Starting phenix.real_space_refine on Mon Sep 14 01:27:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oay_20005/09_2026/6oay_20005.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oay_20005/09_2026/6oay_20005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oay_20005/09_2026/6oay_20005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oay_20005/09_2026/6oay_20005.map" model { file = "/net/cci-nas-00/data/ceres_data/6oay_20005/09_2026/6oay_20005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oay_20005/09_2026/6oay_20005.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6oay_20005/09_2026/6oay_20005.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oay_20005/09_2026/6oay_20005.cif" } resolution = 3.3 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= 0.010 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: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 97 5.16 5 C 17025 2.51 5 N 4946 2.21 5 O 5164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 178 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27261 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4510 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 22, 'TRANS': 547} Chain breaks: 2 Chain: "F" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4426 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 20, 'TRANS': 537} Chain breaks: 3 Chain: "E" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4510 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 22, 'TRANS': 547} Chain breaks: 2 Chain: "D" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4510 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 22, 'TRANS': 547} Chain breaks: 2 Chain: "B" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4510 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 22, 'TRANS': 547} Chain breaks: 2 Chain: "A" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4340 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 21, 'TRANS': 526} Chain breaks: 2 Chain: "P" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.43, per 1000 atoms: 0.24 Number of scatterers: 27261 At special positions: 0 Unit cell: (141.384, 144.48, 116.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 29 15.00 O 5164 8.00 N 4946 7.00 C 17025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6332 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 0 sheets defined 44.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.573A pdb=" N GLN C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.917A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.501A pdb=" N ILE C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 269 removed outlier: 4.078A pdb=" N ASP C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS C 268 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.824A pdb=" N PHE C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 329 through 333' Processing helix chain 'C' and resid 342 through 362 removed outlier: 3.505A pdb=" N ALA C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 377 removed outlier: 3.509A pdb=" N ILE C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 406 removed outlier: 5.506A pdb=" N LYS C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 544 removed outlier: 3.606A pdb=" N ILE C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 567 removed outlier: 3.590A pdb=" N LEU C 559 " --> pdb=" O GLU C 555 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ARG C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 589 removed outlier: 3.658A pdb=" N VAL C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 583 " --> pdb=" O ALA C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 623 Processing helix chain 'C' and resid 655 through 659 removed outlier: 4.671A pdb=" N GLY C 659 " --> pdb=" O GLY C 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 655 through 659' Processing helix chain 'C' and resid 663 through 668 removed outlier: 3.974A pdb=" N ARG C 668 " --> pdb=" O GLU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 696 removed outlier: 5.793A pdb=" N HIS C 683 " --> pdb=" O VAL C 679 " (cutoff:3.500A) Proline residue: C 684 - end of helix removed outlier: 4.201A pdb=" N PHE C 687 " --> pdb=" O HIS C 683 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN C 688 " --> pdb=" O PRO C 684 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE C 689 " --> pdb=" O ASP C 685 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 690 " --> pdb=" O VAL C 686 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLN C 692 " --> pdb=" O ASN C 688 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 693 " --> pdb=" O ILE C 689 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP C 695 " --> pdb=" O LEU C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 728 removed outlier: 4.141A pdb=" N GLN C 726 " --> pdb=" O SER C 722 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU C 727 " --> pdb=" O ASP C 723 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG C 728 " --> pdb=" O LEU C 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 722 through 728' Processing helix chain 'C' and resid 734 through 748 removed outlier: 9.781A pdb=" N LYS C 738 " --> pdb=" O TYR C 734 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLU C 739 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU C 740 " --> pdb=" O HIS C 736 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL C 741 " --> pdb=" O MET C 737 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 742 " --> pdb=" O LYS C 738 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY C 743 " --> pdb=" O GLU C 739 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL C 744 " --> pdb=" O LEU C 740 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS C 747 " --> pdb=" O GLY C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 757 removed outlier: 3.715A pdb=" N ILE C 757 " --> pdb=" O PHE C 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 753 through 757' Processing helix chain 'C' and resid 767 through 785 removed outlier: 3.972A pdb=" N SER C 773 " --> pdb=" O GLN C 769 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C 776 " --> pdb=" O ALA C 772 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 782 " --> pdb=" O GLN C 778 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 784 " --> pdb=" O LYS C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 807 removed outlier: 4.343A pdb=" N LYS C 801 " --> pdb=" O ASP C 797 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU C 802 " --> pdb=" O GLU C 798 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 803 " --> pdb=" O ALA C 799 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER C 804 " --> pdb=" O LEU C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 834 removed outlier: 3.902A pdb=" N GLN C 831 " --> pdb=" O ASN C 827 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLN C 832 " --> pdb=" O PRO C 828 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE C 833 " --> pdb=" O LEU C 829 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU C 834 " --> pdb=" O ALA C 830 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 removed outlier: 3.526A pdb=" N ILE F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 191 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 221 removed outlier: 4.664A pdb=" N VAL F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 264 removed outlier: 4.964A pdb=" N VAL F 262 " --> pdb=" O ARG F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 306 removed outlier: 6.076A pdb=" N ALA F 302 " --> pdb=" O MET F 298 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU F 303 " --> pdb=" O LEU F 299 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ARG F 305 " --> pdb=" O PRO F 301 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY F 306 " --> pdb=" O ALA F 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 298 through 306' Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.680A pdb=" N ARG F 320 " --> pdb=" O LEU F 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 316 through 320' Processing helix chain 'F' and resid 342 through 353 removed outlier: 3.865A pdb=" N LEU F 350 " --> pdb=" O THR F 346 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 376 removed outlier: 5.680A pdb=" N ILE F 370 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL F 371 " --> pdb=" O ASP F 367 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA F 372 " --> pdb=" O PRO F 368 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 406 removed outlier: 4.340A pdb=" N ILE F 391 " --> pdb=" O PRO F 387 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU F 396 " --> pdb=" O ASP F 392 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 397 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET F 403 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLN F 404 " --> pdb=" O SER F 400 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP F 406 " --> pdb=" O ARG F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 545 removed outlier: 3.778A pdb=" N ARG F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 552 removed outlier: 3.951A pdb=" N MET F 551 " --> pdb=" O PRO F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 559 Processing helix chain 'F' and resid 578 through 586 removed outlier: 4.086A pdb=" N ASN F 582 " --> pdb=" O ASP F 578 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ALA F 583 " --> pdb=" O ALA F 579 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 618 removed outlier: 5.018A pdb=" N LEU F 618 " --> pdb=" O LEU F 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 614 through 618' Processing helix chain 'F' and resid 661 through 665 removed outlier: 4.507A pdb=" N ALA F 665 " --> pdb=" O TYR F 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 661 through 665' Processing helix chain 'F' and resid 686 through 691 removed outlier: 3.760A pdb=" N LEU F 690 " --> pdb=" O VAL F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 708 through 712 Processing helix chain 'F' and resid 722 through 728 removed outlier: 5.921A pdb=" N GLN F 726 " --> pdb=" O SER F 722 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N GLU F 727 " --> pdb=" O ASP F 723 " (cutoff:3.500A) removed outlier: 11.720A pdb=" N ARG F 728 " --> pdb=" O LEU F 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 722 through 728' Processing helix chain 'F' and resid 734 through 748 removed outlier: 7.195A pdb=" N LYS F 738 " --> pdb=" O TYR F 734 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU F 739 " --> pdb=" O ALA F 735 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU F 740 " --> pdb=" O HIS F 736 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N VAL F 741 " --> pdb=" O MET F 737 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N LEU F 742 " --> pdb=" O LYS F 738 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLY F 743 " --> pdb=" O GLU F 739 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL F 744 " --> pdb=" O LEU F 740 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL F 745 " --> pdb=" O VAL F 741 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER F 746 " --> pdb=" O LEU F 742 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS F 747 " --> pdb=" O GLY F 743 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASN F 748 " --> pdb=" O VAL F 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 734 through 748' Processing helix chain 'F' and resid 752 through 756 removed outlier: 4.311A pdb=" N ARG F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 752 through 756' Processing helix chain 'F' and resid 769 through 775 removed outlier: 5.988A pdb=" N SER F 773 " --> pdb=" O GLN F 769 " (cutoff:3.500A) Processing helix chain 'F' and resid 779 through 787 removed outlier: 3.609A pdb=" N TYR F 783 " --> pdb=" O LEU F 779 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG F 785 " --> pdb=" O ARG F 781 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU F 786 " --> pdb=" O LEU F 782 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLU F 787 " --> pdb=" O TYR F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 796 through 805 removed outlier: 3.727A pdb=" N LEU F 802 " --> pdb=" O GLU F 798 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU F 803 " --> pdb=" O ALA F 799 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER F 804 " --> pdb=" O LEU F 800 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLU F 805 " --> pdb=" O LYS F 801 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 821 removed outlier: 3.530A pdb=" N ILE F 821 " --> pdb=" O LEU F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 826 through 833 removed outlier: 5.431A pdb=" N GLN F 832 " --> pdb=" O PRO F 828 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE F 833 " --> pdb=" O LEU F 829 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 removed outlier: 3.831A pdb=" N GLN E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 195 removed outlier: 3.528A pdb=" N LEU E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 225 removed outlier: 3.712A pdb=" N GLN E 221 " --> pdb=" O GLU E 217 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 268 removed outlier: 4.359A pdb=" N LEU E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS E 268 " --> pdb=" O ASN E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 283 removed outlier: 4.808A pdb=" N MET E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 279 through 283' Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 315 through 322 removed outlier: 3.824A pdb=" N ARG E 320 " --> pdb=" O LEU E 316 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 359 removed outlier: 3.637A pdb=" N ALA E 348 " --> pdb=" O GLU E 344 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLU E 355 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG E 356 " --> pdb=" O GLY E 352 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 370 Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.998A pdb=" N ILE E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 396 removed outlier: 4.473A pdb=" N ALA E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU E 393 " --> pdb=" O LYS E 389 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E 396 " --> pdb=" O ASP E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 407 removed outlier: 3.817A pdb=" N SER E 407 " --> pdb=" O MET E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 544 removed outlier: 3.725A pdb=" N GLU E 538 " --> pdb=" O ALA E 534 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL E 539 " --> pdb=" O GLU E 535 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG E 542 " --> pdb=" O GLU E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 566 removed outlier: 5.679A pdb=" N LEU E 566 " --> pdb=" O MET E 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 562 through 566' Processing helix chain 'E' and resid 582 through 586 Processing helix chain 'E' and resid 610 through 623 removed outlier: 3.517A pdb=" N CYS E 615 " --> pdb=" O LYS E 611 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA E 619 " --> pdb=" O CYS E 615 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN E 620 " --> pdb=" O LYS E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 646 removed outlier: 3.664A pdb=" N LEU E 646 " --> pdb=" O SER E 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 642 through 646' Processing helix chain 'E' and resid 655 through 669 removed outlier: 4.147A pdb=" N GLY E 659 " --> pdb=" O GLY E 655 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY E 660 " --> pdb=" O TYR E 656 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N TYR E 661 " --> pdb=" O GLU E 657 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU E 662 " --> pdb=" O GLU E 658 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR E 663 " --> pdb=" O GLY E 659 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG E 669 " --> pdb=" O ALA E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 696 removed outlier: 3.850A pdb=" N PHE E 687 " --> pdb=" O HIS E 683 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE E 689 " --> pdb=" O ASP E 685 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLN E 692 " --> pdb=" O ASN E 688 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL E 693 " --> pdb=" O ILE E 689 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 694 " --> pdb=" O LEU E 690 " (cutoff:3.500A) Processing helix chain 'E' and resid 722 through 728 removed outlier: 3.937A pdb=" N GLN E 726 " --> pdb=" O SER E 722 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG E 728 " --> pdb=" O LEU E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 748 removed outlier: 4.877A pdb=" N GLU E 739 " --> pdb=" O ALA E 735 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU E 740 " --> pdb=" O HIS E 736 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU E 742 " --> pdb=" O LYS E 738 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY E 743 " --> pdb=" O GLU E 739 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL E 744 " --> pdb=" O LEU E 740 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL E 745 " --> pdb=" O VAL E 741 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS E 747 " --> pdb=" O GLY E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 757 Processing helix chain 'E' and resid 767 through 786 removed outlier: 4.026A pdb=" N SER E 773 " --> pdb=" O GLN E 769 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN E 776 " --> pdb=" O ALA E 772 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 777 " --> pdb=" O SER E 773 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG E 781 " --> pdb=" O ILE E 777 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU E 782 " --> pdb=" O GLN E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 802 Processing helix chain 'E' and resid 817 through 835 removed outlier: 3.550A pdb=" N GLN E 822 " --> pdb=" O LYS E 818 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU E 826 " --> pdb=" O GLN E 822 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN E 827 " --> pdb=" O GLN E 823 " (cutoff:3.500A) Proline residue: E 828 - end of helix removed outlier: 3.756A pdb=" N GLN E 831 " --> pdb=" O ASN E 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 185 through 194 removed outlier: 3.525A pdb=" N ARG D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 225 removed outlier: 4.155A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 241 through 247 Processing helix chain 'D' and resid 255 through 265 removed outlier: 4.029A pdb=" N ASP D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 283 No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 315 through 322 removed outlier: 4.058A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 321 " --> pdb=" O ASP D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 331 No H-bonds generated for 'chain 'D' and resid 328 through 331' Processing helix chain 'D' and resid 343 through 359 removed outlier: 3.683A pdb=" N ALA D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG D 356 " --> pdb=" O GLY D 352 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 373 removed outlier: 4.135A pdb=" N ALA D 373 " --> pdb=" O ALA D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 390 removed outlier: 5.890A pdb=" N LYS D 389 " --> pdb=" O GLN D 385 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA D 390 " --> pdb=" O LEU D 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 385 through 390' Processing helix chain 'D' and resid 392 through 398 Processing helix chain 'D' and resid 400 through 407 Processing helix chain 'D' and resid 533 through 544 removed outlier: 3.574A pdb=" N ALA D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG D 542 " --> pdb=" O GLU D 538 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 553 removed outlier: 7.138A pdb=" N GLU D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 549 through 553' Processing helix chain 'D' and resid 561 through 570 removed outlier: 4.474A pdb=" N ARG D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 587 removed outlier: 3.982A pdb=" N ALA D 583 " --> pdb=" O ALA D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 622 removed outlier: 3.965A pdb=" N CYS D 615 " --> pdb=" O LYS D 611 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 616 " --> pdb=" O THR D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 637 No H-bonds generated for 'chain 'D' and resid 635 through 637' Processing helix chain 'D' and resid 640 through 645 removed outlier: 5.299A pdb=" N SER D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ARG D 645 " --> pdb=" O HIS D 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 640 through 645' Processing helix chain 'D' and resid 655 through 659 removed outlier: 4.177A pdb=" N GLY D 659 " --> pdb=" O GLY D 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 655 through 659' Processing helix chain 'D' and resid 685 through 695 removed outlier: 4.196A pdb=" N ILE D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU D 690 " --> pdb=" O VAL D 686 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 691 " --> pdb=" O PHE D 687 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN D 692 " --> pdb=" O ASN D 688 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 693 " --> pdb=" O ILE D 689 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 694 " --> pdb=" O LEU D 690 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP D 695 " --> pdb=" O LEU D 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 685 through 695' Processing helix chain 'D' and resid 722 through 728 removed outlier: 4.414A pdb=" N GLU D 727 " --> pdb=" O ASP D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 748 removed outlier: 4.403A pdb=" N LYS D 738 " --> pdb=" O TYR D 734 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 740 " --> pdb=" O HIS D 736 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL D 744 " --> pdb=" O LEU D 740 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL D 745 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER D 746 " --> pdb=" O LEU D 742 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 788 removed outlier: 3.530A pdb=" N SER D 773 " --> pdb=" O GLN D 769 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 777 " --> pdb=" O SER D 773 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 780 " --> pdb=" O GLN D 776 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 784 " --> pdb=" O LYS D 780 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 785 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU D 788 " --> pdb=" O LYS D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 807 removed outlier: 3.591A pdb=" N LEU D 800 " --> pdb=" O SER D 796 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS D 801 " --> pdb=" O ASP D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 834 removed outlier: 3.685A pdb=" N GLN D 822 " --> pdb=" O LYS D 818 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU D 826 " --> pdb=" O GLN D 822 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASN D 827 " --> pdb=" O GLN D 823 " (cutoff:3.500A) Proline residue: D 828 - end of helix removed outlier: 3.800A pdb=" N GLN D 832 " --> pdb=" O PRO D 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 removed outlier: 3.919A pdb=" N GLU B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 174' Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.621A pdb=" N ARG B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 4.154A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.715A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.724A pdb=" N ARG B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 332' Processing helix chain 'B' and resid 342 through 358 removed outlier: 4.401A pdb=" N THR B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 381 removed outlier: 3.553A pdb=" N SER B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 407 removed outlier: 6.265A pdb=" N LYS B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 391 " --> pdb=" O PRO B 387 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 544 removed outlier: 4.139A pdb=" N GLU B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 568 removed outlier: 5.230A pdb=" N LYS B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 559 " --> pdb=" O GLU B 555 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU B 560 " --> pdb=" O ARG B 556 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 589 removed outlier: 3.657A pdb=" N ASN B 582 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 583 " --> pdb=" O ALA B 579 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG B 586 " --> pdb=" O ASN B 582 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 622 Processing helix chain 'B' and resid 640 through 646 removed outlier: 4.969A pdb=" N SER B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG B 645 " --> pdb=" O HIS B 641 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU B 646 " --> pdb=" O SER B 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 646' Processing helix chain 'B' and resid 660 through 665 Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.912A pdb=" N PHE B 687 " --> pdb=" O HIS B 683 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN B 688 " --> pdb=" O PRO B 684 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE B 689 " --> pdb=" O ASP B 685 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 690 " --> pdb=" O VAL B 686 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN B 692 " --> pdb=" O ASN B 688 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 693 " --> pdb=" O ILE B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 728 removed outlier: 6.184A pdb=" N GLN B 726 " --> pdb=" O SER B 722 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLU B 727 " --> pdb=" O ASP B 723 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N ARG B 728 " --> pdb=" O LEU B 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 722 through 728' Processing helix chain 'B' and resid 734 through 748 removed outlier: 4.532A pdb=" N LYS B 738 " --> pdb=" O TYR B 734 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU B 739 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU B 740 " --> pdb=" O HIS B 736 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 741 " --> pdb=" O MET B 737 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 742 " --> pdb=" O LYS B 738 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL B 745 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N HIS B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASN B 748 " --> pdb=" O VAL B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 786 removed outlier: 5.267A pdb=" N ILE B 771 " --> pdb=" O GLY B 767 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 772 " --> pdb=" O GLU B 768 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 775 " --> pdb=" O ILE B 771 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE B 777 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 782 " --> pdb=" O GLN B 778 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS B 784 " --> pdb=" O LYS B 780 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ARG B 785 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU B 786 " --> pdb=" O LEU B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 806 removed outlier: 3.891A pdb=" N LEU B 800 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN B 806 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 823 removed outlier: 3.969A pdb=" N ARG B 819 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 822 " --> pdb=" O LYS B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 832 removed outlier: 4.845A pdb=" N ALA B 830 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN B 831 " --> pdb=" O ASN B 827 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 832 " --> pdb=" O PRO B 828 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 826 through 832' Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.507A pdb=" N ARG A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 removed outlier: 4.583A pdb=" N GLN A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 225 removed outlier: 3.863A pdb=" N ILE A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.775A pdb=" N ASN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 5.123A pdb=" N ARG A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.914A pdb=" N THR A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.927A pdb=" N HIS A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 362' Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.892A pdb=" N VAL A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 407 removed outlier: 3.682A pdb=" N ALA A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N MET A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.648A pdb=" N ILE A 536 " --> pdb=" O THR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 568 removed outlier: 3.561A pdb=" N LEU A 560 " --> pdb=" O ARG A 556 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 588 removed outlier: 7.123A pdb=" N ALA A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 622 removed outlier: 4.962A pdb=" N CYS A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 616 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 617 " --> pdb=" O GLU A 613 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 668 removed outlier: 3.851A pdb=" N GLU A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 removed outlier: 5.271A pdb=" N ALA A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 682' Processing helix chain 'A' and resid 688 through 696 removed outlier: 4.823A pdb=" N GLN A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 728 removed outlier: 7.703A pdb=" N GLN A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 722 through 728' Processing helix chain 'A' and resid 734 through 748 removed outlier: 4.568A pdb=" N LYS A 738 " --> pdb=" O TYR A 734 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 740 " --> pdb=" O HIS A 736 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 741 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASN A 748 " --> pdb=" O VAL A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 removed outlier: 3.829A pdb=" N ILE A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 757 " --> pdb=" O PHE A 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 750 through 757' Processing helix chain 'A' and resid 767 through 776 removed outlier: 3.699A pdb=" N ILE A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE A 774 " --> pdb=" O HIS A 770 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 785 Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.426A pdb=" N GLU A 805 " --> pdb=" O LYS A 801 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 801 through 805' Processing helix chain 'A' and resid 817 through 821 removed outlier: 5.340A pdb=" N ILE A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 817 through 821' Processing helix chain 'A' and resid 825 through 833 removed outlier: 4.327A pdb=" N ALA A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 831 " --> pdb=" O ASN A 827 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLN A 832 " --> pdb=" O PRO A 828 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 9575 1.35 - 1.50: 7650 1.50 - 1.65: 10272 1.65 - 1.80: 134 1.80 - 1.95: 41 Bond restraints: 27672 Sorted by residual: bond pdb=" CA GLY D 743 " pdb=" C GLY D 743 " ideal model delta sigma weight residual 1.514 1.449 0.065 1.41e-02 5.03e+03 2.12e+01 bond pdb=" CG1 ILE D 571 " pdb=" CD1 ILE D 571 " ideal model delta sigma weight residual 1.513 1.383 0.130 3.90e-02 6.57e+02 1.10e+01 bond pdb=" C ARG C 815 " pdb=" N PRO C 816 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.25e-02 6.40e+03 1.04e+01 bond pdb=" CA SER C 600 " pdb=" CB SER C 600 " ideal model delta sigma weight residual 1.526 1.472 0.054 1.70e-02 3.46e+03 1.02e+01 bond pdb=" CB ARG C 196 " pdb=" CG ARG C 196 " ideal model delta sigma weight residual 1.520 1.426 0.094 3.00e-02 1.11e+03 9.87e+00 ... (remaining 27667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 35741 2.59 - 5.17: 1411 5.17 - 7.76: 206 7.76 - 10.34: 36 10.34 - 12.93: 5 Bond angle restraints: 37399 Sorted by residual: angle pdb=" N GLN B 321 " pdb=" CA GLN B 321 " pdb=" C GLN B 321 " ideal model delta sigma weight residual 111.36 100.66 10.70 1.09e+00 8.42e-01 9.64e+01 angle pdb=" N ILE A 793 " pdb=" CA ILE A 793 " pdb=" C ILE A 793 " ideal model delta sigma weight residual 111.88 104.54 7.34 1.06e+00 8.90e-01 4.79e+01 angle pdb=" N GLU C 324 " pdb=" CA GLU C 324 " pdb=" C GLU C 324 " ideal model delta sigma weight residual 114.16 104.62 9.54 1.48e+00 4.57e-01 4.16e+01 angle pdb=" C TYR C 734 " pdb=" CA TYR C 734 " pdb=" CB TYR C 734 " ideal model delta sigma weight residual 116.54 110.29 6.25 1.15e+00 7.56e-01 2.95e+01 angle pdb=" C VAL D 336 " pdb=" N PHE D 337 " pdb=" CA PHE D 337 " ideal model delta sigma weight residual 121.54 131.86 -10.32 1.91e+00 2.74e-01 2.92e+01 ... (remaining 37394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 16352 34.18 - 68.36: 579 68.36 - 102.55: 41 102.55 - 136.73: 4 136.73 - 170.91: 2 Dihedral angle restraints: 16978 sinusoidal: 7166 harmonic: 9812 Sorted by residual: dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 110.91 -170.91 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O1B ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PB ADP B 902 " pdb=" PA ADP B 902 " ideal model delta sinusoidal sigma weight residual 300.00 177.66 122.33 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" O2A ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PA ADP A 902 " pdb=" PB ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 60.83 -120.83 1 2.00e+01 2.50e-03 3.63e+01 ... (remaining 16975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3905 0.115 - 0.229: 300 0.229 - 0.344: 31 0.344 - 0.458: 2 0.458 - 0.573: 2 Chirality restraints: 4240 Sorted by residual: chirality pdb=" CB ILE C 323 " pdb=" CA ILE C 323 " pdb=" CG1 ILE C 323 " pdb=" CG2 ILE C 323 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.57 2.00e-01 2.50e+01 8.21e+00 chirality pdb=" CB VAL C 228 " pdb=" CA VAL C 228 " pdb=" CG1 VAL C 228 " pdb=" CG2 VAL C 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CB VAL C 531 " pdb=" CA VAL C 531 " pdb=" CG1 VAL C 531 " pdb=" CG2 VAL C 531 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 4237 not shown) Planarity restraints: 4870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 367 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO B 368 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 368 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 368 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 367 " -0.059 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO E 368 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO E 368 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 368 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 367 " -0.055 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO D 368 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 368 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 368 " -0.046 5.00e-02 4.00e+02 ... (remaining 4867 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 183 2.43 - 3.05: 15528 3.05 - 3.67: 42609 3.67 - 4.28: 65582 4.28 - 4.90: 106271 Nonbonded interactions: 230173 Sorted by model distance: nonbonded pdb=" O MET E 638 " pdb=" O GLU E 639 " model vdw 1.815 3.040 nonbonded pdb=" O ASP D 696 " pdb=" OD1 ASP D 696 " model vdw 2.092 3.040 nonbonded pdb=" O HIS D 747 " pdb=" OD1 ASN D 748 " model vdw 2.150 3.040 nonbonded pdb=" OH TYR B 322 " pdb=" CB LEU B 329 " model vdw 2.196 3.440 nonbonded pdb=" CG MET E 638 " pdb=" OD2 ASP D 685 " model vdw 2.205 3.440 ... (remaining 230168 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 161 through 648 or resid 661 through 835)) selection = (chain 'B' and (resid 161 through 648 or resid 661 through 835)) selection = (chain 'C' and (resid 161 through 648 or resid 661 through 835)) selection = (chain 'D' and (resid 161 through 648 or resid 661 through 835)) selection = (chain 'E' and (resid 161 through 648 or resid 661 through 835)) selection = (chain 'F' and resid 161 through 835) } 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=1.00 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.870 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.012 0.135 27672 Z= 0.506 Angle : 1.193 12.930 37399 Z= 0.651 Chirality : 0.070 0.573 4240 Planarity : 0.008 0.089 4870 Dihedral : 17.272 170.908 10646 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.89 % Favored : 89.61 % Rotamer: Outliers : 1.36 % Allowed : 13.64 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.50 (0.11), residues: 3348 helix: -4.73 (0.06), residues: 1322 sheet: -3.00 (0.24), residues: 314 loop : -2.82 (0.13), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 789 TYR 0.025 0.003 TYR D 671 PHE 0.031 0.003 PHE D 337 TRP 0.011 0.002 TRP E 543 HIS 0.017 0.002 HIS C 641 Details of bonding type rmsd/Z covalent geometry : bond 0.01207 / 0.51 (27672) covalent geometry : angle 1.19265 / 0.65 (37399) hydrogen bonds : bond 0.30769 / 20.27 ( 503) hydrogen bonds : angle 12.54770 / 8.49 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 536 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 251 TYR cc_start: 0.8331 (m-80) cc_final: 0.7935 (m-80) REVERT: C 283 MET cc_start: 0.8014 (ppp) cc_final: 0.7692 (ppp) REVERT: C 322 TYR cc_start: 0.6439 (t80) cc_final: 0.4145 (t80) REVERT: C 396 GLU cc_start: 0.7860 (pt0) cc_final: 0.7604 (tt0) REVERT: C 636 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8296 (mt-10) REVERT: C 657 GLU cc_start: 0.7384 (pm20) cc_final: 0.7077 (pm20) REVERT: C 669 ARG cc_start: 0.7933 (tpt170) cc_final: 0.7397 (mtp85) REVERT: C 710 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.8116 (mtt180) REVERT: C 728 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7354 (ttt-90) REVERT: C 734 TYR cc_start: 0.1722 (OUTLIER) cc_final: 0.1368 (t80) REVERT: C 750 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7616 (mmm160) REVERT: C 826 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7387 (mt-10) REVERT: F 258 ARG cc_start: 0.5149 (mmm160) cc_final: 0.4685 (tpp-160) REVERT: F 309 HIS cc_start: 0.5364 (t-170) cc_final: 0.4882 (m90) REVERT: F 337 PHE cc_start: 0.6826 (m-80) cc_final: 0.6019 (t80) REVERT: F 395 ASP cc_start: 0.5085 (m-30) cc_final: 0.4792 (m-30) REVERT: E 181 ILE cc_start: 0.7883 (tp) cc_final: 0.7398 (mm) REVERT: E 207 GLU cc_start: 0.7904 (tt0) cc_final: 0.7053 (mp0) REVERT: E 335 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8372 (mtmm) REVERT: E 359 LEU cc_start: 0.8713 (mm) cc_final: 0.8399 (mm) REVERT: E 584 ILE cc_start: 0.8586 (pt) cc_final: 0.8173 (mp) REVERT: E 661 TYR cc_start: 0.8520 (t80) cc_final: 0.7965 (t80) REVERT: E 756 ARG cc_start: 0.7542 (mmt180) cc_final: 0.7072 (mtt180) REVERT: D 180 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8825 (t) REVERT: D 780 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8422 (mtmm) REVERT: D 792 GLU cc_start: 0.7168 (tt0) cc_final: 0.6832 (pt0) REVERT: B 252 ARG cc_start: 0.5412 (ttt90) cc_final: 0.4474 (ttp80) REVERT: B 641 HIS cc_start: 0.6481 (t-90) cc_final: 0.6055 (p90) REVERT: B 664 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6451 (mt-10) REVERT: B 675 LEU cc_start: 0.8792 (tp) cc_final: 0.8572 (tt) REVERT: B 705 ARG cc_start: 0.7709 (mtm180) cc_final: 0.7177 (mtm-85) REVERT: B 750 ARG cc_start: 0.7539 (mtp85) cc_final: 0.7316 (ptp-110) REVERT: A 319 TYR cc_start: 0.5767 (t80) cc_final: 0.5386 (t80) REVERT: A 343 VAL cc_start: 0.6196 (t) cc_final: 0.5992 (t) REVERT: A 353 LEU cc_start: 0.7910 (tp) cc_final: 0.7664 (tt) REVERT: A 542 ARG cc_start: 0.5643 (mtp-110) cc_final: 0.5322 (mtt-85) REVERT: A 629 MET cc_start: 0.4792 (mmt) cc_final: 0.4423 (tpp) REVERT: A 710 ARG cc_start: 0.6903 (ttp80) cc_final: 0.6216 (tpt170) REVERT: A 802 LEU cc_start: -0.0280 (OUTLIER) cc_final: -0.0602 (pp) outliers start: 39 outliers final: 13 residues processed: 569 average time/residue: 0.2315 time to fit residues: 193.5579 Evaluate side-chains 419 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 403 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 734 TYR Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 856 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 GLN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 ASN C 688 ASN C 703 GLN C 776 GLN C 778 GLN C 824 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 641 HIS F 711 ASN F 755 ASN ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 823 GLN F 824 GLN E 321 GLN E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 688 ASN E 770 HIS D 192 GLN D 264 ASN D 334 GLN D 361 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 HIS D 778 GLN D 822 GLN D 823 GLN D 831 GLN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 334 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN B 726 GLN B 764 HIS B 822 GLN B 857 GLN A 174 GLN A 361 HIS A 573 GLN A 726 GLN A 770 HIS ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.213162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164046 restraints weight = 33059.377| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.44 r_work: 0.3494 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27672 Z= 0.161 Angle : 0.714 9.012 37399 Z= 0.366 Chirality : 0.047 0.212 4240 Planarity : 0.006 0.070 4870 Dihedral : 10.094 172.839 3905 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.32 % Favored : 92.53 % Rotamer: Outliers : 2.90 % Allowed : 17.13 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -4.64 (0.12), residues: 3348 helix: -3.83 (0.09), residues: 1394 sheet: -2.94 (0.25), residues: 301 loop : -2.30 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 305 TYR 0.016 0.002 TYR B 322 PHE 0.023 0.002 PHE E 637 TRP 0.009 0.002 TRP C 543 HIS 0.006 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (27672) covalent geometry : angle 0.71420 / 0.37 (37399) hydrogen bonds : bond 0.04430 / 2.91 ( 503) hydrogen bonds : angle 6.79258 / 4.64 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 480 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 169 THR cc_start: 0.8555 (p) cc_final: 0.8351 (p) REVERT: C 170 GLU cc_start: 0.8324 (tt0) cc_final: 0.8105 (tt0) REVERT: C 251 TYR cc_start: 0.8379 (m-80) cc_final: 0.8174 (m-80) REVERT: C 279 GLU cc_start: 0.8459 (mp0) cc_final: 0.7990 (mt-10) REVERT: C 322 TYR cc_start: 0.6745 (t80) cc_final: 0.4405 (t80) REVERT: C 636 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8173 (mt-10) REVERT: C 669 ARG cc_start: 0.8387 (tpt170) cc_final: 0.7865 (mtp-110) REVERT: C 708 ASP cc_start: 0.7798 (t0) cc_final: 0.7180 (t70) REVERT: C 710 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8382 (mtt-85) REVERT: C 728 ARG cc_start: 0.8170 (mtt180) cc_final: 0.6922 (ttt-90) REVERT: F 200 ASN cc_start: 0.5978 (p0) cc_final: 0.5518 (p0) REVERT: F 242 MET cc_start: 0.2809 (OUTLIER) cc_final: 0.2442 (mtt) REVERT: F 337 PHE cc_start: 0.6830 (m-80) cc_final: 0.5967 (t80) REVERT: F 355 GLU cc_start: 0.5614 (mp0) cc_final: 0.5393 (mp0) REVERT: F 634 MET cc_start: 0.7414 (mmp) cc_final: 0.7204 (mmm) REVERT: F 687 PHE cc_start: 0.2057 (m-10) cc_final: 0.1761 (m-80) REVERT: E 207 GLU cc_start: 0.8083 (tt0) cc_final: 0.7205 (mp0) REVERT: E 320 ARG cc_start: 0.7692 (ttp-110) cc_final: 0.7401 (ttp80) REVERT: E 355 GLU cc_start: 0.7970 (mp0) cc_final: 0.7631 (mp0) REVERT: E 359 LEU cc_start: 0.8661 (mm) cc_final: 0.8413 (mm) REVERT: E 392 ASP cc_start: 0.8125 (p0) cc_final: 0.7899 (p0) REVERT: E 560 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7601 (mm) REVERT: E 584 ILE cc_start: 0.8759 (pt) cc_final: 0.8423 (mp) REVERT: E 661 TYR cc_start: 0.8613 (t80) cc_final: 0.8380 (t80) REVERT: E 690 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8713 (tt) REVERT: E 756 ARG cc_start: 0.7718 (mmt180) cc_final: 0.7141 (mtt180) REVERT: D 305 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.8229 (mtp180) REVERT: D 344 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7349 (mm-30) REVERT: D 681 LYS cc_start: 0.4180 (OUTLIER) cc_final: 0.3648 (mmpt) REVERT: D 716 MET cc_start: 0.8860 (mtm) cc_final: 0.8559 (mtm) REVERT: D 792 GLU cc_start: 0.7774 (tt0) cc_final: 0.7480 (pt0) REVERT: B 166 ILE cc_start: 0.8973 (mp) cc_final: 0.8758 (mp) REVERT: B 212 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7778 (mtmm) REVERT: B 252 ARG cc_start: 0.5946 (ttt90) cc_final: 0.5003 (ttp80) REVERT: B 316 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8308 (tp) REVERT: B 591 LEU cc_start: 0.6153 (mm) cc_final: 0.5886 (mm) REVERT: B 641 HIS cc_start: 0.6909 (t-90) cc_final: 0.6355 (p-80) REVERT: B 661 TYR cc_start: 0.7808 (t80) cc_final: 0.7573 (t80) REVERT: A 225 ASN cc_start: 0.7088 (m110) cc_final: 0.6336 (t0) REVERT: A 588 ARG cc_start: 0.6004 (mmt180) cc_final: 0.5188 (mtt180) REVERT: A 629 MET cc_start: 0.4916 (mmt) cc_final: 0.4577 (tpp) REVERT: A 710 ARG cc_start: 0.6823 (ttp80) cc_final: 0.6188 (tpt170) REVERT: A 802 LEU cc_start: -0.0643 (OUTLIER) cc_final: -0.0942 (pp) outliers start: 83 outliers final: 35 residues processed: 537 average time/residue: 0.2087 time to fit residues: 170.3887 Evaluate side-chains 437 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 396 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 797 ASP Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 706 THR Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 200 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 314 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 135 optimal weight: 0.0060 chunk 50 optimal weight: 1.9990 chunk 322 optimal weight: 9.9990 chunk 273 optimal weight: 0.9980 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 ASN C 385 GLN C 776 GLN ** F 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 823 GLN F 824 GLN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 688 ASN E 770 HIS D 281 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 778 GLN D 849 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS B 582 ASN B 692 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 297 ASN A 573 GLN A 824 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.212900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.163714 restraints weight = 33118.105| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.48 r_work: 0.3482 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27672 Z= 0.151 Angle : 0.668 9.459 37399 Z= 0.336 Chirality : 0.046 0.225 4240 Planarity : 0.005 0.067 4870 Dihedral : 9.609 178.633 3897 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.59 % Favored : 92.29 % Rotamer: Outliers : 3.59 % Allowed : 18.98 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -4.04 (0.13), residues: 3348 helix: -3.21 (0.10), residues: 1391 sheet: -2.83 (0.27), residues: 288 loop : -2.06 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 705 TYR 0.017 0.001 TYR B 656 PHE 0.038 0.001 PHE B 753 TRP 0.014 0.001 TRP D 543 HIS 0.010 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (27672) covalent geometry : angle 0.66821 / 0.34 (37399) hydrogen bonds : bond 0.03818 / 2.53 ( 503) hydrogen bonds : angle 5.97578 / 4.06 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 435 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 169 THR cc_start: 0.8541 (p) cc_final: 0.8338 (p) REVERT: C 170 GLU cc_start: 0.8244 (tt0) cc_final: 0.8041 (tt0) REVERT: C 279 GLU cc_start: 0.8492 (mp0) cc_final: 0.8024 (mt-10) REVERT: C 353 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8786 (mp) REVERT: C 636 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8333 (mt-10) REVERT: C 657 GLU cc_start: 0.7697 (pm20) cc_final: 0.7285 (pm20) REVERT: C 658 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7625 (mm-30) REVERT: C 669 ARG cc_start: 0.8542 (tpt170) cc_final: 0.7877 (mtp-110) REVERT: C 705 ARG cc_start: 0.8310 (ptp90) cc_final: 0.8076 (ptp90) REVERT: C 708 ASP cc_start: 0.7894 (t0) cc_final: 0.7312 (t70) REVERT: C 710 ARG cc_start: 0.8741 (mtm-85) cc_final: 0.8499 (mtt-85) REVERT: C 728 ARG cc_start: 0.8010 (mtt180) cc_final: 0.6991 (ttt-90) REVERT: C 745 VAL cc_start: 0.5909 (OUTLIER) cc_final: 0.5551 (p) REVERT: C 826 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7319 (mt-10) REVERT: F 200 ASN cc_start: 0.5625 (p0) cc_final: 0.5264 (p0) REVERT: F 242 MET cc_start: 0.2879 (OUTLIER) cc_final: 0.2534 (mtt) REVERT: F 318 GLU cc_start: 0.4432 (mt-10) cc_final: 0.4179 (pt0) REVERT: F 337 PHE cc_start: 0.6897 (m-80) cc_final: 0.5951 (t80) REVERT: F 560 LEU cc_start: 0.5141 (tt) cc_final: 0.4684 (tp) REVERT: F 687 PHE cc_start: 0.2044 (m-10) cc_final: 0.1738 (m-80) REVERT: E 170 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7806 (mt-10) REVERT: E 181 ILE cc_start: 0.8185 (tp) cc_final: 0.7464 (mm) REVERT: E 207 GLU cc_start: 0.8245 (tt0) cc_final: 0.7373 (mp0) REVERT: E 320 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7602 (ttp80) REVERT: E 392 ASP cc_start: 0.8097 (p0) cc_final: 0.7849 (p0) REVERT: E 560 LEU cc_start: 0.7874 (mm) cc_final: 0.7619 (mm) REVERT: E 584 ILE cc_start: 0.8724 (pt) cc_final: 0.8424 (mp) REVERT: E 629 MET cc_start: 0.8377 (ptt) cc_final: 0.8155 (ptt) REVERT: E 690 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8796 (tt) REVERT: E 756 ARG cc_start: 0.7749 (mmt180) cc_final: 0.7212 (mtt180) REVERT: D 344 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7463 (mm-30) REVERT: D 681 LYS cc_start: 0.3896 (OUTLIER) cc_final: 0.3510 (mmpt) REVERT: D 744 VAL cc_start: 0.3802 (OUTLIER) cc_final: 0.3563 (t) REVERT: D 792 GLU cc_start: 0.7776 (tt0) cc_final: 0.7455 (pt0) REVERT: D 798 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: D 803 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8890 (mp) REVERT: B 166 ILE cc_start: 0.9022 (mp) cc_final: 0.8810 (mp) REVERT: B 212 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7874 (mtmm) REVERT: B 252 ARG cc_start: 0.5887 (ttt180) cc_final: 0.4866 (ttp-170) REVERT: B 641 HIS cc_start: 0.6946 (t-90) cc_final: 0.6342 (p90) REVERT: B 661 TYR cc_start: 0.7858 (t80) cc_final: 0.7647 (t80) REVERT: B 681 LYS cc_start: 0.8587 (mmtp) cc_final: 0.8377 (mmmt) REVERT: B 692 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: B 705 ARG cc_start: 0.8156 (mtm180) cc_final: 0.7632 (mtm-85) REVERT: A 225 ASN cc_start: 0.7075 (m110) cc_final: 0.6369 (t0) REVERT: A 242 MET cc_start: 0.5421 (tpp) cc_final: 0.4433 (tmm) REVERT: A 326 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.5747 (m-30) REVERT: A 588 ARG cc_start: 0.6016 (mmt180) cc_final: 0.5158 (mtt180) REVERT: A 629 MET cc_start: 0.4815 (mmt) cc_final: 0.4567 (tpp) REVERT: A 710 ARG cc_start: 0.6656 (ttp80) cc_final: 0.6051 (tpt170) REVERT: A 802 LEU cc_start: -0.0823 (OUTLIER) cc_final: -0.1147 (pp) outliers start: 103 outliers final: 48 residues processed: 514 average time/residue: 0.2080 time to fit residues: 163.8419 Evaluate side-chains 447 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 388 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 797 ASP Chi-restraints excluded: chain F residue 822 GLN Chi-restraints excluded: chain E residue 334 GLN Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 744 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 301 optimal weight: 10.0000 chunk 333 optimal weight: 0.0020 chunk 14 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 141 optimal weight: 0.0980 chunk 210 optimal weight: 0.9980 chunk 292 optimal weight: 0.0060 chunk 193 optimal weight: 4.9990 chunk 272 optimal weight: 0.3980 chunk 199 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 GLN C 201 ASN C 309 HIS ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN B 692 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN A 823 GLN A 824 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.215688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.166999 restraints weight = 32875.232| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.33 r_work: 0.3542 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27672 Z= 0.111 Angle : 0.629 9.162 37399 Z= 0.316 Chirality : 0.045 0.197 4240 Planarity : 0.005 0.065 4870 Dihedral : 9.109 179.301 3896 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.75 % Favored : 93.13 % Rotamer: Outliers : 3.31 % Allowed : 20.80 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.56 (0.13), residues: 3348 helix: -2.72 (0.11), residues: 1380 sheet: -2.83 (0.28), residues: 269 loop : -1.88 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 542 TYR 0.021 0.001 TYR B 656 PHE 0.038 0.001 PHE B 753 TRP 0.010 0.001 TRP D 543 HIS 0.008 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (27672) covalent geometry : angle 0.62924 / 0.32 (37399) hydrogen bonds : bond 0.03325 / 2.20 ( 503) hydrogen bonds : angle 5.45071 / 3.70 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 452 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 GLN cc_start: 0.8339 (mt0) cc_final: 0.8070 (mt0) REVERT: C 657 GLU cc_start: 0.7721 (pm20) cc_final: 0.7264 (pm20) REVERT: C 669 ARG cc_start: 0.8530 (tpt170) cc_final: 0.7937 (mtp-110) REVERT: C 705 ARG cc_start: 0.8077 (ptp90) cc_final: 0.7844 (ptp90) REVERT: C 708 ASP cc_start: 0.7802 (t0) cc_final: 0.7203 (t70) REVERT: C 728 ARG cc_start: 0.7821 (mtt180) cc_final: 0.6876 (ttt-90) REVERT: C 737 MET cc_start: 0.4341 (tpp) cc_final: 0.1825 (mpp) REVERT: C 826 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7270 (mt-10) REVERT: F 199 LYS cc_start: 0.5641 (ptmt) cc_final: 0.5012 (pttm) REVERT: F 200 ASN cc_start: 0.5798 (p0) cc_final: 0.5436 (p0) REVERT: F 242 MET cc_start: 0.2673 (OUTLIER) cc_final: 0.2430 (mtt) REVERT: F 318 GLU cc_start: 0.4287 (mt-10) cc_final: 0.4078 (pt0) REVERT: F 337 PHE cc_start: 0.6881 (m-80) cc_final: 0.5992 (t80) REVERT: F 556 ARG cc_start: 0.2297 (tpp-160) cc_final: 0.0880 (tpm170) REVERT: F 560 LEU cc_start: 0.4966 (tt) cc_final: 0.3963 (tp) REVERT: F 562 MET cc_start: 0.2294 (ttt) cc_final: 0.1857 (ttp) REVERT: F 616 LYS cc_start: 0.6849 (tttt) cc_final: 0.6507 (tttt) REVERT: F 634 MET cc_start: 0.7558 (mmm) cc_final: 0.7191 (mmm) REVERT: F 638 MET cc_start: -0.1232 (mmp) cc_final: -0.1806 (mmp) REVERT: F 687 PHE cc_start: 0.2016 (m-10) cc_final: 0.1714 (m-80) REVERT: E 185 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7648 (tm-30) REVERT: E 193 VAL cc_start: 0.8602 (p) cc_final: 0.8125 (t) REVERT: E 207 GLU cc_start: 0.8030 (tt0) cc_final: 0.7318 (mp0) REVERT: E 320 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7622 (ttp80) REVERT: E 392 ASP cc_start: 0.8056 (p0) cc_final: 0.7804 (p0) REVERT: E 559 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8519 (tp) REVERT: E 560 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7636 (mm) REVERT: E 584 ILE cc_start: 0.8607 (pt) cc_final: 0.8313 (mp) REVERT: E 661 TYR cc_start: 0.8502 (t80) cc_final: 0.8295 (t80) REVERT: E 690 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8780 (tt) REVERT: E 756 ARG cc_start: 0.7678 (mmt180) cc_final: 0.7210 (mtt180) REVERT: D 344 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7371 (mm-30) REVERT: D 620 ASN cc_start: 0.8703 (t0) cc_final: 0.8484 (t0) REVERT: D 742 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7648 (tp) REVERT: D 744 VAL cc_start: 0.3486 (OUTLIER) cc_final: 0.3258 (t) REVERT: D 792 GLU cc_start: 0.7760 (tt0) cc_final: 0.7513 (pt0) REVERT: D 798 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: B 212 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7769 (mtmm) REVERT: B 252 ARG cc_start: 0.5827 (ttt180) cc_final: 0.4913 (ttp-170) REVERT: B 641 HIS cc_start: 0.6813 (t-90) cc_final: 0.6202 (p90) REVERT: A 225 ASN cc_start: 0.6932 (m110) cc_final: 0.6331 (t0) REVERT: A 242 MET cc_start: 0.5747 (tpp) cc_final: 0.5127 (mmm) REVERT: A 326 ASP cc_start: 0.6014 (OUTLIER) cc_final: 0.5725 (m-30) REVERT: A 588 ARG cc_start: 0.5978 (mmt180) cc_final: 0.5194 (mtt180) REVERT: A 710 ARG cc_start: 0.6740 (ttp80) cc_final: 0.6100 (tpt170) REVERT: A 802 LEU cc_start: -0.0544 (OUTLIER) cc_final: -0.0782 (pp) REVERT: A 823 GLN cc_start: 0.1580 (OUTLIER) cc_final: 0.0412 (mm110) outliers start: 95 outliers final: 42 residues processed: 524 average time/residue: 0.2099 time to fit residues: 167.7038 Evaluate side-chains 451 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 399 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 744 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 179 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 361 HIS F 824 GLN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN B 748 ASN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 824 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.213278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.165104 restraints weight = 32816.330| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.54 r_work: 0.3448 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27672 Z= 0.155 Angle : 0.641 8.020 37399 Z= 0.320 Chirality : 0.046 0.199 4240 Planarity : 0.004 0.065 4870 Dihedral : 8.921 178.433 3889 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.26 % Favored : 92.62 % Rotamer: Outliers : 3.77 % Allowed : 21.32 % Favored : 74.91 % 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: -3.30 (0.13), residues: 3348 helix: -2.42 (0.12), residues: 1377 sheet: -2.77 (0.29), residues: 269 loop : -1.79 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 569 TYR 0.023 0.001 TYR E 656 PHE 0.030 0.001 PHE B 753 TRP 0.012 0.001 TRP D 543 HIS 0.008 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (27672) covalent geometry : angle 0.64088 / 0.32 (37399) hydrogen bonds : bond 0.03348 / 2.23 ( 503) hydrogen bonds : angle 5.29772 / 3.58 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 431 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 561 ARG cc_start: 0.7705 (ptt90) cc_final: 0.7093 (mtm110) REVERT: C 565 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7725 (mm-30) REVERT: C 669 ARG cc_start: 0.8520 (tpt170) cc_final: 0.7909 (mtp-110) REVERT: C 728 ARG cc_start: 0.7879 (mtt180) cc_final: 0.6910 (ttt-90) REVERT: C 737 MET cc_start: 0.4367 (tpp) cc_final: 0.1943 (mpp) REVERT: F 200 ASN cc_start: 0.5634 (p0) cc_final: 0.5365 (p0) REVERT: F 205 ILE cc_start: 0.7417 (mt) cc_final: 0.7031 (tp) REVERT: F 242 MET cc_start: 0.2522 (OUTLIER) cc_final: 0.2289 (mtt) REVERT: F 337 PHE cc_start: 0.6899 (m-80) cc_final: 0.5979 (t80) REVERT: F 556 ARG cc_start: 0.2289 (tpp-160) cc_final: 0.0836 (tpm170) REVERT: F 560 LEU cc_start: 0.4851 (tt) cc_final: 0.4520 (tt) REVERT: F 562 MET cc_start: 0.2201 (ttt) cc_final: 0.1660 (ttp) REVERT: F 616 LYS cc_start: 0.6950 (tttt) cc_final: 0.6584 (tttt) REVERT: F 801 LYS cc_start: 0.6567 (tppt) cc_final: 0.6027 (mmtt) REVERT: E 181 ILE cc_start: 0.8292 (tp) cc_final: 0.7532 (mm) REVERT: E 185 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7689 (tm-30) REVERT: E 207 GLU cc_start: 0.8103 (tt0) cc_final: 0.7324 (mp0) REVERT: E 298 MET cc_start: 0.7907 (mtp) cc_final: 0.7705 (mtt) REVERT: E 320 ARG cc_start: 0.7922 (ttp-110) cc_final: 0.7622 (ttp80) REVERT: E 392 ASP cc_start: 0.8113 (p0) cc_final: 0.7772 (p0) REVERT: E 559 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8559 (tp) REVERT: E 560 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7799 (mm) REVERT: E 584 ILE cc_start: 0.8677 (pt) cc_final: 0.8354 (mp) REVERT: E 661 TYR cc_start: 0.8546 (t80) cc_final: 0.8335 (t80) REVERT: E 690 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8820 (tt) REVERT: E 756 ARG cc_start: 0.7838 (mmt180) cc_final: 0.7378 (mtt180) REVERT: D 344 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7516 (mm-30) REVERT: D 639 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6927 (mm-30) REVERT: D 742 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7639 (tp) REVERT: D 744 VAL cc_start: 0.3972 (OUTLIER) cc_final: 0.3754 (t) REVERT: D 792 GLU cc_start: 0.7809 (tt0) cc_final: 0.7512 (pt0) REVERT: D 798 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7102 (mt-10) REVERT: B 212 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7823 (mtmm) REVERT: B 252 ARG cc_start: 0.5910 (ttt180) cc_final: 0.4955 (ttp-170) REVERT: B 641 HIS cc_start: 0.6863 (t-90) cc_final: 0.6221 (p90) REVERT: B 669 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7741 (ptm160) REVERT: A 588 ARG cc_start: 0.5943 (mmt180) cc_final: 0.5169 (mtt180) REVERT: A 710 ARG cc_start: 0.6576 (ttp80) cc_final: 0.6082 (tpt170) REVERT: A 802 LEU cc_start: -0.0442 (OUTLIER) cc_final: -0.0798 (pp) outliers start: 108 outliers final: 63 residues processed: 509 average time/residue: 0.2076 time to fit residues: 161.7390 Evaluate side-chains 475 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 403 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 822 GLN Chi-restraints excluded: chain F residue 823 GLN Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 744 VAL Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 85 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 231 optimal weight: 0.8980 chunk 222 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 173 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 109 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 ASN C 321 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 GLN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.215400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.167080 restraints weight = 32949.245| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.47 r_work: 0.3523 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27672 Z= 0.112 Angle : 0.614 9.084 37399 Z= 0.307 Chirality : 0.045 0.218 4240 Planarity : 0.004 0.064 4870 Dihedral : 8.666 179.284 3889 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.49 % Rotamer: Outliers : 3.66 % Allowed : 21.84 % Favored : 74.49 % 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: -3.00 (0.14), residues: 3348 helix: -2.16 (0.12), residues: 1393 sheet: -2.69 (0.29), residues: 269 loop : -1.61 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 852 TYR 0.026 0.001 TYR B 656 PHE 0.030 0.001 PHE B 753 TRP 0.008 0.001 TRP D 543 HIS 0.007 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (27672) covalent geometry : angle 0.61355 / 0.31 (37399) hydrogen bonds : bond 0.03087 / 2.03 ( 503) hydrogen bonds : angle 5.07545 / 3.42 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 421 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 551 MET cc_start: 0.4753 (mpp) cc_final: 0.4516 (mpp) REVERT: C 669 ARG cc_start: 0.8500 (tpt170) cc_final: 0.7861 (mtp85) REVERT: C 728 ARG cc_start: 0.7801 (mtt180) cc_final: 0.6814 (ttt-90) REVERT: C 737 MET cc_start: 0.3969 (tpp) cc_final: 0.1978 (mpp) REVERT: F 200 ASN cc_start: 0.5726 (p0) cc_final: 0.5429 (p0) REVERT: F 205 ILE cc_start: 0.7214 (mt) cc_final: 0.6814 (tp) REVERT: F 242 MET cc_start: 0.2595 (OUTLIER) cc_final: 0.2390 (mtt) REVERT: F 337 PHE cc_start: 0.6913 (m-80) cc_final: 0.5936 (t80) REVERT: F 556 ARG cc_start: 0.2268 (tpp-160) cc_final: 0.1151 (tpm170) REVERT: F 634 MET cc_start: 0.7807 (mmm) cc_final: 0.7445 (mmm) REVERT: F 801 LYS cc_start: 0.6331 (tppt) cc_final: 0.6080 (mmtt) REVERT: E 185 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7605 (tm-30) REVERT: E 207 GLU cc_start: 0.8007 (tt0) cc_final: 0.7303 (mp0) REVERT: E 322 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6867 (t80) REVERT: E 392 ASP cc_start: 0.8062 (p0) cc_final: 0.7756 (p0) REVERT: E 559 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8569 (tp) REVERT: E 560 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7735 (mm) REVERT: E 584 ILE cc_start: 0.8616 (pt) cc_final: 0.8346 (mp) REVERT: E 661 TYR cc_start: 0.8478 (t80) cc_final: 0.8229 (t80) REVERT: E 690 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8798 (tt) REVERT: E 756 ARG cc_start: 0.7782 (mmt180) cc_final: 0.7264 (mtt180) REVERT: E 817 LEU cc_start: 0.8678 (tt) cc_final: 0.8317 (tt) REVERT: D 344 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7559 (mm-30) REVERT: D 620 ASN cc_start: 0.8770 (t0) cc_final: 0.8538 (t0) REVERT: D 744 VAL cc_start: 0.3803 (OUTLIER) cc_final: 0.3591 (t) REVERT: D 750 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7577 (mtm110) REVERT: D 792 GLU cc_start: 0.7701 (tt0) cc_final: 0.7492 (pt0) REVERT: D 798 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7010 (mt-10) REVERT: D 834 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8732 (mm) REVERT: B 185 GLU cc_start: 0.8082 (tp30) cc_final: 0.7819 (mp0) REVERT: B 212 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7871 (mtmm) REVERT: B 252 ARG cc_start: 0.5848 (ttt180) cc_final: 0.4978 (ttp-170) REVERT: B 279 GLU cc_start: 0.8387 (mp0) cc_final: 0.8130 (mt-10) REVERT: B 393 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7725 (tp) REVERT: B 396 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7071 (mt-10) REVERT: B 641 HIS cc_start: 0.6839 (t-90) cc_final: 0.6206 (p90) REVERT: B 669 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7910 (ptm160) REVERT: A 551 MET cc_start: 0.3481 (OUTLIER) cc_final: 0.2884 (mtp) REVERT: A 588 ARG cc_start: 0.5883 (mmt180) cc_final: 0.5116 (mtt180) REVERT: A 710 ARG cc_start: 0.6612 (ttp80) cc_final: 0.6116 (tpt170) REVERT: A 757 ILE cc_start: 0.1631 (OUTLIER) cc_final: 0.1290 (mp) REVERT: A 802 LEU cc_start: -0.0826 (OUTLIER) cc_final: -0.1162 (pp) outliers start: 105 outliers final: 64 residues processed: 495 average time/residue: 0.2091 time to fit residues: 157.7133 Evaluate side-chains 480 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 403 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 734 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain E residue 322 TYR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 638 MET Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 708 ASP Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 744 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 92 optimal weight: 0.2980 chunk 222 optimal weight: 0.1980 chunk 171 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 297 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 242 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 HIS ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN B 748 ASN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 692 GLN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.215626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.166900 restraints weight = 32786.098| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.24 r_work: 0.3552 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27672 Z= 0.117 Angle : 0.622 12.866 37399 Z= 0.309 Chirality : 0.045 0.231 4240 Planarity : 0.004 0.062 4870 Dihedral : 8.546 179.389 3887 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 3.70 % Allowed : 22.02 % Favored : 74.28 % 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: -2.87 (0.14), residues: 3348 helix: -2.02 (0.13), residues: 1406 sheet: -2.67 (0.29), residues: 264 loop : -1.56 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 852 TYR 0.027 0.001 TYR E 656 PHE 0.048 0.001 PHE B 753 TRP 0.008 0.001 TRP D 543 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (27672) covalent geometry : angle 0.62191 / 0.31 (37399) hydrogen bonds : bond 0.03092 / 2.04 ( 503) hydrogen bonds : angle 4.97908 / 3.36 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 418 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: C 555 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7121 (mt-10) REVERT: C 669 ARG cc_start: 0.8474 (tpt170) cc_final: 0.7853 (mtp85) REVERT: C 705 ARG cc_start: 0.8125 (ptp90) cc_final: 0.7742 (ptp90) REVERT: F 200 ASN cc_start: 0.5755 (p0) cc_final: 0.5454 (p0) REVERT: F 205 ILE cc_start: 0.7278 (mt) cc_final: 0.6896 (tp) REVERT: F 242 MET cc_start: 0.2695 (OUTLIER) cc_final: 0.2460 (mtt) REVERT: F 337 PHE cc_start: 0.6808 (m-80) cc_final: 0.5914 (t80) REVERT: F 556 ARG cc_start: 0.2283 (tpp-160) cc_final: 0.1220 (tpm170) REVERT: F 560 LEU cc_start: 0.4887 (tt) cc_final: 0.3726 (tp) REVERT: F 562 MET cc_start: 0.2347 (ttt) cc_final: 0.1810 (ttp) REVERT: F 634 MET cc_start: 0.7536 (mmm) cc_final: 0.7150 (mmm) REVERT: F 638 MET cc_start: -0.0795 (mmp) cc_final: -0.1104 (mmp) REVERT: E 185 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7599 (tm-30) REVERT: E 207 GLU cc_start: 0.7947 (tt0) cc_final: 0.7294 (mp0) REVERT: E 322 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6850 (t80) REVERT: E 389 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6434 (tptt) REVERT: E 392 ASP cc_start: 0.8027 (p0) cc_final: 0.7584 (p0) REVERT: E 559 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8568 (tp) REVERT: E 560 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7757 (mm) REVERT: E 584 ILE cc_start: 0.8610 (pt) cc_final: 0.8317 (mp) REVERT: E 690 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8785 (tt) REVERT: E 756 ARG cc_start: 0.7734 (mmt180) cc_final: 0.7301 (mtt180) REVERT: E 817 LEU cc_start: 0.8647 (tt) cc_final: 0.8302 (tt) REVERT: D 620 ASN cc_start: 0.8732 (t0) cc_final: 0.8495 (t0) REVERT: D 742 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7540 (tp) REVERT: D 792 GLU cc_start: 0.7675 (tt0) cc_final: 0.7472 (pt0) REVERT: D 798 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7026 (mt-10) REVERT: D 834 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8760 (mm) REVERT: B 212 LYS cc_start: 0.8215 (mtmt) cc_final: 0.7923 (mtmm) REVERT: B 252 ARG cc_start: 0.5838 (ttt180) cc_final: 0.4975 (ttp-170) REVERT: B 279 GLU cc_start: 0.8342 (mp0) cc_final: 0.8108 (mt-10) REVERT: B 316 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8437 (tp) REVERT: B 396 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7005 (mt-10) REVERT: B 641 HIS cc_start: 0.6867 (t-90) cc_final: 0.6299 (p-80) REVERT: B 749 PHE cc_start: 0.7550 (m-80) cc_final: 0.7324 (m-10) REVERT: A 551 MET cc_start: 0.3478 (OUTLIER) cc_final: 0.2903 (mtp) REVERT: A 557 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6574 (tt0) REVERT: A 588 ARG cc_start: 0.5839 (mmt180) cc_final: 0.5087 (mtt180) REVERT: A 710 ARG cc_start: 0.6643 (ttp80) cc_final: 0.6148 (tpt170) REVERT: A 757 ILE cc_start: 0.1582 (OUTLIER) cc_final: 0.1262 (mp) REVERT: A 802 LEU cc_start: -0.0812 (OUTLIER) cc_final: -0.1110 (pp) outliers start: 106 outliers final: 71 residues processed: 491 average time/residue: 0.2102 time to fit residues: 157.5185 Evaluate side-chains 491 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 407 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 734 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 322 TYR Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 562 MET Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 638 MET Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 612 THR Chi-restraints excluded: chain D residue 625 SER Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 780 LYS Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 158 optimal weight: 3.9990 chunk 157 optimal weight: 0.0270 chunk 51 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 289 optimal weight: 4.9990 chunk 167 optimal weight: 0.1980 chunk 188 optimal weight: 0.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 ASN C 321 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN A 692 GLN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.216083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.167101 restraints weight = 33008.681| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.36 r_work: 0.3534 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27672 Z= 0.117 Angle : 0.629 11.904 37399 Z= 0.310 Chirality : 0.045 0.243 4240 Planarity : 0.004 0.062 4870 Dihedral : 8.433 179.930 3887 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.69 % Favored : 93.19 % Rotamer: Outliers : 3.59 % Allowed : 22.37 % Favored : 74.04 % 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: -2.73 (0.14), residues: 3348 helix: -1.86 (0.13), residues: 1403 sheet: -2.71 (0.29), residues: 279 loop : -1.49 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 852 TYR 0.043 0.001 TYR E 656 PHE 0.045 0.001 PHE B 753 TRP 0.007 0.001 TRP D 543 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (27672) covalent geometry : angle 0.62925 / 0.31 (37399) hydrogen bonds : bond 0.03029 / 1.97 ( 503) hydrogen bonds : angle 4.93509 / 3.35 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 411 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 ARG cc_start: 0.8840 (tmm160) cc_final: 0.8577 (ttp80) REVERT: C 669 ARG cc_start: 0.8449 (tpt170) cc_final: 0.7937 (mtm180) REVERT: F 200 ASN cc_start: 0.5660 (p0) cc_final: 0.5332 (p0) REVERT: F 205 ILE cc_start: 0.7291 (mt) cc_final: 0.6906 (tp) REVERT: F 242 MET cc_start: 0.2565 (OUTLIER) cc_final: 0.2349 (mtt) REVERT: F 254 GLU cc_start: 0.4495 (tp30) cc_final: 0.2949 (mm-30) REVERT: F 337 PHE cc_start: 0.6769 (m-80) cc_final: 0.5888 (t80) REVERT: F 556 ARG cc_start: 0.2263 (tpp-160) cc_final: 0.1221 (tpm170) REVERT: F 560 LEU cc_start: 0.5033 (tt) cc_final: 0.3934 (tp) REVERT: F 562 MET cc_start: 0.2200 (ttt) cc_final: 0.1823 (ttp) REVERT: F 634 MET cc_start: 0.7617 (mmm) cc_final: 0.7246 (mmm) REVERT: F 638 MET cc_start: -0.0807 (mmp) cc_final: -0.1124 (mmp) REVERT: E 207 GLU cc_start: 0.7933 (tt0) cc_final: 0.7305 (mp0) REVERT: E 320 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7919 (ttp-110) REVERT: E 322 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6881 (t80) REVERT: E 389 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6446 (tptt) REVERT: E 392 ASP cc_start: 0.8001 (p0) cc_final: 0.7585 (p0) REVERT: E 559 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8584 (tp) REVERT: E 560 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7761 (mm) REVERT: E 584 ILE cc_start: 0.8597 (pt) cc_final: 0.8328 (mp) REVERT: E 690 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8783 (tt) REVERT: E 817 LEU cc_start: 0.8641 (tt) cc_final: 0.8298 (tt) REVERT: D 620 ASN cc_start: 0.8696 (t0) cc_final: 0.8416 (t0) REVERT: D 742 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7630 (tp) REVERT: D 792 GLU cc_start: 0.7713 (tt0) cc_final: 0.7497 (pt0) REVERT: D 798 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: D 831 GLN cc_start: 0.8010 (tp40) cc_final: 0.7631 (tt0) REVERT: D 834 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8736 (mm) REVERT: B 212 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7938 (mtmm) REVERT: B 252 ARG cc_start: 0.5801 (ttt180) cc_final: 0.4969 (ttp-170) REVERT: B 279 GLU cc_start: 0.8342 (mp0) cc_final: 0.8111 (mt-10) REVERT: B 316 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8270 (tp) REVERT: B 332 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.7635 (mtm180) REVERT: B 337 PHE cc_start: 0.8126 (m-80) cc_final: 0.7873 (m-80) REVERT: B 393 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7797 (mp) REVERT: B 396 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6953 (mt-10) REVERT: B 641 HIS cc_start: 0.6898 (t-90) cc_final: 0.6338 (p-80) REVERT: A 242 MET cc_start: 0.5309 (mmp) cc_final: 0.4856 (mmm) REVERT: A 551 MET cc_start: 0.3345 (OUTLIER) cc_final: 0.2789 (mtp) REVERT: A 557 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6580 (tt0) REVERT: A 588 ARG cc_start: 0.5856 (mmt180) cc_final: 0.5149 (mtt180) REVERT: A 710 ARG cc_start: 0.6662 (ttp80) cc_final: 0.6161 (tpt170) REVERT: A 757 ILE cc_start: 0.1565 (OUTLIER) cc_final: 0.1217 (mp) REVERT: A 802 LEU cc_start: -0.0827 (OUTLIER) cc_final: -0.1123 (pp) outliers start: 103 outliers final: 75 residues processed: 482 average time/residue: 0.2055 time to fit residues: 150.8257 Evaluate side-chains 487 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 397 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 734 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain E residue 322 TYR Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 708 ASP Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 612 THR Chi-restraints excluded: chain D residue 625 SER Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 780 LYS Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 289 optimal weight: 5.9990 chunk 56 optimal weight: 0.0970 chunk 169 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 239 optimal weight: 0.6980 chunk 314 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 276 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 823 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN A 692 GLN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.213019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.164082 restraints weight = 32940.570| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.46 r_work: 0.3480 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 27672 Z= 0.183 Angle : 0.669 11.219 37399 Z= 0.329 Chirality : 0.047 0.252 4240 Planarity : 0.005 0.062 4870 Dihedral : 8.555 178.939 3887 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.14 % Favored : 92.71 % Rotamer: Outliers : 3.38 % Allowed : 22.47 % Favored : 74.15 % 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 (0.14), residues: 3348 helix: -1.86 (0.13), residues: 1415 sheet: -2.71 (0.29), residues: 279 loop : -1.47 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 852 TYR 0.042 0.002 TYR E 656 PHE 0.042 0.001 PHE B 753 TRP 0.011 0.002 TRP D 543 HIS 0.007 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (27672) covalent geometry : angle 0.66928 / 0.33 (37399) hydrogen bonds : bond 0.03188 / 2.09 ( 503) hydrogen bonds : angle 5.02501 / 3.42 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 401 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 ARG cc_start: 0.9072 (tmm160) cc_final: 0.8716 (ttp80) REVERT: C 669 ARG cc_start: 0.8473 (tpt170) cc_final: 0.7852 (mtp85) REVERT: C 705 ARG cc_start: 0.8257 (ptp90) cc_final: 0.7947 (ptp90) REVERT: F 200 ASN cc_start: 0.5581 (p0) cc_final: 0.5109 (p0) REVERT: F 205 ILE cc_start: 0.7320 (mt) cc_final: 0.6954 (tp) REVERT: F 318 GLU cc_start: 0.4778 (pt0) cc_final: 0.4519 (pt0) REVERT: F 337 PHE cc_start: 0.6793 (m-80) cc_final: 0.5872 (t80) REVERT: F 556 ARG cc_start: 0.2351 (tpp-160) cc_final: 0.1313 (tpm170) REVERT: F 560 LEU cc_start: 0.4909 (tt) cc_final: 0.3890 (tp) REVERT: F 562 MET cc_start: 0.2081 (ttt) cc_final: 0.1648 (ttp) REVERT: F 634 MET cc_start: 0.7619 (mmm) cc_final: 0.7227 (mmm) REVERT: F 638 MET cc_start: -0.0793 (mmp) cc_final: -0.1150 (mmp) REVERT: E 181 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7736 (mm) REVERT: E 207 GLU cc_start: 0.8117 (tt0) cc_final: 0.7321 (mp0) REVERT: E 320 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.8007 (ttp-110) REVERT: E 389 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6600 (tptt) REVERT: E 392 ASP cc_start: 0.8201 (p0) cc_final: 0.7768 (p0) REVERT: E 559 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8548 (tp) REVERT: E 560 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7801 (mm) REVERT: E 584 ILE cc_start: 0.8621 (pt) cc_final: 0.8333 (mp) REVERT: E 690 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8828 (tt) REVERT: E 756 ARG cc_start: 0.7627 (mmt180) cc_final: 0.7201 (mtt180) REVERT: E 817 LEU cc_start: 0.8808 (tt) cc_final: 0.8487 (tt) REVERT: D 742 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7747 (tp) REVERT: D 792 GLU cc_start: 0.7744 (tt0) cc_final: 0.7508 (pt0) REVERT: D 798 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7118 (mt-10) REVERT: D 831 GLN cc_start: 0.8152 (tp40) cc_final: 0.7416 (tp40) REVERT: D 834 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8829 (mm) REVERT: B 212 LYS cc_start: 0.8314 (mtmt) cc_final: 0.8021 (mtmm) REVERT: B 252 ARG cc_start: 0.5883 (ttt180) cc_final: 0.4910 (ttp-170) REVERT: B 316 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8347 (tp) REVERT: B 393 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7710 (tp) REVERT: B 638 MET cc_start: 0.8106 (mmm) cc_final: 0.7740 (mpp) REVERT: B 641 HIS cc_start: 0.6986 (t-90) cc_final: 0.6402 (p-80) REVERT: A 242 MET cc_start: 0.5384 (mmp) cc_final: 0.4886 (mmm) REVERT: A 551 MET cc_start: 0.3394 (OUTLIER) cc_final: 0.2810 (mtp) REVERT: A 557 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6650 (tt0) REVERT: A 588 ARG cc_start: 0.5779 (mmt180) cc_final: 0.5055 (mtt180) REVERT: A 710 ARG cc_start: 0.6663 (ttp80) cc_final: 0.6158 (tpt170) REVERT: A 757 ILE cc_start: 0.1508 (OUTLIER) cc_final: 0.1184 (mp) REVERT: A 802 LEU cc_start: -0.0693 (OUTLIER) cc_final: -0.1005 (pp) outliers start: 97 outliers final: 75 residues processed: 469 average time/residue: 0.2106 time to fit residues: 151.5638 Evaluate side-chains 479 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 391 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 734 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 309 HIS Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 708 ASP Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 839 VAL Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 612 THR Chi-restraints excluded: chain D residue 625 SER Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 780 LYS Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 262 optimal weight: 0.0970 chunk 134 optimal weight: 0.7980 chunk 313 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 78 optimal weight: 0.0170 chunk 326 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 325 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 291 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 GLN C 201 ASN C 321 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 703 GLN E 770 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN A 692 GLN A 824 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.215442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.166360 restraints weight = 32985.137| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.34 r_work: 0.3531 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27672 Z= 0.116 Angle : 0.635 11.955 37399 Z= 0.314 Chirality : 0.045 0.257 4240 Planarity : 0.004 0.062 4870 Dihedral : 8.329 176.181 3885 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.36 % Favored : 93.49 % Rotamer: Outliers : 3.21 % Allowed : 22.82 % Favored : 73.97 % 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: -2.56 (0.14), residues: 3348 helix: -1.69 (0.13), residues: 1402 sheet: -2.64 (0.30), residues: 265 loop : -1.43 (0.16), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 750 TYR 0.036 0.001 TYR E 656 PHE 0.043 0.001 PHE B 753 TRP 0.005 0.001 TRP C 543 HIS 0.008 0.001 HIS D 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (27672) covalent geometry : angle 0.63519 / 0.31 (37399) hydrogen bonds : bond 0.03043 / 1.99 ( 503) hydrogen bonds : angle 4.90775 / 3.34 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 401 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 ARG cc_start: 0.8934 (tmm160) cc_final: 0.8605 (ttp80) REVERT: C 669 ARG cc_start: 0.8425 (tpt170) cc_final: 0.7916 (mtm180) REVERT: C 705 ARG cc_start: 0.8119 (ptp90) cc_final: 0.7804 (ptp90) REVERT: C 737 MET cc_start: 0.4267 (tpp) cc_final: 0.2183 (mpp) REVERT: F 200 ASN cc_start: 0.5529 (p0) cc_final: 0.5112 (p0) REVERT: F 205 ILE cc_start: 0.7305 (mt) cc_final: 0.6930 (tp) REVERT: F 337 PHE cc_start: 0.6638 (m-80) cc_final: 0.5736 (t80) REVERT: F 556 ARG cc_start: 0.2275 (tpp-160) cc_final: 0.1170 (tpm170) REVERT: F 560 LEU cc_start: 0.4875 (tt) cc_final: 0.3737 (tp) REVERT: F 562 MET cc_start: 0.2095 (ttt) cc_final: 0.1663 (ttp) REVERT: F 634 MET cc_start: 0.7751 (mmm) cc_final: 0.7270 (mmm) REVERT: E 201 ASN cc_start: 0.8919 (m-40) cc_final: 0.8425 (m110) REVERT: E 207 GLU cc_start: 0.7947 (tt0) cc_final: 0.7282 (mp0) REVERT: E 252 ARG cc_start: 0.7892 (mpp-170) cc_final: 0.7643 (mtm-85) REVERT: E 392 ASP cc_start: 0.8005 (p0) cc_final: 0.7583 (p0) REVERT: E 559 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8532 (tp) REVERT: E 560 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7753 (mm) REVERT: E 584 ILE cc_start: 0.8589 (pt) cc_final: 0.8313 (mp) REVERT: E 690 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8786 (tt) REVERT: E 756 ARG cc_start: 0.7552 (mmt180) cc_final: 0.7131 (mtt180) REVERT: E 817 LEU cc_start: 0.8700 (tt) cc_final: 0.8360 (tt) REVERT: D 742 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7796 (tp) REVERT: D 792 GLU cc_start: 0.7649 (tt0) cc_final: 0.7445 (pt0) REVERT: D 798 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: D 831 GLN cc_start: 0.8097 (tp40) cc_final: 0.7360 (tp40) REVERT: D 834 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8774 (mm) REVERT: B 212 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7939 (mtmm) REVERT: B 252 ARG cc_start: 0.5768 (ttt180) cc_final: 0.4917 (ttp-170) REVERT: B 279 GLU cc_start: 0.8376 (mp0) cc_final: 0.8173 (mt-10) REVERT: B 316 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8342 (tp) REVERT: B 393 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7652 (tp) REVERT: B 641 HIS cc_start: 0.6884 (t-90) cc_final: 0.6343 (p-80) REVERT: A 242 MET cc_start: 0.5313 (mmp) cc_final: 0.4822 (mmm) REVERT: A 551 MET cc_start: 0.3266 (OUTLIER) cc_final: 0.2748 (mtp) REVERT: A 557 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6680 (tt0) REVERT: A 588 ARG cc_start: 0.5779 (mmt180) cc_final: 0.5144 (mtt180) REVERT: A 710 ARG cc_start: 0.6648 (ttp80) cc_final: 0.6151 (tpt170) REVERT: A 752 GLU cc_start: 0.4765 (mm-30) cc_final: 0.4564 (mm-30) REVERT: A 757 ILE cc_start: 0.1454 (OUTLIER) cc_final: 0.1149 (mp) REVERT: A 802 LEU cc_start: -0.0691 (OUTLIER) cc_final: -0.1005 (pp) outliers start: 92 outliers final: 72 residues processed: 464 average time/residue: 0.2100 time to fit residues: 149.2301 Evaluate side-chains 472 residues out of total 2866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 389 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 734 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 703 GLN Chi-restraints excluded: chain E residue 708 ASP Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 839 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 612 THR Chi-restraints excluded: chain D residue 625 SER Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 780 LYS Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 8 optimal weight: 0.0020 chunk 310 optimal weight: 10.0000 chunk 52 optimal weight: 0.4980 chunk 258 optimal weight: 7.9990 chunk 313 optimal weight: 8.9990 chunk 315 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 338 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS D 334 GLN ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.214089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.167310 restraints weight = 32737.383| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.12 r_work: 0.3551 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27672 Z= 0.127 Angle : 0.636 11.926 37399 Z= 0.314 Chirality : 0.045 0.262 4240 Planarity : 0.004 0.062 4870 Dihedral : 8.301 174.997 3885 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.60 % Favored : 93.25 % Rotamer: Outliers : 3.18 % Allowed : 22.92 % Favored : 73.90 % 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: -2.50 (0.14), residues: 3348 helix: -1.61 (0.13), residues: 1405 sheet: -2.64 (0.30), residues: 257 loop : -1.43 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 852 TYR 0.032 0.001 TYR B 656 PHE 0.041 0.001 PHE B 753 TRP 0.007 0.001 TRP D 543 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (27672) covalent geometry : angle 0.63562 / 0.31 (37399) hydrogen bonds : bond 0.03021 / 1.98 ( 503) hydrogen bonds : angle 4.89840 / 3.33 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6613.75 seconds wall clock time: 114 minutes 8.87 seconds (6848.87 seconds total)