Starting phenix.real_space_refine on Fri Aug 7 16:57:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13lo_77139/08_2026/13lo_77139.cif Found real_map, /net/cci-nas-00/data/ceres_data/13lo_77139/08_2026/13lo_77139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13lo_77139/08_2026/13lo_77139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13lo_77139/08_2026/13lo_77139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13lo_77139/08_2026/13lo_77139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13lo_77139/08_2026/13lo_77139.map" } resolution = 3.34 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= 0.001 sd= 0.020 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 128 5.16 5 Na 4 4.78 5 C 14660 2.51 5 N 3464 2.21 5 O 3928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22212 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5188 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "B" Number of atoms: 5188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5188 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "C" Number of atoms: 5188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5188 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "D" Number of atoms: 5188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5188 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "A" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 420 Unusual residues: {' NA': 4, 'POV': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 312 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 4.55, per 1000 atoms: 0.20 Number of scatterers: 22212 At special positions: 0 Unit cell: (146.217, 146.217, 130.662, 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 128 16.00 P 28 15.00 Na 4 11.00 O 3928 8.00 N 3464 7.00 C 14660 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: 1.36 Conformation dependent library (CDL) restraints added in 699.0 milliseconds 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4880 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 56.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.587A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 161 removed outlier: 3.636A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.644A pdb=" N LYS A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.074A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.027A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.542A pdb=" N ALA A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.561A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.522A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.636A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.615A pdb=" N THR A 335 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.671A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.521A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.741A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 434 removed outlier: 3.578A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 461 removed outlier: 3.954A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 507 removed outlier: 3.549A pdb=" N LEU A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 536 removed outlier: 3.863A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 4.570A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 569 through 573 Processing helix chain 'A' and resid 574 through 579 removed outlier: 3.851A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.652A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 607 removed outlier: 4.624A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 634 removed outlier: 3.803A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 660 removed outlier: 3.779A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 Processing helix chain 'A' and resid 669 through 678 removed outlier: 3.539A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 removed outlier: 3.636A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.513A pdb=" N ARG A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 132 through 148 removed outlier: 3.587A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.636A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.645A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA B 175 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 4.074A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 removed outlier: 4.027A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.542A pdb=" N ALA B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.560A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 removed outlier: 3.523A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.636A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.616A pdb=" N THR B 335 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.670A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.520A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.741A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 434 removed outlier: 3.578A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 461 removed outlier: 3.954A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 507 removed outlier: 3.550A pdb=" N LEU B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 536 removed outlier: 3.863A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 561 removed outlier: 4.569A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 564 No H-bonds generated for 'chain 'B' and resid 562 through 564' Processing helix chain 'B' and resid 569 through 573 Processing helix chain 'B' and resid 574 through 579 removed outlier: 3.851A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 584 removed outlier: 3.652A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 607 removed outlier: 4.625A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 607 " --> pdb=" O VAL B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 removed outlier: 3.803A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 660 removed outlier: 3.778A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 665 Processing helix chain 'B' and resid 669 through 678 removed outlier: 3.539A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 686 removed outlier: 3.637A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.513A pdb=" N ARG B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.588A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.636A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.644A pdb=" N LYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA C 175 " --> pdb=" O CYS C 171 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 4.074A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 223 removed outlier: 4.028A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.542A pdb=" N ALA C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.560A pdb=" N HIS C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 307 removed outlier: 3.523A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.636A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 335 removed outlier: 3.616A pdb=" N THR C 335 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.671A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.521A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.740A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 434 removed outlier: 3.578A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 434 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 461 removed outlier: 3.954A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR C 454 " --> pdb=" O PHE C 450 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 507 removed outlier: 3.551A pdb=" N LEU C 484 " --> pdb=" O GLY C 480 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 536 removed outlier: 3.864A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 561 removed outlier: 4.570A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 564 No H-bonds generated for 'chain 'C' and resid 562 through 564' Processing helix chain 'C' and resid 569 through 573 Processing helix chain 'C' and resid 574 through 579 removed outlier: 3.850A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 584 removed outlier: 3.650A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 607 removed outlier: 4.624A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 607 " --> pdb=" O VAL C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 634 removed outlier: 3.803A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 660 removed outlier: 3.779A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 665 Processing helix chain 'C' and resid 669 through 678 removed outlier: 3.540A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 686 removed outlier: 3.636A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.513A pdb=" N ARG C 696 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 132 through 148 removed outlier: 3.587A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 161 removed outlier: 3.636A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.644A pdb=" N LYS D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA D 175 " --> pdb=" O CYS D 171 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.074A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 223 removed outlier: 4.027A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.542A pdb=" N ALA D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.560A pdb=" N HIS D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 307 removed outlier: 3.522A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.636A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 335 removed outlier: 3.616A pdb=" N THR D 335 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.672A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.521A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.740A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 434 removed outlier: 3.578A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 434 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 461 removed outlier: 3.953A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 507 removed outlier: 3.550A pdb=" N LEU D 484 " --> pdb=" O GLY D 480 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 536 removed outlier: 3.864A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 561 removed outlier: 4.569A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 564 No H-bonds generated for 'chain 'D' and resid 562 through 564' Processing helix chain 'D' and resid 569 through 573 Processing helix chain 'D' and resid 574 through 579 removed outlier: 3.851A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 584 removed outlier: 3.651A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 607 removed outlier: 4.625A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 607 " --> pdb=" O VAL D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 634 removed outlier: 3.803A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 660 removed outlier: 3.779A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 665 Processing helix chain 'D' and resid 669 through 678 removed outlier: 3.539A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 686 removed outlier: 3.637A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.513A pdb=" N ARG D 696 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 6.788A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 732 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 731 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 719 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 377 through 382 removed outlier: 6.788A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 732 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 731 " --> pdb=" O GLU B 719 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 719 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 382 removed outlier: 6.788A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 732 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 731 " --> pdb=" O GLU C 719 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 719 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 377 through 382 removed outlier: 6.789A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 732 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS D 731 " --> pdb=" O GLU D 719 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 719 " --> pdb=" O CYS D 731 " (cutoff:3.500A) 709 hydrogen bonds defined for protein. 2079 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: 2.77 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3655 1.32 - 1.45: 5632 1.45 - 1.57: 13077 1.57 - 1.69: 60 1.69 - 1.82: 212 Bond restraints: 22636 Sorted by residual: bond pdb=" CA LEU D 200 " pdb=" C LEU D 200 " ideal model delta sigma weight residual 1.523 1.589 -0.066 1.34e-02 5.57e+03 2.40e+01 bond pdb=" CA LEU B 200 " pdb=" C LEU B 200 " ideal model delta sigma weight residual 1.523 1.588 -0.065 1.34e-02 5.57e+03 2.35e+01 bond pdb=" CA LEU A 200 " pdb=" C LEU A 200 " ideal model delta sigma weight residual 1.523 1.588 -0.065 1.34e-02 5.57e+03 2.33e+01 bond pdb=" CA LEU C 200 " pdb=" C LEU C 200 " ideal model delta sigma weight residual 1.523 1.588 -0.065 1.34e-02 5.57e+03 2.33e+01 bond pdb=" O12 POV D1105 " pdb=" P POV D1105 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 22631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 28546 2.09 - 4.17: 1514 4.17 - 6.26: 161 6.26 - 8.34: 97 8.34 - 10.43: 30 Bond angle restraints: 30348 Sorted by residual: angle pdb=" C LYS B 368 " pdb=" N ARG B 369 " pdb=" CA ARG B 369 " ideal model delta sigma weight residual 121.54 131.97 -10.43 1.91e+00 2.74e-01 2.98e+01 angle pdb=" C LYS C 368 " pdb=" N ARG C 369 " pdb=" CA ARG C 369 " ideal model delta sigma weight residual 121.54 131.96 -10.42 1.91e+00 2.74e-01 2.97e+01 angle pdb=" C LYS A 368 " pdb=" N ARG A 369 " pdb=" CA ARG A 369 " ideal model delta sigma weight residual 121.54 131.96 -10.42 1.91e+00 2.74e-01 2.97e+01 angle pdb=" C LYS D 368 " pdb=" N ARG D 369 " pdb=" CA ARG D 369 " ideal model delta sigma weight residual 121.54 131.94 -10.40 1.91e+00 2.74e-01 2.97e+01 angle pdb=" N ASN A 616 " pdb=" CA ASN A 616 " pdb=" C ASN A 616 " ideal model delta sigma weight residual 113.61 105.78 7.83 1.50e+00 4.44e-01 2.72e+01 ... (remaining 30343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 13438 35.99 - 71.99: 343 71.99 - 107.98: 49 107.98 - 143.98: 32 143.98 - 179.97: 26 Dihedral angle restraints: 13888 sinusoidal: 6364 harmonic: 7524 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual 93.00 147.04 -54.04 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual 93.00 147.03 -54.03 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual 93.00 147.01 -54.01 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 13885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2490 0.060 - 0.119: 688 0.119 - 0.179: 86 0.179 - 0.238: 18 0.238 - 0.298: 14 Chirality restraints: 3296 Sorted by residual: chirality pdb=" CG LEU A 630 " pdb=" CB LEU A 630 " pdb=" CD1 LEU A 630 " pdb=" CD2 LEU A 630 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CG LEU D 630 " pdb=" CB LEU D 630 " pdb=" CD1 LEU D 630 " pdb=" CD2 LEU D 630 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CG LEU B 630 " pdb=" CB LEU B 630 " pdb=" CD1 LEU B 630 " pdb=" CD2 LEU B 630 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3293 not shown) Planarity restraints: 3676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 474 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.04e+00 pdb=" C ALA B 474 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA B 474 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU B 475 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 474 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C ALA C 474 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA C 474 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU C 475 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 474 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C ALA A 474 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA A 474 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 475 " -0.017 2.00e-02 2.50e+03 ... (remaining 3673 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 327 2.67 - 3.22: 18861 3.22 - 3.78: 31244 3.78 - 4.34: 43799 4.34 - 4.90: 73048 Nonbonded interactions: 167279 Sorted by model distance: nonbonded pdb="NA NA A1109 " pdb="NA NA A1110 " model vdw 2.107 1.900 nonbonded pdb=" O PRO A 753 " pdb=" OH TYR B 213 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O PRO D 753 " model vdw 2.266 3.040 nonbonded pdb=" O21 POV A1108 " pdb=" O31 POV A1108 " model vdw 2.280 2.432 nonbonded pdb=" O21 POV C1106 " pdb=" O31 POV C1106 " model vdw 2.283 2.432 ... (remaining 167274 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 118 through 1106) selection = chain 'B' selection = (chain 'C' and resid 118 through 1106) selection = (chain 'D' and resid 118 through 1106) } 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: 1.220 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.770 Find NCS groups from input model: 0.550 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 22640 Z= 0.404 Angle : 1.105 10.430 30356 Z= 0.550 Chirality : 0.058 0.298 3296 Planarity : 0.006 0.052 3676 Dihedral : 19.165 179.972 8996 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.42 % Favored : 90.11 % Rotamer: Outliers : 1.06 % Allowed : 4.78 % Favored : 94.16 % 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: -6.97 (0.09), residues: 2548 helix: -4.80 (0.05), residues: 1480 sheet: -4.53 (0.35), residues: 112 loop : -4.01 (0.14), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 567 TYR 0.013 0.002 TYR D 451 PHE 0.019 0.003 PHE C 259 TRP 0.020 0.003 TRP C 739 HIS 0.008 0.002 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00895 / 0.40 (22636) covalent geometry : angle 1.10425 / 0.55 (30348) SS BOND : bond 0.00063 / 0.03 ( 4) SS BOND : angle 3.07518 / 2.09 ( 8) hydrogen bonds : bond 0.33466 / 22.22 ( 709) hydrogen bonds : angle 10.44526 / 7.24 ( 2079) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 555 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 HIS cc_start: 0.7413 (t-90) cc_final: 0.7002 (t-170) REVERT: A 184 LYS cc_start: 0.8099 (tttt) cc_final: 0.7711 (tppt) REVERT: A 185 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8112 (mm-30) REVERT: A 196 GLU cc_start: 0.8101 (tt0) cc_final: 0.7853 (mm-30) REVERT: A 208 TYR cc_start: 0.7737 (m-10) cc_final: 0.7523 (m-10) REVERT: A 209 THR cc_start: 0.8157 (t) cc_final: 0.7391 (m) REVERT: A 221 ILE cc_start: 0.8016 (mt) cc_final: 0.7814 (mt) REVERT: A 282 MET cc_start: 0.8832 (mtm) cc_final: 0.8590 (mtm) REVERT: A 286 GLN cc_start: 0.8451 (mp10) cc_final: 0.8094 (mp10) REVERT: A 315 ASP cc_start: 0.7636 (p0) cc_final: 0.7300 (p0) REVERT: A 336 THR cc_start: 0.9116 (m) cc_final: 0.8812 (p) REVERT: A 431 MET cc_start: 0.7681 (mtt) cc_final: 0.7123 (mtp) REVERT: A 440 MET cc_start: 0.8579 (mtp) cc_final: 0.8319 (mtm) REVERT: A 497 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7505 (mp) REVERT: A 571 SER cc_start: 0.8454 (m) cc_final: 0.7887 (t) REVERT: A 575 TYR cc_start: 0.8815 (m-80) cc_final: 0.8602 (m-80) REVERT: A 616 ASN cc_start: 0.5932 (OUTLIER) cc_final: 0.5370 (m-40) REVERT: A 617 LYS cc_start: 0.6611 (OUTLIER) cc_final: 0.6132 (tppt) REVERT: A 647 ASN cc_start: 0.7337 (t0) cc_final: 0.6256 (t0) REVERT: A 691 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8141 (mp) REVERT: A 738 LYS cc_start: 0.8099 (tptt) cc_final: 0.7782 (ttmm) REVERT: A 752 ASP cc_start: 0.7115 (t0) cc_final: 0.6495 (p0) REVERT: B 122 ARG cc_start: 0.7371 (mtt180) cc_final: 0.6784 (mtp85) REVERT: B 160 HIS cc_start: 0.7386 (t-90) cc_final: 0.7050 (t-170) REVERT: B 184 LYS cc_start: 0.8239 (tttt) cc_final: 0.7922 (tppt) REVERT: B 196 GLU cc_start: 0.8057 (tt0) cc_final: 0.7742 (mp0) REVERT: B 286 GLN cc_start: 0.8588 (mp10) cc_final: 0.8170 (mp10) REVERT: B 431 MET cc_start: 0.7667 (mtt) cc_final: 0.7035 (mtp) REVERT: B 440 MET cc_start: 0.8532 (mtp) cc_final: 0.8273 (mtm) REVERT: B 497 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7496 (mp) REVERT: B 612 CYS cc_start: 0.3273 (t) cc_final: 0.2991 (m) REVERT: B 617 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.6005 (tppt) REVERT: B 647 ASN cc_start: 0.7365 (t0) cc_final: 0.6444 (t0) REVERT: B 738 LYS cc_start: 0.8306 (tptt) cc_final: 0.8025 (ttmm) REVERT: C 122 ARG cc_start: 0.7294 (mtt180) cc_final: 0.6618 (mtp85) REVERT: C 160 HIS cc_start: 0.7431 (t-90) cc_final: 0.7101 (t-170) REVERT: C 184 LYS cc_start: 0.8211 (tttt) cc_final: 0.7905 (tppt) REVERT: C 196 GLU cc_start: 0.8054 (tt0) cc_final: 0.7726 (mp0) REVERT: C 286 GLN cc_start: 0.8579 (mp10) cc_final: 0.8169 (mp10) REVERT: C 315 ASP cc_start: 0.7813 (p0) cc_final: 0.7499 (p0) REVERT: C 431 MET cc_start: 0.7658 (mtt) cc_final: 0.7020 (mtp) REVERT: C 440 MET cc_start: 0.8549 (mtp) cc_final: 0.8292 (mtm) REVERT: C 497 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7522 (mp) REVERT: C 612 CYS cc_start: 0.3260 (t) cc_final: 0.2901 (m) REVERT: C 617 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6092 (tppt) REVERT: C 647 ASN cc_start: 0.7378 (t0) cc_final: 0.6399 (t0) REVERT: C 738 LYS cc_start: 0.8308 (tptt) cc_final: 0.7942 (ttmm) REVERT: D 122 ARG cc_start: 0.7286 (mtt180) cc_final: 0.6611 (mtp85) REVERT: D 160 HIS cc_start: 0.7434 (t-90) cc_final: 0.7114 (t-170) REVERT: D 184 LYS cc_start: 0.8218 (tttt) cc_final: 0.7921 (tppt) REVERT: D 196 GLU cc_start: 0.8053 (tt0) cc_final: 0.7725 (mp0) REVERT: D 214 GLU cc_start: 0.8021 (tt0) cc_final: 0.7743 (tt0) REVERT: D 286 GLN cc_start: 0.8579 (mp10) cc_final: 0.8172 (mp10) REVERT: D 315 ASP cc_start: 0.7796 (p0) cc_final: 0.7479 (p0) REVERT: D 431 MET cc_start: 0.7698 (mtt) cc_final: 0.7059 (mtp) REVERT: D 497 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7534 (mp) REVERT: D 612 CYS cc_start: 0.3236 (t) cc_final: 0.2995 (m) REVERT: D 617 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.6071 (tppt) REVERT: D 647 ASN cc_start: 0.7427 (t0) cc_final: 0.6443 (t0) REVERT: D 738 LYS cc_start: 0.8331 (tptt) cc_final: 0.7948 (ttmm) outliers start: 24 outliers final: 4 residues processed: 571 average time/residue: 0.1538 time to fit residues: 132.4320 Evaluate side-chains 348 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 334 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 617 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 HIS ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN B 150 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN C 150 HIS ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN D 150 HIS ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 HIS D 561 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.170112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123908 restraints weight = 29613.254| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.73 r_work: 0.3305 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22640 Z= 0.135 Angle : 0.638 7.659 30356 Z= 0.331 Chirality : 0.038 0.140 3296 Planarity : 0.005 0.054 3676 Dihedral : 22.706 170.019 4016 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.56 % Favored : 91.41 % Rotamer: Outliers : 2.79 % Allowed : 10.35 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -5.54 (0.12), residues: 2548 helix: -3.39 (0.09), residues: 1532 sheet: -4.46 (0.40), residues: 88 loop : -3.82 (0.15), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 696 TYR 0.012 0.001 TYR B 213 PHE 0.017 0.001 PHE B 310 TRP 0.016 0.001 TRP A 710 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (22636) covalent geometry : angle 0.63747 / 0.33 (30348) SS BOND : bond 0.00144 / 0.07 ( 4) SS BOND : angle 1.68616 / 1.09 ( 8) hydrogen bonds : bond 0.04664 / 3.11 ( 709) hydrogen bonds : angle 4.75678 / 3.29 ( 2079) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 408 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7581 (mtt180) cc_final: 0.6972 (mtp85) REVERT: A 184 LYS cc_start: 0.7611 (tttt) cc_final: 0.7360 (tppt) REVERT: A 185 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7973 (mm-30) REVERT: A 188 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7642 (mtt-85) REVERT: A 286 GLN cc_start: 0.8422 (mp10) cc_final: 0.8073 (mp10) REVERT: A 315 ASP cc_start: 0.7842 (p0) cc_final: 0.7529 (p0) REVERT: A 429 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8106 (mt) REVERT: A 440 MET cc_start: 0.8792 (mtp) cc_final: 0.8440 (mtm) REVERT: A 509 ARG cc_start: 0.6734 (ptt-90) cc_final: 0.6437 (ptt-90) REVERT: A 571 SER cc_start: 0.8908 (m) cc_final: 0.8409 (t) REVERT: A 575 TYR cc_start: 0.8920 (m-80) cc_final: 0.8405 (m-80) REVERT: A 619 CYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6934 (p) REVERT: A 738 LYS cc_start: 0.8197 (tptt) cc_final: 0.7931 (ttmm) REVERT: B 122 ARG cc_start: 0.7532 (mtt180) cc_final: 0.6938 (mtp85) REVERT: B 185 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8190 (mm-30) REVERT: B 286 GLN cc_start: 0.8590 (mp10) cc_final: 0.8095 (mp10) REVERT: B 440 MET cc_start: 0.8719 (mtp) cc_final: 0.8360 (mtm) REVERT: B 574 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7607 (ptp) REVERT: B 612 CYS cc_start: 0.3417 (t) cc_final: 0.3193 (t) REVERT: B 647 ASN cc_start: 0.7495 (t0) cc_final: 0.6903 (p0) REVERT: B 738 LYS cc_start: 0.8486 (tptt) cc_final: 0.8217 (ttmm) REVERT: C 122 ARG cc_start: 0.7492 (mtt180) cc_final: 0.6920 (mtp85) REVERT: C 185 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8194 (mm-30) REVERT: C 286 GLN cc_start: 0.8585 (mp10) cc_final: 0.8123 (mp10) REVERT: C 440 MET cc_start: 0.8736 (mtp) cc_final: 0.8368 (mtm) REVERT: C 571 SER cc_start: 0.8765 (m) cc_final: 0.8502 (t) REVERT: C 574 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7598 (ptp) REVERT: C 647 ASN cc_start: 0.7514 (t0) cc_final: 0.6862 (p0) REVERT: C 717 MET cc_start: 0.8458 (mmt) cc_final: 0.8145 (mmt) REVERT: C 738 LYS cc_start: 0.8439 (tptt) cc_final: 0.8124 (ttmm) REVERT: D 122 ARG cc_start: 0.7496 (mtt180) cc_final: 0.6898 (mtp85) REVERT: D 185 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8248 (mm-30) REVERT: D 286 GLN cc_start: 0.8579 (mp10) cc_final: 0.8126 (mp10) REVERT: D 571 SER cc_start: 0.8734 (m) cc_final: 0.8527 (t) REVERT: D 574 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7511 (ptp) REVERT: D 647 ASN cc_start: 0.7466 (t0) cc_final: 0.6853 (p0) REVERT: D 717 MET cc_start: 0.8484 (mmt) cc_final: 0.8131 (mmt) REVERT: D 738 LYS cc_start: 0.8458 (tptt) cc_final: 0.8177 (ttmm) outliers start: 63 outliers final: 16 residues processed: 449 average time/residue: 0.1436 time to fit residues: 99.5738 Evaluate side-chains 338 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 317 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 574 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 224 optimal weight: 50.0000 chunk 243 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 153 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 284 HIS A 477 HIS A 671 ASN B 160 HIS B 274 GLN B 284 HIS B 671 ASN C 160 HIS C 274 GLN C 284 HIS C 523 HIS C 671 ASN D 160 HIS D 274 GLN D 284 HIS D 671 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.165561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118762 restraints weight = 29667.334| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.79 r_work: 0.3236 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22640 Z= 0.171 Angle : 0.630 8.595 30356 Z= 0.321 Chirality : 0.040 0.147 3296 Planarity : 0.004 0.047 3676 Dihedral : 21.315 179.565 3988 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.79 % Allowed : 12.92 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.58 (0.13), residues: 2548 helix: -2.53 (0.11), residues: 1560 sheet: -4.27 (0.44), residues: 88 loop : -3.61 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 509 TYR 0.014 0.001 TYR B 451 PHE 0.026 0.002 PHE B 193 TRP 0.018 0.001 TRP A 710 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (22636) covalent geometry : angle 0.62960 / 0.32 (30348) SS BOND : bond 0.00512 / 0.25 ( 4) SS BOND : angle 1.26048 / 0.87 ( 8) hydrogen bonds : bond 0.04011 / 2.66 ( 709) hydrogen bonds : angle 4.14620 / 2.86 ( 2079) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 326 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7090 (mtp85) REVERT: A 185 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8147 (mm-30) REVERT: A 224 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 286 GLN cc_start: 0.8543 (mp10) cc_final: 0.8297 (mp10) REVERT: A 315 ASP cc_start: 0.7895 (p0) cc_final: 0.7601 (p0) REVERT: A 429 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8294 (mt) REVERT: A 440 MET cc_start: 0.8823 (mtp) cc_final: 0.8544 (mtm) REVERT: A 497 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8147 (mp) REVERT: A 575 TYR cc_start: 0.8936 (m-80) cc_final: 0.8433 (m-80) REVERT: A 738 LYS cc_start: 0.8352 (tptt) cc_final: 0.7998 (ttmm) REVERT: B 122 ARG cc_start: 0.7543 (mtt180) cc_final: 0.6945 (mtp85) REVERT: B 184 LYS cc_start: 0.7819 (tppt) cc_final: 0.7587 (tppt) REVERT: B 185 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8207 (mm-30) REVERT: B 286 GLN cc_start: 0.8677 (mp10) cc_final: 0.8349 (mp10) REVERT: B 440 MET cc_start: 0.8765 (mtp) cc_final: 0.8492 (mtm) REVERT: B 497 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8118 (mp) REVERT: B 647 ASN cc_start: 0.7628 (t0) cc_final: 0.7043 (p0) REVERT: B 738 LYS cc_start: 0.8490 (tptt) cc_final: 0.8115 (ttmm) REVERT: C 122 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6901 (mtp85) REVERT: C 184 LYS cc_start: 0.7876 (tppt) cc_final: 0.7652 (tppt) REVERT: C 185 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8207 (mm-30) REVERT: C 282 MET cc_start: 0.9000 (mtm) cc_final: 0.8690 (mtm) REVERT: C 286 GLN cc_start: 0.8660 (mp10) cc_final: 0.8340 (mp10) REVERT: C 366 LYS cc_start: 0.8548 (mttt) cc_final: 0.8228 (mtpp) REVERT: C 440 MET cc_start: 0.8765 (mtp) cc_final: 0.8440 (mtm) REVERT: C 497 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8108 (mp) REVERT: C 535 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9179 (tt) REVERT: C 647 ASN cc_start: 0.7611 (t0) cc_final: 0.7020 (p0) REVERT: C 696 ARG cc_start: 0.8590 (mtp180) cc_final: 0.8215 (mtp180) REVERT: C 738 LYS cc_start: 0.8392 (tptt) cc_final: 0.8030 (tttm) REVERT: D 122 ARG cc_start: 0.7449 (mtt180) cc_final: 0.6907 (mtp85) REVERT: D 184 LYS cc_start: 0.7871 (tppt) cc_final: 0.7650 (tppt) REVERT: D 185 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8217 (mm-30) REVERT: D 282 MET cc_start: 0.8996 (mtm) cc_final: 0.8697 (mtm) REVERT: D 286 GLN cc_start: 0.8654 (mp10) cc_final: 0.8347 (mp10) REVERT: D 366 LYS cc_start: 0.8551 (mttt) cc_final: 0.8234 (mtpp) REVERT: D 497 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8126 (mp) REVERT: D 647 ASN cc_start: 0.7629 (t0) cc_final: 0.6910 (p0) REVERT: D 696 ARG cc_start: 0.8584 (mtp180) cc_final: 0.8215 (mtp180) REVERT: D 738 LYS cc_start: 0.8390 (tptt) cc_final: 0.8057 (ttmm) outliers start: 63 outliers final: 29 residues processed: 361 average time/residue: 0.1525 time to fit residues: 84.6425 Evaluate side-chains 343 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 308 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 668 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 164 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 201 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 523 HIS B 160 HIS B 523 HIS C 160 HIS D 160 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.167726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121225 restraints weight = 29731.422| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.77 r_work: 0.3263 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22640 Z= 0.123 Angle : 0.569 8.093 30356 Z= 0.292 Chirality : 0.038 0.137 3296 Planarity : 0.004 0.038 3676 Dihedral : 20.427 175.180 3988 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.23 % Allowed : 13.50 % Favored : 83.27 % 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: -3.88 (0.14), residues: 2548 helix: -1.91 (0.12), residues: 1560 sheet: -4.24 (0.41), residues: 88 loop : -3.42 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 509 TYR 0.010 0.001 TYR A 451 PHE 0.028 0.001 PHE C 489 TRP 0.020 0.001 TRP A 710 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (22636) covalent geometry : angle 0.56826 / 0.29 (30348) SS BOND : bond 0.00043 / 0.02 ( 4) SS BOND : angle 1.24625 / 0.87 ( 8) hydrogen bonds : bond 0.03163 / 2.10 ( 709) hydrogen bonds : angle 3.86134 / 2.66 ( 2079) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 340 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7092 (mtp85) REVERT: A 185 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8213 (mm-30) REVERT: A 224 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7865 (tm-30) REVERT: A 286 GLN cc_start: 0.8565 (mp10) cc_final: 0.8257 (mp10) REVERT: A 315 ASP cc_start: 0.7835 (p0) cc_final: 0.7535 (p0) REVERT: A 416 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7733 (mtp180) REVERT: A 497 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8040 (mp) REVERT: A 575 TYR cc_start: 0.8956 (m-80) cc_final: 0.8436 (m-80) REVERT: A 717 MET cc_start: 0.8489 (mmt) cc_final: 0.7732 (mmt) REVERT: A 738 LYS cc_start: 0.8328 (tptt) cc_final: 0.7916 (mtpp) REVERT: B 122 ARG cc_start: 0.7527 (mtt180) cc_final: 0.6930 (mtp85) REVERT: B 184 LYS cc_start: 0.7751 (tppt) cc_final: 0.7511 (tppt) REVERT: B 185 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8236 (mm-30) REVERT: B 286 GLN cc_start: 0.8647 (mp10) cc_final: 0.8311 (mp10) REVERT: B 440 MET cc_start: 0.8764 (mtp) cc_final: 0.8527 (mtm) REVERT: B 497 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 647 ASN cc_start: 0.7621 (t0) cc_final: 0.7149 (p0) REVERT: B 738 LYS cc_start: 0.8382 (tptt) cc_final: 0.8079 (ttmm) REVERT: C 122 ARG cc_start: 0.7415 (mtt180) cc_final: 0.6915 (mtp85) REVERT: C 184 LYS cc_start: 0.7744 (tppt) cc_final: 0.7486 (tppt) REVERT: C 185 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8272 (mm-30) REVERT: C 286 GLN cc_start: 0.8660 (mp10) cc_final: 0.8319 (mp10) REVERT: C 416 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7989 (ttp80) REVERT: C 440 MET cc_start: 0.8698 (mtp) cc_final: 0.8465 (mtm) REVERT: C 497 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8018 (mp) REVERT: C 647 ASN cc_start: 0.7537 (t0) cc_final: 0.7078 (p0) REVERT: C 696 ARG cc_start: 0.8569 (mtp180) cc_final: 0.8250 (mtp180) REVERT: C 738 LYS cc_start: 0.8348 (tptt) cc_final: 0.8046 (ttmm) REVERT: D 122 ARG cc_start: 0.7436 (mtt180) cc_final: 0.6942 (mtp85) REVERT: D 184 LYS cc_start: 0.7782 (tppt) cc_final: 0.7535 (tppt) REVERT: D 185 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8285 (mm-30) REVERT: D 286 GLN cc_start: 0.8600 (mp10) cc_final: 0.8291 (mp10) REVERT: D 497 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8035 (mp) REVERT: D 647 ASN cc_start: 0.7561 (t0) cc_final: 0.7106 (p0) REVERT: D 696 ARG cc_start: 0.8542 (mtp180) cc_final: 0.8214 (mtp180) REVERT: D 738 LYS cc_start: 0.8362 (tptt) cc_final: 0.7966 (ttmm) outliers start: 73 outliers final: 40 residues processed: 377 average time/residue: 0.1688 time to fit residues: 96.1296 Evaluate side-chains 342 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 196 optimal weight: 4.9990 chunk 209 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS B 160 HIS C 160 HIS C 523 HIS D 160 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.167320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121077 restraints weight = 29579.720| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.77 r_work: 0.3267 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22640 Z= 0.121 Angle : 0.543 8.268 30356 Z= 0.279 Chirality : 0.038 0.119 3296 Planarity : 0.004 0.031 3676 Dihedral : 19.470 167.858 3988 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.12 % Allowed : 13.32 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.15), residues: 2548 helix: -1.43 (0.12), residues: 1572 sheet: -4.11 (0.42), residues: 88 loop : -3.12 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 509 TYR 0.011 0.001 TYR A 451 PHE 0.031 0.001 PHE A 489 TRP 0.024 0.001 TRP A 710 HIS 0.008 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (22636) covalent geometry : angle 0.54244 / 0.28 (30348) SS BOND : bond 0.00226 / 0.11 ( 4) SS BOND : angle 1.61021 / 1.14 ( 8) hydrogen bonds : bond 0.02929 / 1.95 ( 709) hydrogen bonds : angle 3.68628 / 2.55 ( 2079) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 316 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7110 (mtp85) REVERT: A 185 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8259 (mm-30) REVERT: A 286 GLN cc_start: 0.8530 (mp10) cc_final: 0.8211 (mp10) REVERT: A 299 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8725 (tp) REVERT: A 315 ASP cc_start: 0.7827 (p0) cc_final: 0.7562 (p0) REVERT: A 416 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8004 (mtp180) REVERT: A 497 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8009 (mp) REVERT: A 575 TYR cc_start: 0.8953 (m-80) cc_final: 0.8439 (m-80) REVERT: A 717 MET cc_start: 0.8497 (mmt) cc_final: 0.8165 (mmm) REVERT: A 738 LYS cc_start: 0.8371 (tptt) cc_final: 0.7943 (mtpp) REVERT: B 122 ARG cc_start: 0.7539 (mtt180) cc_final: 0.6947 (mtp85) REVERT: B 184 LYS cc_start: 0.7740 (tppt) cc_final: 0.7517 (tppt) REVERT: B 185 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8216 (mm-30) REVERT: B 224 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 286 GLN cc_start: 0.8655 (mp10) cc_final: 0.8314 (mp10) REVERT: B 299 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8724 (tp) REVERT: B 416 ARG cc_start: 0.8295 (ttp80) cc_final: 0.8013 (mtp180) REVERT: B 440 MET cc_start: 0.8785 (mtp) cc_final: 0.8528 (mtm) REVERT: B 497 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8003 (mp) REVERT: B 647 ASN cc_start: 0.7622 (t0) cc_final: 0.7080 (p0) REVERT: C 122 ARG cc_start: 0.7426 (mtt180) cc_final: 0.6945 (mtp85) REVERT: C 184 LYS cc_start: 0.7743 (tppt) cc_final: 0.7526 (tppt) REVERT: C 185 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8279 (mm-30) REVERT: C 286 GLN cc_start: 0.8631 (mp10) cc_final: 0.8307 (mp10) REVERT: C 299 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8734 (tp) REVERT: C 440 MET cc_start: 0.8765 (mtp) cc_final: 0.8484 (mtm) REVERT: C 497 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8012 (mp) REVERT: C 647 ASN cc_start: 0.7617 (t0) cc_final: 0.7064 (p0) REVERT: C 696 ARG cc_start: 0.8593 (mtp180) cc_final: 0.8239 (mtp180) REVERT: C 738 LYS cc_start: 0.8360 (tptt) cc_final: 0.7937 (mtpp) REVERT: D 122 ARG cc_start: 0.7426 (mtt180) cc_final: 0.6944 (mtp85) REVERT: D 184 LYS cc_start: 0.7755 (tppt) cc_final: 0.7540 (tppt) REVERT: D 185 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8274 (mm-30) REVERT: D 286 GLN cc_start: 0.8604 (mp10) cc_final: 0.8267 (mp10) REVERT: D 299 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8741 (tp) REVERT: D 497 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7969 (mp) REVERT: D 512 ASP cc_start: 0.6649 (m-30) cc_final: 0.6423 (m-30) REVERT: D 647 ASN cc_start: 0.7594 (t0) cc_final: 0.7052 (p0) REVERT: D 696 ARG cc_start: 0.8574 (mtp180) cc_final: 0.8241 (mtp180) REVERT: D 738 LYS cc_start: 0.8377 (tptt) cc_final: 0.7943 (ttmm) outliers start: 93 outliers final: 51 residues processed: 373 average time/residue: 0.1396 time to fit residues: 81.2376 Evaluate side-chains 350 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 291 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 68 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 150 optimal weight: 0.0570 chunk 137 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 212 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 297 ASN A 417 HIS B 160 HIS B 417 HIS B 523 HIS C 160 HIS C 417 HIS C 523 HIS D 160 HIS D 297 ASN D 417 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.168871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122855 restraints weight = 29787.305| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.78 r_work: 0.3286 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22640 Z= 0.099 Angle : 0.522 8.972 30356 Z= 0.267 Chirality : 0.037 0.116 3296 Planarity : 0.003 0.031 3676 Dihedral : 18.599 164.425 3986 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.05 % Allowed : 14.65 % Favored : 82.30 % 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: -2.72 (0.16), residues: 2548 helix: -0.95 (0.13), residues: 1572 sheet: -4.05 (0.40), residues: 88 loop : -3.00 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 416 TYR 0.010 0.001 TYR B 213 PHE 0.033 0.001 PHE B 489 TRP 0.025 0.001 TRP A 710 HIS 0.011 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (22636) covalent geometry : angle 0.52118 / 0.27 (30348) SS BOND : bond 0.00472 / 0.25 ( 4) SS BOND : angle 1.38521 / 1.00 ( 8) hydrogen bonds : bond 0.02589 / 1.72 ( 709) hydrogen bonds : angle 3.54939 / 2.45 ( 2079) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 333 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7110 (mtp85) REVERT: A 184 LYS cc_start: 0.7526 (tppt) cc_final: 0.7212 (tppt) REVERT: A 185 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8132 (mm-30) REVERT: A 286 GLN cc_start: 0.8485 (mp10) cc_final: 0.8196 (mp10) REVERT: A 315 ASP cc_start: 0.7951 (p0) cc_final: 0.7654 (p0) REVERT: A 416 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7957 (mtp180) REVERT: A 575 TYR cc_start: 0.8866 (m-80) cc_final: 0.8333 (m-80) REVERT: A 717 MET cc_start: 0.8542 (mmt) cc_final: 0.8207 (mmm) REVERT: A 738 LYS cc_start: 0.8397 (tptt) cc_final: 0.7940 (mtpp) REVERT: B 122 ARG cc_start: 0.7554 (mtt180) cc_final: 0.6994 (mtp85) REVERT: B 184 LYS cc_start: 0.7645 (tppt) cc_final: 0.7430 (tppt) REVERT: B 185 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 224 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 286 GLN cc_start: 0.8572 (mp10) cc_final: 0.8278 (mp10) REVERT: B 416 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7860 (mtp180) REVERT: B 431 MET cc_start: 0.8337 (mtt) cc_final: 0.8069 (mtp) REVERT: B 440 MET cc_start: 0.8765 (mtp) cc_final: 0.8515 (mtm) REVERT: B 497 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7973 (mp) REVERT: B 509 ARG cc_start: 0.6757 (ptt-90) cc_final: 0.6378 (mmt180) REVERT: B 647 ASN cc_start: 0.7592 (t0) cc_final: 0.7158 (p0) REVERT: B 738 LYS cc_start: 0.8283 (tptp) cc_final: 0.7796 (mtpp) REVERT: C 122 ARG cc_start: 0.7435 (mtt180) cc_final: 0.6977 (mtp85) REVERT: C 185 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8251 (mm-30) REVERT: C 224 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7695 (tm-30) REVERT: C 286 GLN cc_start: 0.8570 (mp10) cc_final: 0.8263 (mp10) REVERT: C 288 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: C 327 ARG cc_start: 0.7902 (tpt-90) cc_final: 0.7563 (mmm160) REVERT: C 416 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7896 (mtp180) REVERT: C 440 MET cc_start: 0.8760 (mtp) cc_final: 0.8484 (mtm) REVERT: C 509 ARG cc_start: 0.6788 (ptt-90) cc_final: 0.6394 (mmt180) REVERT: C 645 GLN cc_start: 0.7592 (pm20) cc_final: 0.7372 (pm20) REVERT: C 647 ASN cc_start: 0.7595 (t0) cc_final: 0.7169 (p0) REVERT: C 696 ARG cc_start: 0.8586 (mtp180) cc_final: 0.8326 (mtp180) REVERT: C 738 LYS cc_start: 0.8415 (tptt) cc_final: 0.7954 (mtpp) REVERT: D 122 ARG cc_start: 0.7426 (mtt180) cc_final: 0.6968 (mtp85) REVERT: D 185 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8248 (mm-30) REVERT: D 286 GLN cc_start: 0.8573 (mp10) cc_final: 0.8257 (mp10) REVERT: D 327 ARG cc_start: 0.7933 (tpt-90) cc_final: 0.7478 (tpt90) REVERT: D 414 ASP cc_start: 0.7759 (t0) cc_final: 0.7534 (p0) REVERT: D 512 ASP cc_start: 0.6647 (m-30) cc_final: 0.6321 (m-30) REVERT: D 647 ASN cc_start: 0.7580 (t0) cc_final: 0.7140 (p0) REVERT: D 696 ARG cc_start: 0.8570 (mtp180) cc_final: 0.8315 (mtp180) REVERT: D 738 LYS cc_start: 0.8430 (tptt) cc_final: 0.8004 (mtpp) outliers start: 69 outliers final: 39 residues processed: 379 average time/residue: 0.1527 time to fit residues: 90.5766 Evaluate side-chains 353 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 312 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 668 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 130 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 0.0000 chunk 49 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS B 160 HIS B 297 ASN B 523 HIS C 160 HIS C 297 ASN D 160 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.168991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123192 restraints weight = 29758.423| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.76 r_work: 0.3295 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22640 Z= 0.101 Angle : 0.533 9.224 30356 Z= 0.269 Chirality : 0.037 0.140 3296 Planarity : 0.003 0.030 3676 Dihedral : 17.960 156.290 3986 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.32 % Allowed : 15.18 % Favored : 81.50 % 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: -2.48 (0.16), residues: 2548 helix: -0.70 (0.13), residues: 1600 sheet: -3.93 (0.42), residues: 88 loop : -3.10 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 733 TYR 0.009 0.001 TYR B 213 PHE 0.037 0.001 PHE A 489 TRP 0.026 0.001 TRP A 710 HIS 0.007 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (22636) covalent geometry : angle 0.53206 / 0.27 (30348) SS BOND : bond 0.00316 / 0.17 ( 4) SS BOND : angle 1.65581 / 1.15 ( 8) hydrogen bonds : bond 0.02550 / 1.69 ( 709) hydrogen bonds : angle 3.52641 / 2.44 ( 2079) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 334 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7127 (mtp85) REVERT: A 184 LYS cc_start: 0.7446 (tppt) cc_final: 0.7229 (tppt) REVERT: A 185 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8113 (mm-30) REVERT: A 224 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 286 GLN cc_start: 0.8454 (mp10) cc_final: 0.8176 (mp10) REVERT: A 299 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8676 (tp) REVERT: A 315 ASP cc_start: 0.7852 (p0) cc_final: 0.7570 (p0) REVERT: A 416 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7953 (mtp180) REVERT: A 430 HIS cc_start: 0.7671 (t70) cc_final: 0.7445 (t-90) REVERT: A 575 TYR cc_start: 0.8951 (m-80) cc_final: 0.8425 (m-80) REVERT: A 642 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7846 (tt) REVERT: A 717 MET cc_start: 0.8579 (mmt) cc_final: 0.8323 (mmm) REVERT: A 738 LYS cc_start: 0.8435 (tptt) cc_final: 0.7955 (mtpp) REVERT: B 122 ARG cc_start: 0.7549 (mtt180) cc_final: 0.6995 (mtp85) REVERT: B 184 LYS cc_start: 0.7691 (tppt) cc_final: 0.7466 (tppt) REVERT: B 185 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8234 (mm-30) REVERT: B 224 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 286 GLN cc_start: 0.8537 (mp10) cc_final: 0.8242 (mp10) REVERT: B 299 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8685 (tp) REVERT: B 416 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7856 (mtp180) REVERT: B 431 MET cc_start: 0.8332 (mtt) cc_final: 0.8050 (mtp) REVERT: B 440 MET cc_start: 0.8780 (mtp) cc_final: 0.8510 (mtm) REVERT: B 647 ASN cc_start: 0.7586 (t0) cc_final: 0.7136 (p0) REVERT: B 738 LYS cc_start: 0.8253 (tptp) cc_final: 0.7874 (mtpp) REVERT: C 122 ARG cc_start: 0.7458 (mtt180) cc_final: 0.7025 (mtp85) REVERT: C 185 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8275 (mm-30) REVERT: C 286 GLN cc_start: 0.8547 (mp10) cc_final: 0.8249 (mp10) REVERT: C 288 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: C 299 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8690 (tp) REVERT: C 416 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7934 (mtp180) REVERT: C 440 MET cc_start: 0.8757 (mtp) cc_final: 0.8494 (mtm) REVERT: C 642 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7818 (tt) REVERT: C 645 GLN cc_start: 0.7542 (pm20) cc_final: 0.7324 (pm20) REVERT: C 647 ASN cc_start: 0.7624 (t0) cc_final: 0.7077 (p0) REVERT: C 696 ARG cc_start: 0.8575 (mtp180) cc_final: 0.8342 (mtp180) REVERT: C 738 LYS cc_start: 0.8444 (tptt) cc_final: 0.7957 (mtpp) REVERT: D 122 ARG cc_start: 0.7453 (mtt180) cc_final: 0.7014 (mtp85) REVERT: D 185 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8281 (mm-30) REVERT: D 286 GLN cc_start: 0.8524 (mp10) cc_final: 0.8228 (mp10) REVERT: D 299 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8688 (tp) REVERT: D 509 ARG cc_start: 0.6990 (ptt-90) cc_final: 0.6571 (mmt180) REVERT: D 642 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7838 (tt) REVERT: D 647 ASN cc_start: 0.7621 (t0) cc_final: 0.7076 (p0) REVERT: D 696 ARG cc_start: 0.8578 (mtp180) cc_final: 0.8333 (mtp180) REVERT: D 738 LYS cc_start: 0.8461 (tptt) cc_final: 0.8013 (mtpp) outliers start: 75 outliers final: 43 residues processed: 376 average time/residue: 0.1625 time to fit residues: 95.5028 Evaluate side-chains 368 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 493 TRP Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 493 TRP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 80 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS B 160 HIS B 197 ASN B 523 HIS C 160 HIS C 523 HIS D 160 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.169428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123611 restraints weight = 29439.130| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.75 r_work: 0.3296 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22640 Z= 0.105 Angle : 0.538 9.736 30356 Z= 0.272 Chirality : 0.037 0.156 3296 Planarity : 0.003 0.030 3676 Dihedral : 17.410 146.731 3982 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.61 % Allowed : 16.46 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 2548 helix: -0.49 (0.13), residues: 1596 sheet: -3.89 (0.42), residues: 88 loop : -2.99 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 416 TYR 0.010 0.001 TYR B 451 PHE 0.036 0.001 PHE A 489 TRP 0.023 0.001 TRP A 710 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (22636) covalent geometry : angle 0.53777 / 0.27 (30348) SS BOND : bond 0.00089 / 0.05 ( 4) SS BOND : angle 1.69518 / 1.16 ( 8) hydrogen bonds : bond 0.02497 / 1.65 ( 709) hydrogen bonds : angle 3.48476 / 2.41 ( 2079) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 331 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7636 (mtt180) cc_final: 0.7120 (mtp85) REVERT: A 184 LYS cc_start: 0.7540 (tppt) cc_final: 0.7274 (tppt) REVERT: A 185 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 224 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 286 GLN cc_start: 0.8437 (mp10) cc_final: 0.8146 (mp10) REVERT: A 299 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8662 (tp) REVERT: A 315 ASP cc_start: 0.7804 (p0) cc_final: 0.7506 (p0) REVERT: A 327 ARG cc_start: 0.8128 (tpt-90) cc_final: 0.7770 (mtp-110) REVERT: A 416 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7950 (mtp180) REVERT: A 430 HIS cc_start: 0.7690 (t70) cc_final: 0.7449 (t-90) REVERT: A 575 TYR cc_start: 0.8925 (m-80) cc_final: 0.8445 (m-80) REVERT: A 642 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.7932 (tt) REVERT: A 717 MET cc_start: 0.8547 (mmt) cc_final: 0.7997 (mmm) REVERT: A 738 LYS cc_start: 0.8445 (tptt) cc_final: 0.7964 (mtpp) REVERT: B 122 ARG cc_start: 0.7554 (mtt180) cc_final: 0.6992 (mtp85) REVERT: B 185 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8206 (mm-30) REVERT: B 224 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 286 GLN cc_start: 0.8548 (mp10) cc_final: 0.8232 (mp10) REVERT: B 299 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8698 (tp) REVERT: B 416 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7820 (mtp180) REVERT: B 440 MET cc_start: 0.8796 (mtp) cc_final: 0.8532 (mtm) REVERT: B 509 ARG cc_start: 0.6894 (ptt-90) cc_final: 0.6412 (mmt180) REVERT: B 642 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7929 (tt) REVERT: B 647 ASN cc_start: 0.7607 (t0) cc_final: 0.7139 (p0) REVERT: B 738 LYS cc_start: 0.8301 (tptp) cc_final: 0.7919 (mtpp) REVERT: C 122 ARG cc_start: 0.7456 (mtt180) cc_final: 0.7026 (mtp85) REVERT: C 184 LYS cc_start: 0.7550 (tppt) cc_final: 0.7255 (tppt) REVERT: C 185 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8271 (mm-30) REVERT: C 286 GLN cc_start: 0.8563 (mp10) cc_final: 0.8225 (mp10) REVERT: C 299 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8694 (tp) REVERT: C 327 ARG cc_start: 0.7863 (tpt-90) cc_final: 0.7374 (tpt90) REVERT: C 416 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7839 (mtp180) REVERT: C 440 MET cc_start: 0.8776 (mtp) cc_final: 0.8517 (mtm) REVERT: C 544 TYR cc_start: 0.7545 (m-80) cc_final: 0.7278 (m-80) REVERT: C 645 GLN cc_start: 0.7546 (pm20) cc_final: 0.7321 (pm20) REVERT: C 647 ASN cc_start: 0.7640 (t0) cc_final: 0.7111 (p0) REVERT: C 696 ARG cc_start: 0.8594 (mtp180) cc_final: 0.8332 (mtp180) REVERT: C 738 LYS cc_start: 0.8462 (tptt) cc_final: 0.7955 (mtpp) REVERT: D 122 ARG cc_start: 0.7430 (mtt180) cc_final: 0.6994 (mtp85) REVERT: D 184 LYS cc_start: 0.7552 (tppt) cc_final: 0.7256 (tppt) REVERT: D 185 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8245 (mm-30) REVERT: D 286 GLN cc_start: 0.8549 (mp10) cc_final: 0.8229 (mp10) REVERT: D 299 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8692 (tp) REVERT: D 327 ARG cc_start: 0.7897 (tpt-90) cc_final: 0.7404 (tpt90) REVERT: D 544 TYR cc_start: 0.7501 (m-80) cc_final: 0.7248 (m-80) REVERT: D 647 ASN cc_start: 0.7605 (t0) cc_final: 0.7066 (p0) REVERT: D 696 ARG cc_start: 0.8575 (mtp180) cc_final: 0.8356 (mtp180) REVERT: D 738 LYS cc_start: 0.8468 (tptt) cc_final: 0.8007 (mtpp) outliers start: 59 outliers final: 49 residues processed: 367 average time/residue: 0.1598 time to fit residues: 91.1025 Evaluate side-chains 372 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 317 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 493 TRP Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 493 TRP Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 493 TRP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 123 optimal weight: 0.0170 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 235 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 523 HIS B 160 HIS B 523 HIS C 160 HIS C 523 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.169412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123420 restraints weight = 29643.171| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.76 r_work: 0.3293 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22640 Z= 0.107 Angle : 0.538 9.739 30356 Z= 0.271 Chirality : 0.037 0.121 3296 Planarity : 0.003 0.030 3676 Dihedral : 16.916 136.857 3982 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.70 % Allowed : 16.73 % Favored : 80.58 % 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: -2.02 (0.17), residues: 2548 helix: -0.34 (0.13), residues: 1600 sheet: -3.87 (0.43), residues: 88 loop : -2.92 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 733 TYR 0.011 0.001 TYR C 451 PHE 0.035 0.001 PHE B 489 TRP 0.030 0.001 TRP A 710 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (22636) covalent geometry : angle 0.53812 / 0.27 (30348) SS BOND : bond 0.00113 / 0.06 ( 4) SS BOND : angle 1.33459 / 0.93 ( 8) hydrogen bonds : bond 0.02488 / 1.65 ( 709) hydrogen bonds : angle 3.45820 / 2.40 ( 2079) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 322 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7651 (mtt180) cc_final: 0.7113 (mtp85) REVERT: A 184 LYS cc_start: 0.7535 (tppt) cc_final: 0.7286 (tppt) REVERT: A 185 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8135 (mm-30) REVERT: A 224 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 283 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7156 (mm-30) REVERT: A 286 GLN cc_start: 0.8451 (mp10) cc_final: 0.8161 (mp10) REVERT: A 299 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8705 (tp) REVERT: A 315 ASP cc_start: 0.7754 (p0) cc_final: 0.7491 (p0) REVERT: A 416 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7920 (mtp180) REVERT: A 430 HIS cc_start: 0.7826 (t70) cc_final: 0.7588 (t-90) REVERT: A 544 TYR cc_start: 0.7651 (m-80) cc_final: 0.7373 (m-80) REVERT: A 575 TYR cc_start: 0.9001 (m-80) cc_final: 0.8461 (m-80) REVERT: A 642 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.7958 (tt) REVERT: A 647 ASN cc_start: 0.7783 (t0) cc_final: 0.7314 (p0) REVERT: A 717 MET cc_start: 0.8544 (mmt) cc_final: 0.8017 (mmm) REVERT: A 738 LYS cc_start: 0.8455 (tptt) cc_final: 0.7991 (mtpp) REVERT: B 122 ARG cc_start: 0.7557 (mtt180) cc_final: 0.7029 (mtp85) REVERT: B 185 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8260 (mm-30) REVERT: B 224 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7695 (tm-30) REVERT: B 282 MET cc_start: 0.8923 (mtm) cc_final: 0.8625 (mtm) REVERT: B 286 GLN cc_start: 0.8528 (mp10) cc_final: 0.8223 (mp10) REVERT: B 299 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8710 (tp) REVERT: B 416 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7791 (mtp180) REVERT: B 440 MET cc_start: 0.8786 (mtp) cc_final: 0.8517 (mtm) REVERT: B 642 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7928 (tt) REVERT: B 647 ASN cc_start: 0.7610 (t0) cc_final: 0.7168 (p0) REVERT: B 738 LYS cc_start: 0.8257 (tptp) cc_final: 0.7865 (mtpp) REVERT: C 122 ARG cc_start: 0.7436 (mtt180) cc_final: 0.6999 (mtp85) REVERT: C 184 LYS cc_start: 0.7505 (tppt) cc_final: 0.7231 (tppt) REVERT: C 185 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8265 (mm-30) REVERT: C 286 GLN cc_start: 0.8555 (mp10) cc_final: 0.8231 (mp10) REVERT: C 299 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8713 (tp) REVERT: C 416 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7836 (mtp180) REVERT: C 440 MET cc_start: 0.8835 (mtp) cc_final: 0.8570 (mtm) REVERT: C 544 TYR cc_start: 0.7579 (m-80) cc_final: 0.7278 (m-80) REVERT: C 642 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.7999 (tt) REVERT: C 645 GLN cc_start: 0.7687 (pm20) cc_final: 0.7447 (pm20) REVERT: C 647 ASN cc_start: 0.7628 (t0) cc_final: 0.7132 (p0) REVERT: C 696 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8364 (mtp180) REVERT: C 738 LYS cc_start: 0.8460 (tptt) cc_final: 0.7988 (mtpp) REVERT: D 122 ARG cc_start: 0.7440 (mtt180) cc_final: 0.7006 (mtp85) REVERT: D 184 LYS cc_start: 0.7558 (tppt) cc_final: 0.7285 (tppt) REVERT: D 185 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8254 (mm-30) REVERT: D 286 GLN cc_start: 0.8559 (mp10) cc_final: 0.8239 (mp10) REVERT: D 299 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8712 (tp) REVERT: D 430 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.7140 (t70) REVERT: D 647 ASN cc_start: 0.7619 (t0) cc_final: 0.7190 (p0) REVERT: D 738 LYS cc_start: 0.8478 (tptt) cc_final: 0.8004 (mtpp) outliers start: 61 outliers final: 46 residues processed: 362 average time/residue: 0.1656 time to fit residues: 93.3100 Evaluate side-chains 365 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 493 TRP Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 493 TRP Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 493 TRP Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 99 optimal weight: 7.9990 chunk 220 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 59 optimal weight: 0.0050 chunk 178 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS B 160 HIS C 160 HIS C 523 HIS D 160 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.168403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122514 restraints weight = 29789.166| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.75 r_work: 0.3286 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22640 Z= 0.114 Angle : 0.551 11.281 30356 Z= 0.276 Chirality : 0.038 0.121 3296 Planarity : 0.003 0.030 3676 Dihedral : 16.667 131.339 3982 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.74 % Allowed : 17.04 % Favored : 80.22 % 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: -1.90 (0.17), residues: 2548 helix: -0.24 (0.13), residues: 1600 sheet: -3.84 (0.43), residues: 88 loop : -2.88 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 733 TYR 0.011 0.001 TYR C 451 PHE 0.035 0.001 PHE B 489 TRP 0.027 0.001 TRP A 710 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (22636) covalent geometry : angle 0.55067 / 0.28 (30348) SS BOND : bond 0.00148 / 0.08 ( 4) SS BOND : angle 1.49994 / 1.12 ( 8) hydrogen bonds : bond 0.02545 / 1.68 ( 709) hydrogen bonds : angle 3.47031 / 2.40 ( 2079) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 312 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7647 (mtt180) cc_final: 0.7109 (mtp85) REVERT: A 184 LYS cc_start: 0.7534 (tppt) cc_final: 0.7280 (tppt) REVERT: A 185 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8127 (mm-30) REVERT: A 224 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 283 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7148 (mm-30) REVERT: A 286 GLN cc_start: 0.8466 (mp10) cc_final: 0.8175 (mp10) REVERT: A 299 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8724 (tp) REVERT: A 315 ASP cc_start: 0.7784 (p0) cc_final: 0.7535 (p0) REVERT: A 416 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7901 (mtp180) REVERT: A 430 HIS cc_start: 0.7851 (t70) cc_final: 0.7628 (t-90) REVERT: A 544 TYR cc_start: 0.7663 (m-80) cc_final: 0.7379 (m-80) REVERT: A 575 TYR cc_start: 0.8994 (m-80) cc_final: 0.8481 (m-80) REVERT: A 647 ASN cc_start: 0.7782 (t0) cc_final: 0.7339 (p0) REVERT: A 717 MET cc_start: 0.8547 (mmt) cc_final: 0.8049 (mmm) REVERT: A 738 LYS cc_start: 0.8484 (tptt) cc_final: 0.8039 (mtpp) REVERT: B 122 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7079 (mtp85) REVERT: B 184 LYS cc_start: 0.7462 (tppt) cc_final: 0.7213 (tppt) REVERT: B 185 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8269 (mm-30) REVERT: B 224 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7684 (tm-30) REVERT: B 282 MET cc_start: 0.8936 (mtm) cc_final: 0.8642 (mtm) REVERT: B 286 GLN cc_start: 0.8516 (mp10) cc_final: 0.8208 (mp10) REVERT: B 299 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8713 (tp) REVERT: B 416 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7793 (mtp180) REVERT: B 440 MET cc_start: 0.8800 (mtp) cc_final: 0.8591 (mtm) REVERT: B 544 TYR cc_start: 0.7557 (m-80) cc_final: 0.7263 (m-80) REVERT: B 642 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.7927 (tt) REVERT: B 647 ASN cc_start: 0.7595 (t0) cc_final: 0.7182 (p0) REVERT: B 738 LYS cc_start: 0.8298 (tptp) cc_final: 0.7902 (mtpp) REVERT: C 122 ARG cc_start: 0.7441 (mtt180) cc_final: 0.7001 (mtp85) REVERT: C 184 LYS cc_start: 0.7505 (tppt) cc_final: 0.7223 (tppt) REVERT: C 185 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8259 (mm-30) REVERT: C 286 GLN cc_start: 0.8543 (mp10) cc_final: 0.8214 (mp10) REVERT: C 299 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8717 (tp) REVERT: C 327 ARG cc_start: 0.8029 (tpt-90) cc_final: 0.7673 (mmm160) REVERT: C 416 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7832 (mtp180) REVERT: C 440 MET cc_start: 0.8826 (mtp) cc_final: 0.8557 (mtm) REVERT: C 544 TYR cc_start: 0.7567 (m-80) cc_final: 0.7262 (m-80) REVERT: C 642 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8018 (tt) REVERT: C 647 ASN cc_start: 0.7631 (t0) cc_final: 0.7237 (p0) REVERT: C 696 ARG cc_start: 0.8597 (mtp180) cc_final: 0.8394 (mtp180) REVERT: C 738 LYS cc_start: 0.8449 (tptt) cc_final: 0.7978 (mtpp) REVERT: D 122 ARG cc_start: 0.7427 (mtt180) cc_final: 0.6985 (mtp85) REVERT: D 184 LYS cc_start: 0.7510 (tppt) cc_final: 0.7236 (tppt) REVERT: D 185 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8248 (mm-30) REVERT: D 286 GLN cc_start: 0.8549 (mp10) cc_final: 0.8223 (mp10) REVERT: D 299 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8717 (tp) REVERT: D 327 ARG cc_start: 0.8032 (tpt-90) cc_final: 0.7669 (mmm160) REVERT: D 544 TYR cc_start: 0.7552 (m-80) cc_final: 0.7273 (m-80) REVERT: D 642 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.7955 (tt) REVERT: D 647 ASN cc_start: 0.7615 (t0) cc_final: 0.7136 (p0) REVERT: D 738 LYS cc_start: 0.8451 (tptt) cc_final: 0.7989 (mtpp) outliers start: 62 outliers final: 50 residues processed: 351 average time/residue: 0.1651 time to fit residues: 90.2527 Evaluate side-chains 363 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 306 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 493 TRP Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 493 TRP Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 32 optimal weight: 0.5980 chunk 199 optimal weight: 0.6980 chunk 156 optimal weight: 0.0770 chunk 185 optimal weight: 0.0670 chunk 244 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS B 160 HIS B 523 HIS C 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.170655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125110 restraints weight = 29562.701| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.74 r_work: 0.3334 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22640 Z= 0.094 Angle : 0.535 9.359 30356 Z= 0.270 Chirality : 0.037 0.143 3296 Planarity : 0.003 0.029 3676 Dihedral : 16.209 123.298 3982 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.57 % Allowed : 17.88 % Favored : 79.56 % 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: -1.70 (0.17), residues: 2548 helix: -0.06 (0.13), residues: 1596 sheet: -3.70 (0.45), residues: 88 loop : -2.86 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 733 TYR 0.009 0.001 TYR B 213 PHE 0.034 0.001 PHE C 489 TRP 0.027 0.001 TRP A 710 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 (22636) covalent geometry : angle 0.53432 / 0.27 (30348) SS BOND : bond 0.00141 / 0.07 ( 4) SS BOND : angle 1.56693 / 1.16 ( 8) hydrogen bonds : bond 0.02348 / 1.56 ( 709) hydrogen bonds : angle 3.42365 / 2.37 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4748.04 seconds wall clock time: 82 minutes 14.29 seconds (4934.29 seconds total)