Starting phenix.real_space_refine on Sat Jul 4 19:05:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mio_23858/07_2026/7mio_23858.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mio_23858/07_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_23858/07_2026/7mio_23858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mio_23858/07_2026/7mio_23858.map" model { file = "/net/cci-nas-00/data/ceres_data/7mio_23858/07_2026/7mio_23858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mio_23858/07_2026/7mio_23858.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mio_23858/07_2026/7mio_23858.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mio_23858/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 5.00, per 1000 atoms: 0.22 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: 1.81 Conformation dependent library (CDL) restraints added in 948.8 milliseconds 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: 0.41 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: 3.47 Time building geometry restraints manager: 2.50 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: 13591 31.42 - 62.84: 548 62.84 - 94.26: 49 94.26 - 125.67: 20 125.67 - 157.09: 20 Dihedral angle restraints: 14228 sinusoidal: 6440 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 14225 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.760 Find NCS groups from input model: 0.500 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 : 17.545 157.093 9152 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/Z covalent geometry : bond 0.01054 / 0.48 (23376) covalent geometry : angle 1.32280 / 0.58 (31332) SS BOND : bond 0.00025 / 0.01 ( 4) SS BOND : angle 0.49762 / 0.24 ( 8) hydrogen bonds : bond 0.36214 / 23.68 ( 838) hydrogen bonds : angle 9.19867 / 6.33 ( 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 : 0.856 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: 0.1570 time to fit residues: 122.7877 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 : 0.875 ------------------------------------------------------------------------------- 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... 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 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 394 ASN D 647 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.160256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.113605 restraints weight = 27293.346| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.32 r_work: 0.2876 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- 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 = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2127 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 : 0.552 7.652 31340 Z= 0.286 Chirality : 0.039 0.135 3412 Planarity : 0.004 0.038 3788 Dihedral : 18.627 138.189 3904 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.90 % Allowed : 9.35 % 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: -0.31 (0.55), residues: 88 loop : -2.21 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 363 TYR 0.013 0.001 TYR A 208 PHE 0.019 0.001 PHE C 449 TRP 0.011 0.001 TRP A 559 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (23376) covalent geometry : angle 0.55155 / 0.29 (31332) SS BOND : bond 0.00079 / 0.04 ( 4) SS BOND : angle 0.40906 / 0.20 ( 8) hydrogen bonds : bond 0.05753 / 3.73 ( 838) hydrogen bonds : angle 4.11322 / 2.87 ( 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 448 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 403 time to evaluate : 0.859 Fit side-chains REVERT: A 136 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7718 (mmm-85) REVERT: A 162 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7459 (mt) REVERT: A 185 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7197 (mp0) REVERT: A 254 TYR cc_start: 0.8433 (m-10) cc_final: 0.8069 (m-80) REVERT: A 323 MET cc_start: 0.9016 (ttp) cc_final: 0.8799 (ttm) REVERT: A 330 ASN cc_start: 0.8720 (m-40) cc_final: 0.7846 (t0) REVERT: A 332 GLU cc_start: 0.8040 (mp0) cc_final: 0.7476 (mp0) REVERT: A 334 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8747 (mt-10) REVERT: A 435 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8521 (mtpm) REVERT: A 690 ARG cc_start: 0.8564 (mtt-85) cc_final: 0.7469 (mtm110) REVERT: B 137 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7915 (mm-30) REVERT: B 140 GLN cc_start: 0.7309 (pt0) cc_final: 0.7076 (mm-40) REVERT: B 202 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7763 (mtp85) REVERT: B 254 TYR cc_start: 0.8407 (m-10) cc_final: 0.8057 (m-80) REVERT: B 323 MET cc_start: 0.8997 (ttp) cc_final: 0.8761 (ttm) REVERT: B 330 ASN cc_start: 0.8720 (m-40) cc_final: 0.8277 (m-40) REVERT: B 332 GLU cc_start: 0.8025 (mp0) cc_final: 0.7703 (mp0) REVERT: B 435 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8518 (mtpm) REVERT: B 690 ARG cc_start: 0.8592 (mtt-85) cc_final: 0.7484 (mtm110) REVERT: C 136 ARG cc_start: 0.8071 (mtt180) cc_final: 0.7692 (mmm-85) REVERT: C 137 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7924 (mm-30) REVERT: C 140 GLN cc_start: 0.7283 (pt0) cc_final: 0.7039 (mm-40) REVERT: C 162 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7303 (mt) REVERT: C 323 MET cc_start: 0.8983 (ttp) cc_final: 0.8750 (ttm) REVERT: C 330 ASN cc_start: 0.8547 (m-40) cc_final: 0.8263 (m-40) REVERT: C 332 GLU cc_start: 0.8003 (mp0) cc_final: 0.7718 (mp0) REVERT: C 334 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8529 (mm-30) REVERT: C 690 ARG cc_start: 0.8649 (mtt-85) cc_final: 0.7526 (mtm110) REVERT: D 137 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7786 (mm-30) REVERT: D 202 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7755 (mtp85) REVERT: D 323 MET cc_start: 0.8979 (ttp) cc_final: 0.8756 (ttm) REVERT: D 330 ASN cc_start: 0.8729 (m-40) cc_final: 0.8282 (m-40) REVERT: D 332 GLU cc_start: 0.8033 (mp0) cc_final: 0.7721 (mp0) REVERT: D 435 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8530 (mtpm) REVERT: D 690 ARG cc_start: 0.8580 (mtt-85) cc_final: 0.7484 (mtm110) outliers start: 45 outliers final: 28 residues processed: 436 average time/residue: 0.1772 time to fit residues: 116.0537 Evaluate side-chains 380 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 348 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 204 ILE 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 128 SER 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 128 SER 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 128 SER 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: 30.0000 chunk 111 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 245 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS ** 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 = 0.3612 r_free = 0.3612 target = 0.158222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.112636 restraints weight = 27390.809| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.23 r_work: 0.2809 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23380 Z= 0.201 Angle : 0.603 7.674 31340 Z= 0.310 Chirality : 0.042 0.168 3412 Planarity : 0.004 0.034 3788 Dihedral : 17.431 91.242 3904 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.17 % Allowed : 10.24 % Favored : 86.59 % 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: -2.34 (0.15), residues: 2620 helix: -1.22 (0.12), residues: 1608 sheet: 0.11 (0.55), residues: 88 loop : -2.12 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 696 TYR 0.019 0.002 TYR A 451 PHE 0.018 0.002 PHE D 489 TRP 0.015 0.002 TRP A 521 HIS 0.010 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (23376) covalent geometry : angle 0.60266 / 0.31 (31332) SS BOND : bond 0.00079 / 0.04 ( 4) SS BOND : angle 0.45869 / 0.23 ( 8) hydrogen bonds : bond 0.06037 / 3.91 ( 838) hydrogen bonds : angle 3.92085 / 2.72 ( 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 426 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 351 time to evaluate : 0.867 Fit side-chains REVERT: A 136 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7725 (mmm-85) REVERT: A 185 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7202 (mp0) REVERT: A 246 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7643 (pmmt) REVERT: A 323 MET cc_start: 0.9071 (ttp) cc_final: 0.8828 (ttm) REVERT: A 330 ASN cc_start: 0.8657 (m-40) cc_final: 0.8086 (t0) REVERT: A 334 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8543 (mm-30) REVERT: A 435 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8583 (mtpp) REVERT: A 545 LYS cc_start: 0.7489 (pptt) cc_final: 0.7198 (pptt) REVERT: A 690 ARG cc_start: 0.8682 (mtt-85) cc_final: 0.7666 (mtm110) REVERT: B 136 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7671 (mmm-85) REVERT: B 246 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7664 (pmmt) REVERT: B 323 MET cc_start: 0.9023 (ttp) cc_final: 0.8678 (ttm) REVERT: B 330 ASN cc_start: 0.8666 (m-40) cc_final: 0.8105 (t0) REVERT: B 422 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8072 (mt) REVERT: B 435 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8570 (mtpp) REVERT: B 545 LYS cc_start: 0.7512 (pptt) cc_final: 0.7206 (pptt) REVERT: B 690 ARG cc_start: 0.8691 (mtt-85) cc_final: 0.7660 (mtm110) REVERT: C 136 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7780 (mmm-85) REVERT: C 137 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8103 (mm-30) REVERT: C 246 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7648 (pmmt) REVERT: C 323 MET cc_start: 0.9020 (ttp) cc_final: 0.8678 (ttm) REVERT: C 330 ASN cc_start: 0.8553 (m-40) cc_final: 0.8079 (t0) REVERT: C 334 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8525 (mm-30) REVERT: C 422 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8010 (mt) REVERT: C 690 ARG cc_start: 0.8726 (mtt-85) cc_final: 0.7714 (mtm110) REVERT: D 136 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7663 (mmm-85) REVERT: D 140 GLN cc_start: 0.7466 (pt0) cc_final: 0.7259 (mm-40) REVERT: D 246 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7659 (pmmt) REVERT: D 323 MET cc_start: 0.9021 (ttp) cc_final: 0.8679 (ttm) REVERT: D 330 ASN cc_start: 0.8698 (m-40) cc_final: 0.8107 (t0) REVERT: D 435 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8573 (mtpp) REVERT: D 525 VAL cc_start: 0.8926 (t) cc_final: 0.8678 (m) REVERT: D 690 ARG cc_start: 0.8667 (mtt-85) cc_final: 0.7632 (mtm110) outliers start: 75 outliers final: 43 residues processed: 417 average time/residue: 0.1694 time to fit residues: 106.7695 Evaluate side-chains 384 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 333 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 0.0050 chunk 28 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.161522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.116657 restraints weight = 27501.727| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.23 r_work: 0.2878 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3094 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= 0.099 Angle : 0.478 7.587 31340 Z= 0.245 Chirality : 0.038 0.135 3412 Planarity : 0.003 0.032 3788 Dihedral : 15.852 85.380 3904 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.28 % Allowed : 12.52 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.51 (0.16), residues: 2620 helix: -0.50 (0.13), residues: 1604 sheet: 0.93 (0.66), residues: 64 loop : -1.89 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 202 TYR 0.012 0.001 TYR B 208 PHE 0.013 0.001 PHE A 449 TRP 0.011 0.001 TRP D 380 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (23376) covalent geometry : angle 0.47786 / 0.25 (31332) SS BOND : bond 0.00058 / 0.03 ( 4) SS BOND : angle 0.39378 / 0.20 ( 8) hydrogen bonds : bond 0.03958 / 2.57 ( 838) hydrogen bonds : angle 3.54174 / 2.46 ( 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 428 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 374 time to evaluate : 0.878 Fit side-chains REVERT: A 134 GLU cc_start: 0.7788 (mp0) cc_final: 0.7376 (mp0) REVERT: A 136 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7754 (mmm-85) REVERT: A 202 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7827 (mtp85) REVERT: A 330 ASN cc_start: 0.8607 (m-40) cc_final: 0.8310 (m-40) REVERT: A 334 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8561 (mm-30) REVERT: A 690 ARG cc_start: 0.8532 (mtt-85) cc_final: 0.7510 (mtm110) REVERT: B 136 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7538 (mmm-85) REVERT: B 137 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7714 (mm-30) REVERT: B 545 LYS cc_start: 0.7450 (pptt) cc_final: 0.7218 (pptt) REVERT: B 690 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.7507 (mtm110) REVERT: C 136 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7536 (mmm-85) REVERT: C 137 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7909 (mm-30) REVERT: C 202 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7765 (mtp85) REVERT: C 334 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8544 (mm-30) REVERT: C 690 ARG cc_start: 0.8567 (mtt-85) cc_final: 0.7600 (mtm110) REVERT: D 136 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7547 (mmm-85) REVERT: D 137 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7817 (mm-30) REVERT: D 330 ASN cc_start: 0.8616 (m-40) cc_final: 0.8331 (m-40) REVERT: D 690 ARG cc_start: 0.8537 (mtt-85) cc_final: 0.7490 (mtm110) outliers start: 54 outliers final: 36 residues processed: 418 average time/residue: 0.1751 time to fit residues: 111.2812 Evaluate side-chains 371 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 333 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 584 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 A residue 749 LEU Chi-restraints excluded: chain B residue 63 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 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 229 ASP 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 251 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 chunk 257 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 250 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 514 GLN ** D 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 = 0.3621 r_free = 0.3621 target = 0.159488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.113722 restraints weight = 27451.704| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.30 r_work: 0.2833 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 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 = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3257 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 : 0.487 7.667 31340 Z= 0.250 Chirality : 0.038 0.142 3412 Planarity : 0.003 0.030 3788 Dihedral : 15.328 86.145 3904 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.92 % Allowed : 12.94 % Favored : 84.14 % 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: -1.09 (0.16), residues: 2620 helix: -0.11 (0.13), residues: 1616 sheet: 1.03 (0.66), residues: 64 loop : -1.83 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 202 TYR 0.014 0.001 TYR A 208 PHE 0.012 0.001 PHE B 449 TRP 0.010 0.001 TRP B 380 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (23376) covalent geometry : angle 0.48704 / 0.25 (31332) SS BOND : bond 0.00043 / 0.02 ( 4) SS BOND : angle 0.38188 / 0.19 ( 8) hydrogen bonds : bond 0.04247 / 2.76 ( 838) hydrogen bonds : angle 3.52372 / 2.44 ( 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 421 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 352 time to evaluate : 0.838 Fit side-chains REVERT: A 134 GLU cc_start: 0.7680 (mp0) cc_final: 0.7205 (mp0) REVERT: A 140 GLN cc_start: 0.6273 (mm-40) cc_final: 0.5998 (mm-40) REVERT: A 334 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8685 (mm-30) REVERT: A 690 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.7469 (mtm110) REVERT: B 136 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7502 (mmm-85) REVERT: B 137 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7838 (mm-30) REVERT: B 690 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.7541 (mtm110) REVERT: C 136 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7482 (mmm-85) REVERT: C 137 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7814 (mm-30) REVERT: C 334 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8656 (mm-30) REVERT: C 690 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.7578 (mtm110) REVERT: C 702 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8332 (mm-30) REVERT: D 137 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7849 (mm-30) REVERT: D 140 GLN cc_start: 0.6421 (mm-40) cc_final: 0.6187 (mm-40) REVERT: D 690 ARG cc_start: 0.8547 (mtt-85) cc_final: 0.7516 (mtm110) outliers start: 69 outliers final: 50 residues processed: 404 average time/residue: 0.1667 time to fit residues: 102.9921 Evaluate side-chains 393 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 340 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 204 ILE 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 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 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 702 GLU 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 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 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: 0.8980 chunk 242 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 23 optimal weight: 0.0970 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 514 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.152979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.106465 restraints weight = 27918.370| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.35 r_work: 0.2768 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23380 Z= 0.182 Angle : 0.557 8.861 31340 Z= 0.284 Chirality : 0.041 0.147 3412 Planarity : 0.003 0.030 3788 Dihedral : 15.528 86.848 3904 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.51 % Allowed : 12.48 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.07 (0.16), residues: 2620 helix: -0.02 (0.13), residues: 1588 sheet: 0.36 (0.55), residues: 88 loop : -1.93 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 202 TYR 0.017 0.002 TYR C 208 PHE 0.015 0.001 PHE D 489 TRP 0.011 0.001 TRP A 380 HIS 0.009 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (23376) covalent geometry : angle 0.55665 / 0.28 (31332) SS BOND : bond 0.00033 / 0.02 ( 4) SS BOND : angle 0.36782 / 0.18 ( 8) hydrogen bonds : bond 0.05165 / 3.35 ( 838) hydrogen bonds : angle 3.67677 / 2.54 ( 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 429 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 346 time to evaluate : 0.842 Fit side-chains REVERT: A 134 GLU cc_start: 0.7685 (mp0) cc_final: 0.7070 (mp0) REVERT: A 140 GLN cc_start: 0.6392 (mm-40) cc_final: 0.6078 (mm-40) REVERT: A 246 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7551 (pmmt) REVERT: A 334 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8572 (mm-30) REVERT: A 690 ARG cc_start: 0.8638 (mtt-85) cc_final: 0.7520 (mtm110) REVERT: B 136 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7616 (mmm-85) REVERT: B 137 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7844 (mm-30) REVERT: B 246 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7598 (pmmt) REVERT: B 690 ARG cc_start: 0.8670 (mtt-85) cc_final: 0.7596 (mtm110) REVERT: C 136 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7528 (mmm-85) REVERT: C 246 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7584 (pmmt) REVERT: C 334 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8669 (mm-30) REVERT: C 690 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.7659 (mtm110) REVERT: D 137 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7793 (mt-10) REVERT: D 140 GLN cc_start: 0.6438 (mm-40) cc_final: 0.6171 (mm-40) REVERT: D 246 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7562 (pmmt) REVERT: D 690 ARG cc_start: 0.8651 (mtt-85) cc_final: 0.7586 (mtm110) outliers start: 83 outliers final: 62 residues processed: 412 average time/residue: 0.1590 time to fit residues: 101.0491 Evaluate side-chains 405 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 337 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 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 207 GLU 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 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 207 GLU 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 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 176 LEU Chi-restraints excluded: chain D residue 207 GLU 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: 0.5980 chunk 97 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 561 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.158711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.114082 restraints weight = 27751.966| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.23 r_work: 0.2830 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3505 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= 0.123 Angle : 0.495 7.652 31340 Z= 0.255 Chirality : 0.039 0.152 3412 Planarity : 0.003 0.029 3788 Dihedral : 14.652 88.938 3904 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.38 % Allowed : 12.56 % Favored : 84.05 % 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: -0.81 (0.16), residues: 2620 helix: 0.21 (0.13), residues: 1592 sheet: 0.28 (0.56), residues: 88 loop : -1.87 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 202 TYR 0.015 0.001 TYR C 208 PHE 0.013 0.001 PHE B 449 TRP 0.012 0.001 TRP C 380 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (23376) covalent geometry : angle 0.49504 / 0.25 (31332) SS BOND : bond 0.00025 / 0.01 ( 4) SS BOND : angle 0.38482 / 0.19 ( 8) hydrogen bonds : bond 0.04225 / 2.74 ( 838) hydrogen bonds : angle 3.55415 / 2.46 ( 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 427 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 347 time to evaluate : 0.849 Fit side-chains REVERT: A 134 GLU cc_start: 0.7686 (mp0) cc_final: 0.7090 (mp0) REVERT: A 140 GLN cc_start: 0.6360 (mm-40) cc_final: 0.5988 (mm-40) REVERT: A 202 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8000 (mtp85) REVERT: A 246 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7530 (pmmt) REVERT: A 334 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8601 (mm-30) REVERT: A 690 ARG cc_start: 0.8605 (mtt-85) cc_final: 0.7443 (mtm110) REVERT: B 137 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7868 (mm-30) REVERT: B 246 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7459 (pmmt) REVERT: B 609 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8810 (pp) REVERT: B 690 ARG cc_start: 0.8578 (mtt-85) cc_final: 0.7542 (mtm110) REVERT: C 136 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7498 (mmm-85) REVERT: C 137 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7873 (mm-30) REVERT: C 202 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7841 (mtp85) REVERT: C 246 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7526 (pmmt) REVERT: C 334 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8631 (mm-30) REVERT: C 690 ARG cc_start: 0.8560 (mtt-85) cc_final: 0.7539 (mtm110) REVERT: D 137 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7753 (mt-10) REVERT: D 140 GLN cc_start: 0.6467 (mm-40) cc_final: 0.6177 (mm-40) REVERT: D 246 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7530 (pmmt) REVERT: D 690 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.7513 (mtm110) outliers start: 80 outliers final: 58 residues processed: 410 average time/residue: 0.1620 time to fit residues: 102.3520 Evaluate side-chains 403 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 338 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 229 ASP 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 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 246 LYS Chi-restraints excluded: chain B residue 281 LEU 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 609 ILE 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 207 GLU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 281 LEU 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 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 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: 0.8980 chunk 187 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 259 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 246 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3622 r_free = 0.3622 target = 0.159565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.115275 restraints weight = 27363.376| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.19 r_work: 0.2858 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- 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: 20 | |-----------------------------------------------------------------------------| |-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: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3624 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= 0.108 Angle : 0.488 8.078 31340 Z= 0.249 Chirality : 0.038 0.157 3412 Planarity : 0.003 0.028 3788 Dihedral : 14.116 89.078 3904 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.79 % Allowed : 13.11 % Favored : 84.09 % 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: -0.54 (0.16), residues: 2620 helix: 0.42 (0.13), residues: 1592 sheet: 1.32 (0.64), residues: 64 loop : -1.78 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 202 TYR 0.013 0.001 TYR C 208 PHE 0.014 0.001 PHE D 193 TRP 0.012 0.001 TRP B 380 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (23376) covalent geometry : angle 0.48815 / 0.25 (31332) SS BOND : bond 0.00010 / 0.00 ( 4) SS BOND : angle 0.38107 / 0.19 ( 8) hydrogen bonds : bond 0.03934 / 2.55 ( 838) hydrogen bonds : angle 3.50577 / 2.42 ( 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 423 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 357 time to evaluate : 0.874 Fit side-chains REVERT: A 134 GLU cc_start: 0.7732 (mp0) cc_final: 0.7139 (mp0) REVERT: A 140 GLN cc_start: 0.6377 (mm-40) cc_final: 0.6063 (mm110) REVERT: A 202 ARG cc_start: 0.8349 (mtp85) cc_final: 0.8044 (mtp85) REVERT: A 246 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7393 (pmmt) REVERT: A 334 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8624 (mm-30) REVERT: A 690 ARG cc_start: 0.8592 (mtt-85) cc_final: 0.7451 (mtm110) REVERT: A 702 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8395 (mm-30) REVERT: B 137 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7849 (mm-30) REVERT: B 246 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7440 (pmmt) REVERT: B 690 ARG cc_start: 0.8568 (mtt-85) cc_final: 0.7577 (mtm110) REVERT: B 702 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8394 (mm-30) REVERT: C 137 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7821 (mm-30) REVERT: C 202 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7909 (mtp85) REVERT: C 246 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7435 (pmmt) REVERT: C 334 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8622 (mm-30) REVERT: C 690 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.7547 (mtm110) REVERT: C 702 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8377 (mm-30) REVERT: D 137 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7748 (mt-10) REVERT: D 140 GLN cc_start: 0.6534 (mm-40) cc_final: 0.6165 (mm-40) REVERT: D 246 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7410 (pmmt) REVERT: D 690 ARG cc_start: 0.8527 (mtt-85) cc_final: 0.7523 (mtm110) REVERT: D 702 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8402 (mm-30) outliers start: 66 outliers final: 51 residues processed: 409 average time/residue: 0.1770 time to fit residues: 111.4021 Evaluate side-chains 401 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 344 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 229 ASP 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 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 63 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 207 GLU 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 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 207 GLU 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 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 207 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.160996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.117378 restraints weight = 27176.934| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.15 r_work: 0.2871 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3719 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= 0.110 Angle : 0.490 7.500 31340 Z= 0.250 Chirality : 0.038 0.158 3412 Planarity : 0.003 0.029 3788 Dihedral : 13.822 88.687 3904 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.83 % Allowed : 13.49 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.42 (0.16), residues: 2620 helix: 0.51 (0.13), residues: 1592 sheet: 1.52 (0.66), residues: 64 loop : -1.73 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 202 TYR 0.013 0.001 TYR C 208 PHE 0.013 0.001 PHE A 449 TRP 0.012 0.001 TRP A 380 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (23376) covalent geometry : angle 0.48964 / 0.25 (31332) SS BOND : bond 0.00016 / 0.01 ( 4) SS BOND : angle 0.38351 / 0.19 ( 8) hydrogen bonds : bond 0.03969 / 2.58 ( 838) hydrogen bonds : angle 3.52693 / 2.44 ( 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 404 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 337 time to evaluate : 0.830 Fit side-chains REVERT: A 134 GLU cc_start: 0.7753 (mp0) cc_final: 0.7174 (mp0) REVERT: A 140 GLN cc_start: 0.6402 (mm-40) cc_final: 0.6079 (mm110) REVERT: A 202 ARG cc_start: 0.8367 (mtp85) cc_final: 0.8043 (mtp85) REVERT: A 246 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7449 (pmmt) REVERT: A 334 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8623 (mm-30) REVERT: A 690 ARG cc_start: 0.8596 (mtt-85) cc_final: 0.7459 (mtm110) REVERT: A 702 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8263 (mm-30) REVERT: B 137 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7761 (mm-30) REVERT: B 246 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7518 (pmmt) REVERT: B 518 SER cc_start: 0.8752 (t) cc_final: 0.8527 (p) REVERT: B 690 ARG cc_start: 0.8571 (mtt-85) cc_final: 0.7578 (mtm110) REVERT: B 702 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8246 (mm-30) REVERT: C 137 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7781 (mm-30) REVERT: C 202 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7960 (mtp85) REVERT: C 246 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7504 (pmmt) REVERT: C 334 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8632 (mm-30) REVERT: C 690 ARG cc_start: 0.8535 (mtt-85) cc_final: 0.7546 (mtm110) REVERT: C 702 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8224 (mm-30) REVERT: D 137 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7675 (mt-10) REVERT: D 140 GLN cc_start: 0.6362 (mm-40) cc_final: 0.6101 (mm110) REVERT: D 246 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7461 (pmmt) REVERT: D 690 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.7551 (mtm110) REVERT: D 702 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8278 (mm-30) outliers start: 67 outliers final: 53 residues processed: 392 average time/residue: 0.1713 time to fit residues: 103.6588 Evaluate side-chains 390 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 331 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 229 ASP 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 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 207 GLU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 285 GLU 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 207 GLU 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 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 207 GLU 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: 6.9990 chunk 237 optimal weight: 4.9990 chunk 189 optimal weight: 0.0980 chunk 182 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 103 optimal weight: 0.0670 chunk 201 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS B 585 HIS C 585 HIS D 585 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.165212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.122254 restraints weight = 26965.093| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.14 r_work: 0.2927 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3926 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= 0.084 Angle : 0.452 7.491 31340 Z= 0.232 Chirality : 0.037 0.158 3412 Planarity : 0.003 0.029 3788 Dihedral : 13.190 89.578 3904 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.12 % Allowed : 14.81 % 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: -0.14 (0.17), residues: 2620 helix: 0.76 (0.13), residues: 1592 sheet: 1.41 (0.69), residues: 64 loop : -1.64 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 202 TYR 0.010 0.001 TYR D 208 PHE 0.013 0.001 PHE D 449 TRP 0.010 0.001 TRP A 380 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.08 (23376) covalent geometry : angle 0.45223 / 0.23 (31332) SS BOND : bond 0.00009 / 0.00 ( 4) SS BOND : angle 0.38111 / 0.19 ( 8) hydrogen bonds : bond 0.03189 / 2.08 ( 838) hydrogen bonds : angle 3.45857 / 2.39 ( 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 407 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 357 time to evaluate : 0.853 Fit side-chains REVERT: A 134 GLU cc_start: 0.7685 (mp0) cc_final: 0.7111 (mp0) REVERT: A 140 GLN cc_start: 0.6365 (mm-40) cc_final: 0.6016 (mm110) REVERT: A 161 LYS cc_start: 0.8131 (mmpt) cc_final: 0.7922 (mmmt) REVERT: A 202 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7969 (mtp85) REVERT: A 334 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8611 (mm-30) REVERT: A 690 ARG cc_start: 0.8543 (mtt-85) cc_final: 0.7409 (mtm110) REVERT: A 702 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8262 (mm-30) REVERT: B 137 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7725 (mm-30) REVERT: B 202 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7846 (mtp85) REVERT: B 690 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.7497 (mtm110) REVERT: B 702 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8239 (mm-30) REVERT: C 137 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7749 (mm-30) REVERT: C 202 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7861 (mtp85) REVERT: C 334 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8615 (mm-30) REVERT: C 690 ARG cc_start: 0.8442 (mtt-85) cc_final: 0.7440 (mtm110) REVERT: C 702 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8212 (mm-30) REVERT: D 137 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7638 (mt-10) REVERT: D 140 GLN cc_start: 0.6457 (mm-40) cc_final: 0.6191 (mm110) REVERT: D 690 ARG cc_start: 0.8433 (mtt-85) cc_final: 0.7470 (mtm110) REVERT: D 702 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8264 (mm-30) outliers start: 50 outliers final: 38 residues processed: 397 average time/residue: 0.1734 time to fit residues: 106.1941 Evaluate side-chains 383 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 343 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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 B residue 128 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 229 ASP 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 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 229 ASP 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 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 737 VAL 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 414 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 137 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 237 optimal weight: 0.0010 chunk 49 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.160529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.116387 restraints weight = 27276.563| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.18 r_work: 0.2838 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23380 Z= 0.164 Angle : 0.544 8.235 31340 Z= 0.277 Chirality : 0.041 0.158 3412 Planarity : 0.003 0.028 3788 Dihedral : 13.906 87.297 3904 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.28 % Allowed : 14.85 % Favored : 82.87 % 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: -0.42 (0.16), residues: 2620 helix: 0.52 (0.13), residues: 1592 sheet: 0.79 (0.59), residues: 88 loop : -1.73 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 202 TYR 0.016 0.002 TYR B 208 PHE 0.013 0.001 PHE A 449 TRP 0.011 0.001 TRP A 380 HIS 0.008 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 (23376) covalent geometry : angle 0.54439 / 0.28 (31332) SS BOND : bond 0.00010 / 0.01 ( 4) SS BOND : angle 0.38925 / 0.19 ( 8) hydrogen bonds : bond 0.04777 / 3.11 ( 838) hydrogen bonds : angle 3.60686 / 2.49 ( 2478) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5070.30 seconds wall clock time: 87 minutes 45.64 seconds (5265.64 seconds total)