253 LYS cc_start: 0.8504 (mmtm) cc_final: 0.8292 (ttmm) REVERT: B 254 TYR cc_start: 0.8334 (m-10) cc_final: 0.7939 (m-80) REVERT: B 282 MET cc_start: 0.8157 (mtm) cc_final: 0.7794 (mtp) REVERT: B 330 ASN cc_start: 0.8521 (m-40) cc_final: 0.8306 (m-40) REVERT: B 371 ARG cc_start: 0.8192 (tpt170) cc_final: 0.7861 (tpt170) REVERT: B 419 MET cc_start: 0.9375 (mtm) cc_final: 0.9132 (mtp) REVERT: B 487 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7473 (ttm170) REVERT: B 525 VAL cc_start: 0.9206 (t) cc_final: 0.8939 (m) REVERT: B 690 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7293 (mtm110) REVERT: C 253 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8329 (ttmm) REVERT: C 254 TYR cc_start: 0.8351 (m-10) cc_final: 0.7952 (m-80) REVERT: C 282 MET cc_start: 0.8119 (mtm) cc_final: 0.7761 (mtp) REVERT: C 435 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8392 (mtpp) REVERT: C 487 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7492 (ttm170) REVERT: C 525 VAL cc_start: 0.9186 (t) cc_final: 0.8951 (m) REVERT: C 690 ARG cc_start: 0.8240 (mtt-85) cc_final: 0.7354 (mtm110) REVERT: D 254 TYR cc_start: 0.8332 (m-10) cc_final: 0.7956 (m-80) REVERT: D 282 MET cc_start: 0.8136 (mtm) cc_final: 0.7799 (mtp) REVERT: D 330 ASN cc_start: 0.8516 (m-40) cc_final: 0.8226 (m-40) REVERT: D 371 ARG cc_start: 0.8172 (tpt170) cc_final: 0.7839 (tpt170) REVERT: D 419 MET cc_start: 0.9374 (mtm) cc_final: 0.9137 (mtp) REVERT: D 435 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8359 (mtpp) REVERT: D 487 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7472 (ttm170) REVERT: D 525 VAL cc_start: 0.9201 (t) cc_final: 0.8951 (m) REVERT: D 690 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7255 (mtm110) outliers start: 8 outliers final: 4 residues processed: 497 average time/residue: 0.1560 time to fit residues: 121.0699 Evaluate side-chains 340 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 336 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain D residue 737 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 258 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 178 ASN A 197 ASN A 205 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 647 ASN B 178 ASN B 197 ASN B 205 ASN B 256 HIS ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 647 ASN C 197 ASN C 205 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 647 ASN D 178 ASN D 197 ASN D 205 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 647 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.160297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.114001 restraints weight = 27273.568| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.30 r_work: 0.2882 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23380 Z= 0.124 Angle : 0.557 7.525 31340 Z= 0.288 Chirality : 0.039 0.138 3412 Planarity : 0.004 0.038 3788 Dihedral : 19.233 136.557 4072 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.73 % Allowed : 9.52 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.14), residues: 2620 helix: -2.32 (0.11), residues: 1580 sheet: -0.32 (0.55), residues: 88 loop : -2.20 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 363 TYR 0.014 0.001 TYR A 208 PHE 0.019 0.001 PHE C 449 TRP 0.011 0.001 TRP B 559 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00277 (23376) covalent geometry : angle 0.55697 (31332) SS BOND : bond 0.00070 ( 4) SS BOND : angle 0.40642 ( 8) hydrogen bonds : bond 0.05599 ( 838) hydrogen bonds : angle 4.10708 ( 2478) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 404 time to evaluate : 0.810 Fit side-chains REVERT: A 136 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7725 (mmm-85) REVERT: A 162 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7484 (mt) REVERT: A 185 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7182 (mp0) REVERT: A 254 TYR cc_start: 0.8435 (m-10) cc_final: 0.8072 (m-80) REVERT: A 323 MET cc_start: 0.9022 (ttp) cc_final: 0.8800 (ttm) REVERT: A 330 ASN cc_start: 0.8716 (m-40) cc_final: 0.7848 (t0) REVERT: A 332 GLU cc_start: 0.8036 (mp0) cc_final: 0.7475 (mp0) REVERT: A 334 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8745 (mt-10) REVERT: A 435 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8511 (mtpm) REVERT: A 690 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.7477 (mtm110) REVERT: B 137 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7915 (mm-30) REVERT: B 140 GLN cc_start: 0.7297 (pt0) cc_final: 0.7061 (mm-40) REVERT: B 202 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7772 (mtp85) REVERT: B 254 TYR cc_start: 0.8402 (m-10) cc_final: 0.8053 (m-80) REVERT: B 323 MET cc_start: 0.8999 (ttp) cc_final: 0.8772 (ttm) REVERT: B 330 ASN cc_start: 0.8704 (m-40) cc_final: 0.8262 (m-40) REVERT: B 332 GLU cc_start: 0.8034 (mp0) cc_final: 0.7711 (mp0) REVERT: B 435 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8505 (mtpm) REVERT: B 690 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.7448 (mtm110) REVERT: C 136 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7695 (mmm-85) REVERT: C 137 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7954 (mm-30) REVERT: C 140 GLN cc_start: 0.7289 (pt0) cc_final: 0.7049 (mm-40) REVERT: C 162 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7319 (mt) REVERT: C 323 MET cc_start: 0.8977 (ttp) cc_final: 0.8751 (ttm) REVERT: C 330 ASN cc_start: 0.8542 (m-40) cc_final: 0.8254 (m-40) REVERT: C 332 GLU cc_start: 0.8004 (mp0) cc_final: 0.7726 (mp0) REVERT: C 334 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8541 (mm-30) REVERT: C 690 ARG cc_start: 0.8645 (mtt-85) cc_final: 0.7521 (mtm110) REVERT: D 137 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7815 (mm-30) REVERT: D 202 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7764 (mtp85) REVERT: D 323 MET cc_start: 0.8969 (ttp) cc_final: 0.8746 (ttm) REVERT: D 330 ASN cc_start: 0.8722 (m-40) cc_final: 0.8273 (m-40) REVERT: D 332 GLU cc_start: 0.8035 (mp0) cc_final: 0.7726 (mp0) REVERT: D 435 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8512 (mtpm) REVERT: D 690 ARG cc_start: 0.8575 (mtt-85) cc_final: 0.7483 (mtm110) outliers start: 41 outliers final: 23 residues processed: 433 average time/residue: 0.1816 time to fit residues: 117.2204 Evaluate side-chains 376 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 349 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 737 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 94 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 250 optimal weight: 0.1980 chunk 158 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN C 256 HIS ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 GLN D 256 HIS ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.161488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.116165 restraints weight = 27289.392| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.23 r_work: 0.2846 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23380 Z= 0.144 Angle : 0.543 7.665 31340 Z= 0.279 Chirality : 0.040 0.138 3412 Planarity : 0.003 0.033 3788 Dihedral : 17.588 86.039 4072 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.83 % Allowed : 11.08 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.15), residues: 2620 helix: -1.10 (0.12), residues: 1604 sheet: 0.15 (0.56), residues: 88 loop : -2.08 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 696 TYR 0.016 0.002 TYR D 451 PHE 0.016 0.001 PHE B 449 TRP 0.012 0.001 TRP A 521 HIS 0.007 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00341 (23376) covalent geometry : angle 0.54267 (31332) SS BOND : bond 0.00037 ( 4) SS BOND : angle 0.44614 ( 8) hydrogen bonds : bond 0.05258 ( 838) hydrogen bonds : angle 3.77245 ( 2478) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 362 time to evaluate : 0.784 Fit side-chains REVERT: A 136 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7747 (mmm-85) REVERT: A 137 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7944 (mt-10) REVERT: A 185 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7214 (mp0) REVERT: A 246 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7601 (pmmt) REVERT: A 323 MET cc_start: 0.9036 (ttp) cc_final: 0.8794 (ttm) REVERT: A 330 ASN cc_start: 0.8649 (m-40) cc_final: 0.8052 (t0) REVERT: A 334 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8530 (mm-30) REVERT: A 422 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7804 (mt) REVERT: A 435 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8515 (mttm) REVERT: A 545 LYS cc_start: 0.7386 (pptt) cc_final: 0.7143 (pptt) REVERT: A 690 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.7622 (mtm110) REVERT: B 136 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7718 (mmm-85) REVERT: B 137 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7995 (mm-30) REVERT: B 246 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7598 (pmmt) REVERT: B 254 TYR cc_start: 0.8464 (m-10) cc_final: 0.8113 (m-80) REVERT: B 330 ASN cc_start: 0.8643 (m-40) cc_final: 0.8194 (t0) REVERT: B 422 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7825 (mt) REVERT: B 545 LYS cc_start: 0.7401 (pptt) cc_final: 0.7138 (pptt) REVERT: B 690 ARG cc_start: 0.8625 (mtt-85) cc_final: 0.7566 (mtm110) REVERT: C 136 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7756 (mmm-85) REVERT: C 137 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8013 (mm-30) REVERT: C 246 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7595 (pmmt) REVERT: C 330 ASN cc_start: 0.8499 (m-40) cc_final: 0.8046 (t0) REVERT: C 334 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8592 (mm-30) REVERT: C 422 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7760 (mt) REVERT: C 690 ARG cc_start: 0.8662 (mtt-85) cc_final: 0.7678 (mtm110) REVERT: D 136 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7637 (mmm-85) REVERT: D 137 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7942 (mm-30) REVERT: D 246 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7613 (pmmt) REVERT: D 330 ASN cc_start: 0.8672 (m-40) cc_final: 0.8208 (t0) REVERT: D 422 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7819 (mt) REVERT: D 435 LYS cc_start: 0.8698 (mtpt) cc_final: 0.8494 (mttm) REVERT: D 690 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.7602 (mtm110) outliers start: 67 outliers final: 40 residues processed: 420 average time/residue: 0.1725 time to fit residues: 108.9518 Evaluate side-chains 390 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 340 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 737 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 72 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.151356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.104664 restraints weight = 27694.863| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.33 r_work: 0.2751 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 23380 Z= 0.237 Angle : 0.629 9.471 31340 Z= 0.322 Chirality : 0.044 0.175 3412 Planarity : 0.004 0.033 3788 Dihedral : 17.986 93.711 4072 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.38 % Allowed : 12.31 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.16), residues: 2620 helix: -0.81 (0.13), residues: 1616 sheet: 0.29 (0.55), residues: 88 loop : -2.02 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 202 TYR 0.020 0.002 TYR C 208 PHE 0.019 0.002 PHE D 489 TRP 0.015 0.002 TRP B 521 HIS 0.011 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00577 (23376) covalent geometry : angle 0.62861 (31332) SS BOND : bond 0.00088 ( 4) SS BOND : angle 0.41004 ( 8) hydrogen bonds : bond 0.06079 ( 838) hydrogen bonds : angle 3.90984 ( 2478) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 358 time to evaluate : 0.823 Fit side-chains REVERT: A 136 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7656 (mmm-85) REVERT: A 137 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7964 (mt-10) REVERT: A 246 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7660 (pmmt) REVERT: A 323 MET cc_start: 0.9099 (ttp) cc_final: 0.8826 (ttm) REVERT: A 330 ASN cc_start: 0.8672 (m-40) cc_final: 0.8350 (m-40) REVERT: A 334 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8558 (mm-30) REVERT: A 435 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8612 (mtpp) REVERT: A 668 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8794 (tt) REVERT: A 690 ARG cc_start: 0.8723 (mtt-85) cc_final: 0.7643 (mtm110) REVERT: B 136 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7732 (mmm-85) REVERT: B 246 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7642 (pmmt) REVERT: B 330 ASN cc_start: 0.8613 (m-40) cc_final: 0.8230 (t0) REVERT: B 668 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8788 (tt) REVERT: B 690 ARG cc_start: 0.8785 (mtt-85) cc_final: 0.7539 (mtm110) REVERT: C 136 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7713 (mmm-85) REVERT: C 246 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7619 (pmmt) REVERT: C 334 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8636 (mm-30) REVERT: C 668 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8798 (tt) REVERT: C 690 ARG cc_start: 0.8742 (mtt-85) cc_final: 0.7709 (mtm110) REVERT: D 136 ARG cc_start: 0.7897 (mtt180) cc_final: 0.7523 (mmm-85) REVERT: D 137 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7732 (mm-30) REVERT: D 246 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7653 (pmmt) REVERT: D 330 ASN cc_start: 0.8627 (m-40) cc_final: 0.8196 (t0) REVERT: D 435 LYS cc_start: 0.8907 (mtpt) cc_final: 0.8605 (mtpp) REVERT: D 668 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8784 (tt) REVERT: D 690 ARG cc_start: 0.8766 (mtt-85) cc_final: 0.7567 (mtm110) outliers start: 80 outliers final: 51 residues processed: 430 average time/residue: 0.1724 time to fit residues: 112.6793 Evaluate side-chains 402 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 341 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 251 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 257 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 250 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.158763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.113839 restraints weight = 27393.619| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.22 r_work: 0.2815 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23380 Z= 0.138 Angle : 0.513 7.540 31340 Z= 0.265 Chirality : 0.039 0.137 3412 Planarity : 0.003 0.032 3788 Dihedral : 16.801 91.338 4072 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.30 % Allowed : 13.28 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.16), residues: 2620 helix: -0.26 (0.13), residues: 1588 sheet: 0.18 (0.56), residues: 88 loop : -2.01 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 202 TYR 0.016 0.001 TYR B 208 PHE 0.012 0.001 PHE A 449 TRP 0.012 0.001 TRP B 380 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00332 (23376) covalent geometry : angle 0.51332 (31332) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.41053 ( 8) hydrogen bonds : bond 0.04614 ( 838) hydrogen bonds : angle 3.66366 ( 2478) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 356 time to evaluate : 0.911 Fit side-chains REVERT: A 136 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7608 (mmm-85) REVERT: A 137 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7545 (mm-30) REVERT: A 246 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7590 (pmmt) REVERT: A 323 MET cc_start: 0.9000 (ttp) cc_final: 0.8779 (ttm) REVERT: A 334 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8537 (mm-30) REVERT: A 435 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8476 (mttm) REVERT: A 545 LYS cc_start: 0.7517 (pptt) cc_final: 0.7219 (pptt) REVERT: A 690 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.7430 (mtm110) REVERT: B 136 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7558 (mmm-85) REVERT: B 137 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7849 (mm-30) REVERT: B 330 ASN cc_start: 0.8608 (m-40) cc_final: 0.8181 (t0) REVERT: B 545 LYS cc_start: 0.7529 (pptt) cc_final: 0.7214 (pptt) REVERT: B 690 ARG cc_start: 0.8721 (mtt-85) cc_final: 0.7505 (mtm110) REVERT: C 136 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7558 (mmm-85) REVERT: C 137 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7900 (mm-30) REVERT: C 334 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8533 (mm-30) REVERT: C 690 ARG cc_start: 0.8617 (mtt-85) cc_final: 0.7607 (mtm110) REVERT: D 136 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7499 (mmm-85) REVERT: D 137 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7719 (mm-30) REVERT: D 246 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7557 (pmmt) REVERT: D 330 ASN cc_start: 0.8614 (m-40) cc_final: 0.8183 (t0) REVERT: D 435 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8482 (mttm) REVERT: D 690 ARG cc_start: 0.8691 (mtt-85) cc_final: 0.7518 (mtm110) outliers start: 78 outliers final: 54 residues processed: 424 average time/residue: 0.1663 time to fit residues: 108.1169 Evaluate side-chains 395 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 337 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 50 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 242 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.154273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.109112 restraints weight = 27879.051| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.24 r_work: 0.2801 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23380 Z= 0.140 Angle : 0.521 9.540 31340 Z= 0.266 Chirality : 0.040 0.139 3412 Planarity : 0.003 0.031 3788 Dihedral : 16.101 91.897 4072 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.55 % Allowed : 13.37 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.16), residues: 2620 helix: -0.03 (0.13), residues: 1588 sheet: 0.26 (0.56), residues: 88 loop : -2.00 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 202 TYR 0.016 0.001 TYR B 208 PHE 0.013 0.001 PHE A 193 TRP 0.012 0.001 TRP C 380 HIS 0.007 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00336 (23376) covalent geometry : angle 0.52118 (31332) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.39511 ( 8) hydrogen bonds : bond 0.04638 ( 838) hydrogen bonds : angle 3.64324 ( 2478) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 350 time to evaluate : 0.727 Fit side-chains REVERT: A 136 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7585 (mmm-85) REVERT: A 137 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7497 (mm-30) REVERT: A 246 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7522 (pmmt) REVERT: A 323 MET cc_start: 0.9035 (ttp) cc_final: 0.8820 (ttm) REVERT: A 334 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8594 (mm-30) REVERT: A 435 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8488 (mttm) REVERT: A 690 ARG cc_start: 0.8595 (mtt-85) cc_final: 0.7454 (mtm110) REVERT: B 136 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7613 (mmm-85) REVERT: B 137 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7815 (mm-30) REVERT: B 202 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7889 (mtp85) REVERT: B 246 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7579 (pmmt) REVERT: B 330 ASN cc_start: 0.8625 (m-40) cc_final: 0.8187 (t0) REVERT: B 690 ARG cc_start: 0.8719 (mtt-85) cc_final: 0.7517 (mtm110) REVERT: C 136 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7555 (mmm-85) REVERT: C 137 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7856 (mm-30) REVERT: C 246 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7564 (pmmt) REVERT: C 334 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8635 (mm-30) REVERT: C 690 ARG cc_start: 0.8641 (mtt-85) cc_final: 0.7587 (mtm110) REVERT: D 136 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7465 (mmm-85) REVERT: D 137 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7614 (mm-30) REVERT: D 202 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7879 (mtp85) REVERT: D 246 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7525 (pmmt) REVERT: D 330 ASN cc_start: 0.8629 (m-40) cc_final: 0.8305 (m-40) REVERT: D 435 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8466 (mttm) REVERT: D 690 ARG cc_start: 0.8710 (mtt-85) cc_final: 0.7494 (mtm110) outliers start: 84 outliers final: 56 residues processed: 421 average time/residue: 0.1647 time to fit residues: 105.8404 Evaluate side-chains 401 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 339 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 190 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 151 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.160130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.115822 restraints weight = 27687.278| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.21 r_work: 0.2831 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23380 Z= 0.119 Angle : 0.490 7.872 31340 Z= 0.252 Chirality : 0.039 0.142 3412 Planarity : 0.003 0.030 3788 Dihedral : 15.521 90.560 4072 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.92 % Allowed : 13.66 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.16), residues: 2620 helix: 0.24 (0.13), residues: 1588 sheet: 0.27 (0.57), residues: 88 loop : -1.90 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 202 TYR 0.014 0.001 TYR B 208 PHE 0.010 0.001 PHE C 316 TRP 0.012 0.001 TRP A 380 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00282 (23376) covalent geometry : angle 0.49049 (31332) SS BOND : bond 0.00045 ( 4) SS BOND : angle 0.41059 ( 8) hydrogen bonds : bond 0.04147 ( 838) hydrogen bonds : angle 3.55128 ( 2478) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 350 time to evaluate : 0.874 Fit side-chains REVERT: A 134 GLU cc_start: 0.7674 (mp0) cc_final: 0.7035 (mp0) REVERT: A 137 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7570 (mm-30) REVERT: A 334 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8591 (mm-30) REVERT: A 435 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8375 (mttm) REVERT: A 690 ARG cc_start: 0.8607 (mtt-85) cc_final: 0.7452 (mtm110) REVERT: B 136 ARG cc_start: 0.7901 (mtt180) cc_final: 0.7577 (mmm-85) REVERT: B 137 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7794 (mm-30) REVERT: B 246 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7477 (pmmt) REVERT: B 330 ASN cc_start: 0.8542 (m-40) cc_final: 0.8268 (m-40) REVERT: B 690 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.7478 (mtm110) REVERT: C 136 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7597 (mmm-85) REVERT: C 137 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7915 (mm-30) REVERT: C 246 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7460 (pmmt) REVERT: C 334 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8574 (mm-30) REVERT: C 690 ARG cc_start: 0.8587 (mtt-85) cc_final: 0.7498 (mtm110) REVERT: D 136 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7440 (mmm-85) REVERT: D 137 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7531 (mm-30) REVERT: D 330 ASN cc_start: 0.8556 (m-40) cc_final: 0.8283 (m-40) REVERT: D 435 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8366 (mttm) REVERT: D 690 ARG cc_start: 0.8664 (mtt-85) cc_final: 0.7488 (mtm110) outliers start: 69 outliers final: 53 residues processed: 406 average time/residue: 0.1740 time to fit residues: 107.7289 Evaluate side-chains 395 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 338 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 216 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 217 optimal weight: 0.7980 chunk 246 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.161400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.117500 restraints weight = 27308.348| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.17 r_work: 0.2880 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23380 Z= 0.093 Angle : 0.465 7.891 31340 Z= 0.239 Chirality : 0.037 0.145 3412 Planarity : 0.003 0.030 3788 Dihedral : 14.989 87.284 4072 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.58 % Allowed : 14.00 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.17), residues: 2620 helix: 0.52 (0.13), residues: 1588 sheet: 1.38 (0.68), residues: 64 loop : -1.74 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 202 TYR 0.011 0.001 TYR D 208 PHE 0.015 0.001 PHE A 193 TRP 0.012 0.001 TRP A 380 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00208 (23376) covalent geometry : angle 0.46484 (31332) SS BOND : bond 0.00024 ( 4) SS BOND : angle 0.42270 ( 8) hydrogen bonds : bond 0.03566 ( 838) hydrogen bonds : angle 3.47043 ( 2478) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 367 time to evaluate : 0.747 Fit side-chains REVERT: A 134 GLU cc_start: 0.7642 (mp0) cc_final: 0.7008 (mp0) REVERT: A 137 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7562 (mm-30) REVERT: A 334 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8601 (mm-30) REVERT: A 555 MET cc_start: 0.8742 (mtp) cc_final: 0.8471 (mtp) REVERT: A 690 ARG cc_start: 0.8588 (mtt-85) cc_final: 0.7435 (mtm110) REVERT: A 702 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8235 (mm-30) REVERT: B 137 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7789 (mm-30) REVERT: B 202 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7378 (ttm-80) REVERT: B 246 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7411 (pmmt) REVERT: B 690 ARG cc_start: 0.8630 (mtt-85) cc_final: 0.7429 (mtm110) REVERT: B 702 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8248 (mm-30) REVERT: C 137 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7892 (mm-30) REVERT: C 246 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7409 (pmmt) REVERT: C 334 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8593 (mm-30) REVERT: C 690 ARG cc_start: 0.8497 (mtt-85) cc_final: 0.7455 (mtm110) REVERT: C 702 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8209 (mm-30) REVERT: D 137 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7658 (mm-30) REVERT: D 202 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7850 (mtp85) REVERT: D 690 ARG cc_start: 0.8610 (mtt-85) cc_final: 0.7431 (mtm110) REVERT: D 702 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8240 (mm-30) outliers start: 61 outliers final: 44 residues processed: 420 average time/residue: 0.1694 time to fit residues: 109.5150 Evaluate side-chains 381 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 333 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.152696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.107553 restraints weight = 27700.362| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.22 r_work: 0.2783 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 23380 Z= 0.194 Angle : 0.570 7.739 31340 Z= 0.291 Chirality : 0.042 0.153 3412 Planarity : 0.003 0.030 3788 Dihedral : 15.794 91.918 4072 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.34 % Allowed : 14.09 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.16), residues: 2620 helix: 0.28 (0.13), residues: 1596 sheet: 0.59 (0.58), residues: 88 loop : -1.85 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 202 TYR 0.017 0.002 TYR B 451 PHE 0.014 0.001 PHE D 489 TRP 0.011 0.001 TRP B 380 HIS 0.009 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00476 (23376) covalent geometry : angle 0.57028 (31332) SS BOND : bond 0.00037 ( 4) SS BOND : angle 0.37611 ( 8) hydrogen bonds : bond 0.05228 ( 838) hydrogen bonds : angle 3.67456 ( 2478) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 337 time to evaluate : 0.850 Fit side-chains REVERT: A 137 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7551 (mm-30) REVERT: A 219 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7870 (tt) REVERT: A 246 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7572 (pmmt) REVERT: A 334 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8589 (mm-30) REVERT: A 392 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8565 (mp) REVERT: A 690 ARG cc_start: 0.8694 (mtt-85) cc_final: 0.7555 (mtm110) REVERT: B 137 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7723 (mm-30) REVERT: B 202 ARG cc_start: 0.8355 (mtp85) cc_final: 0.7999 (mtp85) REVERT: B 219 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7823 (tt) REVERT: B 246 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7588 (pmmt) REVERT: B 392 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8567 (mp) REVERT: B 690 ARG cc_start: 0.8745 (mtt-85) cc_final: 0.7516 (mtm110) REVERT: C 137 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7811 (mm-30) REVERT: C 246 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7579 (pmmt) REVERT: C 334 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8587 (mm-30) REVERT: C 392 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8571 (mp) REVERT: C 418 GLU cc_start: 0.8226 (pm20) cc_final: 0.7971 (tt0) REVERT: C 690 ARG cc_start: 0.8693 (mtt-85) cc_final: 0.7509 (mtm110) REVERT: D 137 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7564 (mm-30) REVERT: D 202 ARG cc_start: 0.8339 (mtp85) cc_final: 0.7970 (mtp85) REVERT: D 219 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7869 (tt) REVERT: D 246 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7580 (pmmt) REVERT: D 690 ARG cc_start: 0.8747 (mtt-85) cc_final: 0.7576 (mtm110) outliers start: 79 outliers final: 53 residues processed: 409 average time/residue: 0.1704 time to fit residues: 107.2646 Evaluate side-chains 399 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 334 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 6 optimal weight: 0.7980 chunk 237 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 197 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 585 HIS B 205 ASN B 286 GLN B 585 HIS C 140 GLN C 205 ASN C 286 GLN C 585 HIS D 205 ASN D 286 GLN D 585 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.160611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.115771 restraints weight = 27400.471| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.26 r_work: 0.2875 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23380 Z= 0.086 Angle : 0.461 7.819 31340 Z= 0.237 Chirality : 0.037 0.145 3412 Planarity : 0.003 0.029 3788 Dihedral : 14.618 85.308 4072 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.71 % Allowed : 14.64 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2620 helix: 0.63 (0.13), residues: 1596 sheet: 1.42 (0.69), residues: 64 loop : -1.64 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 202 TYR 0.013 0.001 TYR B 359 PHE 0.014 0.001 PHE A 449 TRP 0.011 0.001 TRP D 380 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00185 (23376) covalent geometry : angle 0.46103 (31332) SS BOND : bond 0.00018 ( 4) SS BOND : angle 0.41820 ( 8) hydrogen bonds : bond 0.03264 ( 838) hydrogen bonds : angle 3.49133 ( 2478) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 347 time to evaluate : 0.831 Fit side-chains REVERT: A 137 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7524 (mm-30) REVERT: A 334 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8635 (mm-30) REVERT: A 555 MET cc_start: 0.8812 (mtp) cc_final: 0.8492 (mtp) REVERT: A 690 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.7354 (mtm110) REVERT: A 702 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8281 (mm-30) REVERT: B 137 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7723 (mm-30) REVERT: B 202 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7963 (mtp85) REVERT: B 690 ARG cc_start: 0.8648 (mtt-85) cc_final: 0.7403 (mtm110) REVERT: B 702 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8288 (mm-30) REVERT: C 137 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7806 (mm-30) REVERT: C 334 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8679 (mm-30) REVERT: C 418 GLU cc_start: 0.8182 (pm20) cc_final: 0.7881 (tt0) REVERT: C 555 MET cc_start: 0.8771 (mtp) cc_final: 0.8445 (mtp) REVERT: C 690 ARG cc_start: 0.8526 (mtt-85) cc_final: 0.7316 (mtm110) REVERT: C 702 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8247 (mm-30) REVERT: D 137 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7490 (mm-30) REVERT: D 202 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7947 (mtp85) REVERT: D 690 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.7410 (mtm110) REVERT: D 702 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8442 (mm-30) outliers start: 64 outliers final: 44 residues processed: 398 average time/residue: 0.1651 time to fit residues: 101.4036 Evaluate side-chains 379 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 333 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 137 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 145 optimal weight: 0.0770 chunk 114 optimal weight: 1.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.161767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.117904 restraints weight = 27447.753| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.17 r_work: 0.2851 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23380 Z= 0.112 Angle : 0.489 7.969 31340 Z= 0.250 Chirality : 0.038 0.147 3412 Planarity : 0.003 0.028 3788 Dihedral : 14.500 82.977 4068 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.28 % Allowed : 15.31 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2620 helix: 0.67 (0.13), residues: 1596 sheet: 1.48 (0.66), residues: 64 loop : -1.61 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 202 TYR 0.014 0.001 TYR C 208 PHE 0.013 0.001 PHE B 449 TRP 0.012 0.001 TRP C 380 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00263 (23376) covalent geometry : angle 0.48913 (31332) SS BOND : bond 0.00012 ( 4) SS BOND : angle 0.39469 ( 8) hydrogen bonds : bond 0.03929 ( 838) hydrogen bonds : angle 3.51028 ( 2478) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5118.10 seconds wall clock time: 88 minutes 26.24 seconds (5306.24 seconds total)