Starting phenix.real_space_refine on Sat Mar 7 13:12:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wz3_66380/03_2026/9wz3_66380.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wz3_66380/03_2026/9wz3_66380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wz3_66380/03_2026/9wz3_66380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wz3_66380/03_2026/9wz3_66380.map" model { file = "/net/cci-nas-00/data/ceres_data/9wz3_66380/03_2026/9wz3_66380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wz3_66380/03_2026/9wz3_66380.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 198 5.16 5 C 27432 2.51 5 N 7416 2.21 5 O 8100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43146 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "B" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "C" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "D" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "E" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "F" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "G" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "H" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "I" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "J" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "K" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "L" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "M" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "N" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "O" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "P" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "Q" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Chain: "R" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2397 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Time building chain proxies: 9.16, per 1000 atoms: 0.21 Number of scatterers: 43146 At special positions: 0 Unit cell: (136.9, 133.94, 233.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 198 16.00 O 8100 8.00 N 7416 7.00 C 27432 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: 3.40 Conformation dependent library (CDL) restraints added in 1.8 seconds 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10044 Finding SS restraints... Secondary structure from input PDB file: 244 helices and 18 sheets defined 81.8% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 418 through 430 Proline residue: A 424 - end of helix removed outlier: 3.527A pdb=" N ALA A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 449 removed outlier: 3.753A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N TRP A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 477 Processing helix chain 'A' and resid 494 through 514 removed outlier: 3.876A pdb=" N LEU A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 545 removed outlier: 4.314A pdb=" N LEU A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 575 removed outlier: 3.911A pdb=" N GLY A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 607 removed outlier: 3.833A pdb=" N ALA A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'A' and resid 638 through 652 removed outlier: 4.078A pdb=" N ARG A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 Processing helix chain 'A' and resid 670 through 698 removed outlier: 4.184A pdb=" N PHE A 674 " --> pdb=" O GLY A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 Processing helix chain 'B' and resid 418 through 430 Proline residue: B 424 - end of helix Processing helix chain 'B' and resid 435 through 449 removed outlier: 3.583A pdb=" N GLN B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 477 Processing helix chain 'B' and resid 494 through 513 removed outlier: 4.085A pdb=" N LEU B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 517 through 544 removed outlier: 4.287A pdb=" N LEU B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 561 through 575 removed outlier: 3.767A pdb=" N PHE B 565 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 607 removed outlier: 3.855A pdb=" N THR B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 607 " --> pdb=" O ASN B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.632A pdb=" N ARG B 642 " --> pdb=" O ASN B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 670 through 698 removed outlier: 4.167A pdb=" N PHE B 674 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 713 Processing helix chain 'C' and resid 418 through 430 Proline residue: C 424 - end of helix removed outlier: 3.606A pdb=" N TYR C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 449 removed outlier: 3.567A pdb=" N GLN C 439 " --> pdb=" O GLY C 435 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TRP C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 477 removed outlier: 3.514A pdb=" N ASP C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 492 through 513 removed outlier: 4.076A pdb=" N GLN C 496 " --> pdb=" O PHE C 492 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR C 497 " --> pdb=" O GLY C 493 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C 498 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 506 " --> pdb=" O ASN C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 544 removed outlier: 4.212A pdb=" N LEU C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 522 " --> pdb=" O ALA C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 561 Processing helix chain 'C' and resid 564 through 575 removed outlier: 4.016A pdb=" N PHE C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 573 " --> pdb=" O GLY C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 607 removed outlier: 3.548A pdb=" N THR C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 638 through 652 removed outlier: 3.594A pdb=" N ARG C 642 " --> pdb=" O ASN C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 Processing helix chain 'C' and resid 670 through 698 removed outlier: 4.017A pdb=" N PHE C 674 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 713 Processing helix chain 'D' and resid 418 through 430 Proline residue: D 424 - end of helix removed outlier: 3.706A pdb=" N ILE D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 449 removed outlier: 3.512A pdb=" N GLN D 439 " --> pdb=" O GLY D 435 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL D 446 " --> pdb=" O ASP D 442 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TRP D 447 " --> pdb=" O ALA D 443 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 477 removed outlier: 3.522A pdb=" N ASP D 477 " --> pdb=" O ASP D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 Processing helix chain 'D' and resid 494 through 513 removed outlier: 3.676A pdb=" N ILE D 498 " --> pdb=" O LEU D 494 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU D 505 " --> pdb=" O ALA D 501 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 544 removed outlier: 3.841A pdb=" N ASN D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 575 removed outlier: 3.525A pdb=" N GLY D 562 " --> pdb=" O GLU D 558 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 564 " --> pdb=" O LYS D 560 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE D 565 " --> pdb=" O THR D 561 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 573 " --> pdb=" O GLY D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 607 removed outlier: 3.570A pdb=" N ALA D 607 " --> pdb=" O ASN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 635 Processing helix chain 'D' and resid 638 through 652 removed outlier: 3.829A pdb=" N ARG D 642 " --> pdb=" O ASN D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 670 Processing helix chain 'D' and resid 670 through 698 removed outlier: 3.924A pdb=" N PHE D 674 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 713 Processing helix chain 'E' and resid 418 through 430 Proline residue: E 424 - end of helix removed outlier: 3.791A pdb=" N ILE E 428 " --> pdb=" O PRO E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 449 removed outlier: 4.249A pdb=" N VAL E 446 " --> pdb=" O ASP E 442 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP E 447 " --> pdb=" O ALA E 443 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 477 Processing helix chain 'E' and resid 488 through 493 Processing helix chain 'E' and resid 494 through 513 removed outlier: 3.663A pdb=" N ILE E 498 " --> pdb=" O LEU E 494 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU E 505 " --> pdb=" O ALA E 501 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL E 506 " --> pdb=" O ASN E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 516 No H-bonds generated for 'chain 'E' and resid 514 through 516' Processing helix chain 'E' and resid 517 through 544 removed outlier: 4.203A pdb=" N LEU E 521 " --> pdb=" O ASP E 517 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU E 522 " --> pdb=" O ALA E 518 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN E 530 " --> pdb=" O GLU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 575 removed outlier: 4.562A pdb=" N LEU E 564 " --> pdb=" O LYS E 560 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE E 565 " --> pdb=" O THR E 561 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE E 568 " --> pdb=" O LEU E 564 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA E 573 " --> pdb=" O GLY E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 607 removed outlier: 3.668A pdb=" N ALA E 607 " --> pdb=" O ASN E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 635 Processing helix chain 'E' and resid 638 through 652 removed outlier: 3.820A pdb=" N ARG E 642 " --> pdb=" O ASN E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 670 Processing helix chain 'E' and resid 670 through 698 removed outlier: 4.102A pdb=" N PHE E 674 " --> pdb=" O GLY E 670 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN E 676 " --> pdb=" O LEU E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 713 removed outlier: 3.825A pdb=" N LEU E 706 " --> pdb=" O PHE E 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 430 Proline residue: F 424 - end of helix Processing helix chain 'F' and resid 435 through 449 removed outlier: 3.580A pdb=" N GLN F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL F 446 " --> pdb=" O ASP F 442 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TRP F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 477 Processing helix chain 'F' and resid 488 through 493 removed outlier: 3.621A pdb=" N GLY F 493 " --> pdb=" O HIS F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 514 removed outlier: 3.659A pdb=" N ILE F 498 " --> pdb=" O LEU F 494 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU F 505 " --> pdb=" O ALA F 501 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL F 506 " --> pdb=" O ASN F 502 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN F 513 " --> pdb=" O LEU F 509 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS F 514 " --> pdb=" O GLN F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 544 removed outlier: 4.310A pdb=" N LEU F 522 " --> pdb=" O ALA F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 575 removed outlier: 3.646A pdb=" N GLY F 563 " --> pdb=" O HIS F 559 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU F 564 " --> pdb=" O LYS F 560 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE F 565 " --> pdb=" O THR F 561 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE F 568 " --> pdb=" O LEU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 610 removed outlier: 3.878A pdb=" N THR F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR F 610 " --> pdb=" O SER F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 635 Processing helix chain 'F' and resid 638 through 652 removed outlier: 3.824A pdb=" N ARG F 642 " --> pdb=" O ASN F 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 670 Processing helix chain 'F' and resid 670 through 698 removed outlier: 4.172A pdb=" N PHE F 674 " --> pdb=" O GLY F 670 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN F 676 " --> pdb=" O LEU F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 713 Processing helix chain 'G' and resid 418 through 430 Proline residue: G 424 - end of helix removed outlier: 3.654A pdb=" N ILE G 428 " --> pdb=" O PRO G 424 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 430 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 449 removed outlier: 4.144A pdb=" N VAL G 446 " --> pdb=" O ASP G 442 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TRP G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 478 Processing helix chain 'G' and resid 488 through 491 Processing helix chain 'G' and resid 494 through 513 removed outlier: 3.639A pdb=" N ILE G 498 " --> pdb=" O LEU G 494 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU G 505 " --> pdb=" O ALA G 501 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL G 506 " --> pdb=" O ASN G 502 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN G 513 " --> pdb=" O LEU G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 545 removed outlier: 3.679A pdb=" N ASN G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP G 538 " --> pdb=" O GLY G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 561 Processing helix chain 'G' and resid 561 through 575 removed outlier: 4.071A pdb=" N PHE G 565 " --> pdb=" O THR G 561 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE G 568 " --> pdb=" O LEU G 564 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA G 573 " --> pdb=" O GLY G 569 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 607 removed outlier: 3.616A pdb=" N ALA G 607 " --> pdb=" O ASN G 603 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 635 Processing helix chain 'G' and resid 638 through 652 removed outlier: 3.762A pdb=" N ARG G 642 " --> pdb=" O ASN G 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 655 through 670 Processing helix chain 'G' and resid 670 through 698 removed outlier: 4.019A pdb=" N PHE G 674 " --> pdb=" O GLY G 670 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN G 676 " --> pdb=" O LEU G 672 " (cutoff:3.500A) Processing helix chain 'G' and resid 702 through 713 Processing helix chain 'H' and resid 418 through 430 Proline residue: H 424 - end of helix removed outlier: 3.625A pdb=" N ILE H 428 " --> pdb=" O PRO H 424 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA H 430 " --> pdb=" O GLU H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 449 removed outlier: 3.562A pdb=" N GLN H 439 " --> pdb=" O GLY H 435 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL H 446 " --> pdb=" O ASP H 442 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TRP H 447 " --> pdb=" O ALA H 443 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 478 Processing helix chain 'H' and resid 488 through 493 Processing helix chain 'H' and resid 494 through 513 removed outlier: 3.810A pdb=" N ILE H 498 " --> pdb=" O LEU H 494 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU H 505 " --> pdb=" O ALA H 501 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL H 506 " --> pdb=" O ASN H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 518 through 545 removed outlier: 4.419A pdb=" N LEU H 522 " --> pdb=" O ALA H 518 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 523 " --> pdb=" O ARG H 519 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN H 530 " --> pdb=" O GLU H 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 549 through 575 removed outlier: 4.070A pdb=" N LEU H 564 " --> pdb=" O LYS H 560 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE H 565 " --> pdb=" O THR H 561 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE H 568 " --> pdb=" O LEU H 564 " (cutoff:3.500A) Processing helix chain 'H' and resid 584 through 607 removed outlier: 3.647A pdb=" N ALA H 607 " --> pdb=" O ASN H 603 " (cutoff:3.500A) Processing helix chain 'H' and resid 625 through 635 Processing helix chain 'H' and resid 638 through 652 removed outlier: 4.289A pdb=" N ARG H 642 " --> pdb=" O ASN H 638 " (cutoff:3.500A) Processing helix chain 'H' and resid 655 through 670 Processing helix chain 'H' and resid 670 through 698 removed outlier: 4.014A pdb=" N PHE H 674 " --> pdb=" O GLY H 670 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN H 676 " --> pdb=" O LEU H 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 702 through 713 Processing helix chain 'I' and resid 418 through 429 Proline residue: I 424 - end of helix Processing helix chain 'I' and resid 435 through 449 removed outlier: 3.686A pdb=" N GLN I 439 " --> pdb=" O GLY I 435 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL I 446 " --> pdb=" O ASP I 442 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TRP I 447 " --> pdb=" O ALA I 443 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 477 Processing helix chain 'I' and resid 488 through 513 removed outlier: 8.372A pdb=" N LEU I 494 " --> pdb=" O ASN I 490 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N GLY I 495 " --> pdb=" O ILE I 491 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN I 496 " --> pdb=" O PHE I 492 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR I 497 " --> pdb=" O GLY I 493 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE I 498 " --> pdb=" O LEU I 494 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL I 506 " --> pdb=" O ASN I 502 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN I 513 " --> pdb=" O LEU I 509 " (cutoff:3.500A) Processing helix chain 'I' and resid 518 through 544 removed outlier: 3.995A pdb=" N LEU I 522 " --> pdb=" O ALA I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 549 through 575 removed outlier: 4.829A pdb=" N LEU I 564 " --> pdb=" O LYS I 560 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE I 565 " --> pdb=" O THR I 561 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE I 568 " --> pdb=" O LEU I 564 " (cutoff:3.500A) Processing helix chain 'I' and resid 584 through 607 removed outlier: 3.749A pdb=" N ALA I 607 " --> pdb=" O ASN I 603 " (cutoff:3.500A) Processing helix chain 'I' and resid 625 through 635 Processing helix chain 'I' and resid 638 through 652 removed outlier: 3.682A pdb=" N ARG I 642 " --> pdb=" O ASN I 638 " (cutoff:3.500A) Processing helix chain 'I' and resid 655 through 670 Processing helix chain 'I' and resid 670 through 698 removed outlier: 4.136A pdb=" N PHE I 674 " --> pdb=" O GLY I 670 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN I 676 " --> pdb=" O LEU I 672 " (cutoff:3.500A) Processing helix chain 'I' and resid 702 through 713 Processing helix chain 'J' and resid 418 through 430 Proline residue: J 424 - end of helix removed outlier: 3.512A pdb=" N ILE J 428 " --> pdb=" O PRO J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 449 removed outlier: 3.501A pdb=" N GLN J 439 " --> pdb=" O GLY J 435 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL J 446 " --> pdb=" O ASP J 442 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP J 447 " --> pdb=" O ALA J 443 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 478 Processing helix chain 'J' and resid 488 through 491 Processing helix chain 'J' and resid 494 through 513 removed outlier: 3.896A pdb=" N LEU J 505 " --> pdb=" O ALA J 501 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL J 506 " --> pdb=" O ASN J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 518 through 544 removed outlier: 3.950A pdb=" N LEU J 522 " --> pdb=" O ALA J 518 " (cutoff:3.500A) Processing helix chain 'J' and resid 549 through 561 Processing helix chain 'J' and resid 561 through 575 removed outlier: 3.838A pdb=" N PHE J 565 " --> pdb=" O THR J 561 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE J 568 " --> pdb=" O LEU J 564 " (cutoff:3.500A) Processing helix chain 'J' and resid 584 through 607 removed outlier: 3.812A pdb=" N ALA J 607 " --> pdb=" O ASN J 603 " (cutoff:3.500A) Processing helix chain 'J' and resid 625 through 635 Processing helix chain 'J' and resid 638 through 652 removed outlier: 3.834A pdb=" N ARG J 642 " --> pdb=" O ASN J 638 " (cutoff:3.500A) Processing helix chain 'J' and resid 655 through 670 Processing helix chain 'J' and resid 670 through 698 removed outlier: 4.227A pdb=" N PHE J 674 " --> pdb=" O GLY J 670 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN J 676 " --> pdb=" O LEU J 672 " (cutoff:3.500A) Processing helix chain 'J' and resid 702 through 713 Processing helix chain 'K' and resid 418 through 430 Proline residue: K 424 - end of helix removed outlier: 3.543A pdb=" N ILE K 428 " --> pdb=" O PRO K 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 449 removed outlier: 4.850A pdb=" N VAL K 446 " --> pdb=" O ASP K 442 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP K 447 " --> pdb=" O ALA K 443 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 478 Processing helix chain 'K' and resid 488 through 491 Processing helix chain 'K' and resid 494 through 513 removed outlier: 3.559A pdb=" N ILE K 498 " --> pdb=" O LEU K 494 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU K 505 " --> pdb=" O ALA K 501 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL K 506 " --> pdb=" O ASN K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 514 through 516 No H-bonds generated for 'chain 'K' and resid 514 through 516' Processing helix chain 'K' and resid 517 through 544 removed outlier: 4.318A pdb=" N LEU K 521 " --> pdb=" O ASP K 517 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU K 522 " --> pdb=" O ALA K 518 " (cutoff:3.500A) Processing helix chain 'K' and resid 549 through 575 removed outlier: 4.914A pdb=" N LEU K 564 " --> pdb=" O LYS K 560 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE K 565 " --> pdb=" O THR K 561 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE K 568 " --> pdb=" O LEU K 564 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS K 575 " --> pdb=" O LEU K 571 " (cutoff:3.500A) Processing helix chain 'K' and resid 584 through 607 removed outlier: 3.876A pdb=" N ALA K 607 " --> pdb=" O ASN K 603 " (cutoff:3.500A) Processing helix chain 'K' and resid 625 through 635 Processing helix chain 'K' and resid 638 through 652 removed outlier: 3.664A pdb=" N ARG K 642 " --> pdb=" O ASN K 638 " (cutoff:3.500A) Processing helix chain 'K' and resid 655 through 670 Processing helix chain 'K' and resid 670 through 698 removed outlier: 4.055A pdb=" N PHE K 674 " --> pdb=" O GLY K 670 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN K 676 " --> pdb=" O LEU K 672 " (cutoff:3.500A) Processing helix chain 'K' and resid 702 through 713 Processing helix chain 'L' and resid 418 through 430 Proline residue: L 424 - end of helix removed outlier: 3.620A pdb=" N ILE L 428 " --> pdb=" O PRO L 424 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA L 430 " --> pdb=" O GLU L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 449 removed outlier: 3.624A pdb=" N GLN L 439 " --> pdb=" O GLY L 435 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL L 446 " --> pdb=" O ASP L 442 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TRP L 447 " --> pdb=" O ALA L 443 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 478 Processing helix chain 'L' and resid 488 through 493 Processing helix chain 'L' and resid 494 through 514 removed outlier: 3.768A pdb=" N ILE L 498 " --> pdb=" O LEU L 494 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU L 505 " --> pdb=" O ALA L 501 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL L 506 " --> pdb=" O ASN L 502 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS L 514 " --> pdb=" O GLN L 510 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 545 removed outlier: 3.586A pdb=" N VAL L 523 " --> pdb=" O ARG L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 549 through 575 removed outlier: 4.875A pdb=" N LEU L 564 " --> pdb=" O LYS L 560 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE L 565 " --> pdb=" O THR L 561 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE L 568 " --> pdb=" O LEU L 564 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 610 removed outlier: 3.509A pdb=" N THR L 588 " --> pdb=" O LEU L 584 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR L 610 " --> pdb=" O SER L 606 " (cutoff:3.500A) Processing helix chain 'L' and resid 618 through 622 Processing helix chain 'L' and resid 625 through 635 Processing helix chain 'L' and resid 638 through 652 removed outlier: 3.588A pdb=" N ARG L 642 " --> pdb=" O ASN L 638 " (cutoff:3.500A) Processing helix chain 'L' and resid 655 through 670 Processing helix chain 'L' and resid 670 through 698 removed outlier: 3.933A pdb=" N PHE L 674 " --> pdb=" O GLY L 670 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN L 676 " --> pdb=" O LEU L 672 " (cutoff:3.500A) Processing helix chain 'L' and resid 702 through 713 Processing helix chain 'M' and resid 418 through 430 Proline residue: M 424 - end of helix removed outlier: 3.608A pdb=" N ILE M 428 " --> pdb=" O PRO M 424 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 449 removed outlier: 3.560A pdb=" N GLN M 439 " --> pdb=" O GLY M 435 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL M 446 " --> pdb=" O ASP M 442 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TRP M 447 " --> pdb=" O ALA M 443 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 478 Processing helix chain 'M' and resid 488 through 491 Processing helix chain 'M' and resid 492 through 513 removed outlier: 4.378A pdb=" N GLN M 496 " --> pdb=" O PHE M 492 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR M 497 " --> pdb=" O GLY M 493 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE M 498 " --> pdb=" O LEU M 494 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU M 505 " --> pdb=" O ALA M 501 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL M 506 " --> pdb=" O ASN M 502 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN M 513 " --> pdb=" O LEU M 509 " (cutoff:3.500A) Processing helix chain 'M' and resid 517 through 545 removed outlier: 4.620A pdb=" N LEU M 521 " --> pdb=" O ASP M 517 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU M 522 " --> pdb=" O ALA M 518 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN M 530 " --> pdb=" O GLU M 526 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU M 531 " --> pdb=" O GLU M 527 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET M 537 " --> pdb=" O VAL M 533 " (cutoff:3.500A) Processing helix chain 'M' and resid 549 through 561 Processing helix chain 'M' and resid 562 through 575 removed outlier: 3.683A pdb=" N ARG M 566 " --> pdb=" O GLY M 562 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU M 567 " --> pdb=" O GLY M 563 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE M 568 " --> pdb=" O LEU M 564 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA M 573 " --> pdb=" O GLY M 569 " (cutoff:3.500A) Processing helix chain 'M' and resid 584 through 607 removed outlier: 3.539A pdb=" N THR M 588 " --> pdb=" O LEU M 584 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA M 607 " --> pdb=" O ASN M 603 " (cutoff:3.500A) Processing helix chain 'M' and resid 625 through 635 Processing helix chain 'M' and resid 638 through 652 removed outlier: 3.656A pdb=" N ARG M 642 " --> pdb=" O ASN M 638 " (cutoff:3.500A) Processing helix chain 'M' and resid 655 through 670 Processing helix chain 'M' and resid 670 through 698 removed outlier: 3.991A pdb=" N PHE M 674 " --> pdb=" O GLY M 670 " (cutoff:3.500A) Processing helix chain 'M' and resid 702 through 713 Processing helix chain 'N' and resid 417 through 430 removed outlier: 4.596A pdb=" N LEU N 421 " --> pdb=" O ASP N 417 " (cutoff:3.500A) Proline residue: N 424 - end of helix removed outlier: 3.636A pdb=" N ILE N 428 " --> pdb=" O PRO N 424 " (cutoff:3.500A) Processing helix chain 'N' and resid 435 through 449 removed outlier: 3.616A pdb=" N GLN N 439 " --> pdb=" O GLY N 435 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL N 446 " --> pdb=" O ASP N 442 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TRP N 447 " --> pdb=" O ALA N 443 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) Processing helix chain 'N' and resid 451 through 478 Processing helix chain 'N' and resid 492 through 513 removed outlier: 4.481A pdb=" N GLN N 496 " --> pdb=" O PHE N 492 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR N 497 " --> pdb=" O GLY N 493 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE N 498 " --> pdb=" O LEU N 494 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU N 505 " --> pdb=" O ALA N 501 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL N 506 " --> pdb=" O ASN N 502 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN N 513 " --> pdb=" O LEU N 509 " (cutoff:3.500A) Processing helix chain 'N' and resid 517 through 545 removed outlier: 4.508A pdb=" N LEU N 521 " --> pdb=" O ASP N 517 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU N 522 " --> pdb=" O ALA N 518 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET N 537 " --> pdb=" O VAL N 533 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP N 538 " --> pdb=" O GLY N 534 " (cutoff:3.500A) Processing helix chain 'N' and resid 549 through 561 Processing helix chain 'N' and resid 562 through 575 removed outlier: 3.637A pdb=" N ARG N 566 " --> pdb=" O GLY N 562 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU N 567 " --> pdb=" O GLY N 563 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE N 568 " --> pdb=" O LEU N 564 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA N 573 " --> pdb=" O GLY N 569 " (cutoff:3.500A) Processing helix chain 'N' and resid 584 through 607 removed outlier: 3.575A pdb=" N THR N 588 " --> pdb=" O LEU N 584 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA N 607 " --> pdb=" O ASN N 603 " (cutoff:3.500A) Processing helix chain 'N' and resid 625 through 635 Processing helix chain 'N' and resid 638 through 652 removed outlier: 3.868A pdb=" N ARG N 642 " --> pdb=" O ASN N 638 " (cutoff:3.500A) Processing helix chain 'N' and resid 655 through 670 Processing helix chain 'N' and resid 670 through 698 removed outlier: 3.928A pdb=" N PHE N 674 " --> pdb=" O GLY N 670 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN N 676 " --> pdb=" O LEU N 672 " (cutoff:3.500A) Processing helix chain 'N' and resid 702 through 713 Processing helix chain 'O' and resid 417 through 430 removed outlier: 4.608A pdb=" N LEU O 421 " --> pdb=" O ASP O 417 " (cutoff:3.500A) Proline residue: O 424 - end of helix removed outlier: 3.663A pdb=" N ILE O 428 " --> pdb=" O PRO O 424 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 449 removed outlier: 3.540A pdb=" N GLN O 439 " --> pdb=" O GLY O 435 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL O 446 " --> pdb=" O ASP O 442 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TRP O 447 " --> pdb=" O ALA O 443 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE O 448 " --> pdb=" O LEU O 444 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 477 Processing helix chain 'O' and resid 488 through 491 Processing helix chain 'O' and resid 492 through 513 removed outlier: 4.412A pdb=" N GLN O 496 " --> pdb=" O PHE O 492 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR O 497 " --> pdb=" O GLY O 493 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE O 498 " --> pdb=" O LEU O 494 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU O 505 " --> pdb=" O ALA O 501 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL O 506 " --> pdb=" O ASN O 502 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN O 513 " --> pdb=" O LEU O 509 " (cutoff:3.500A) Processing helix chain 'O' and resid 517 through 545 removed outlier: 4.230A pdb=" N LEU O 521 " --> pdb=" O ASP O 517 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU O 522 " --> pdb=" O ALA O 518 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET O 537 " --> pdb=" O VAL O 533 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP O 538 " --> pdb=" O GLY O 534 " (cutoff:3.500A) Processing helix chain 'O' and resid 549 through 561 Processing helix chain 'O' and resid 562 through 575 removed outlier: 3.875A pdb=" N PHE O 568 " --> pdb=" O LEU O 564 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA O 573 " --> pdb=" O GLY O 569 " (cutoff:3.500A) Processing helix chain 'O' and resid 584 through 607 removed outlier: 3.521A pdb=" N THR O 588 " --> pdb=" O LEU O 584 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA O 607 " --> pdb=" O ASN O 603 " (cutoff:3.500A) Processing helix chain 'O' and resid 625 through 635 Processing helix chain 'O' and resid 638 through 652 removed outlier: 3.625A pdb=" N ARG O 642 " --> pdb=" O ASN O 638 " (cutoff:3.500A) Processing helix chain 'O' and resid 655 through 670 Processing helix chain 'O' and resid 670 through 698 removed outlier: 4.085A pdb=" N PHE O 674 " --> pdb=" O GLY O 670 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN O 676 " --> pdb=" O LEU O 672 " (cutoff:3.500A) Processing helix chain 'O' and resid 702 through 713 Processing helix chain 'P' and resid 418 through 430 Proline residue: P 424 - end of helix removed outlier: 3.603A pdb=" N ILE P 428 " --> pdb=" O PRO P 424 " (cutoff:3.500A) Processing helix chain 'P' and resid 435 through 449 removed outlier: 3.563A pdb=" N GLN P 439 " --> pdb=" O GLY P 435 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL P 446 " --> pdb=" O ASP P 442 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TRP P 447 " --> pdb=" O ALA P 443 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE P 448 " --> pdb=" O LEU P 444 " (cutoff:3.500A) Processing helix chain 'P' and resid 451 through 477 Processing helix chain 'P' and resid 488 through 491 Processing helix chain 'P' and resid 492 through 513 removed outlier: 4.345A pdb=" N GLN P 496 " --> pdb=" O PHE P 492 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR P 497 " --> pdb=" O GLY P 493 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE P 498 " --> pdb=" O LEU P 494 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU P 505 " --> pdb=" O ALA P 501 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL P 506 " --> pdb=" O ASN P 502 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN P 513 " --> pdb=" O LEU P 509 " (cutoff:3.500A) Processing helix chain 'P' and resid 517 through 545 removed outlier: 4.552A pdb=" N LEU P 521 " --> pdb=" O ASP P 517 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU P 522 " --> pdb=" O ALA P 518 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN P 530 " --> pdb=" O GLU P 526 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR P 532 " --> pdb=" O LEU P 528 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET P 537 " --> pdb=" O VAL P 533 " (cutoff:3.500A) Processing helix chain 'P' and resid 549 through 561 Processing helix chain 'P' and resid 562 through 575 removed outlier: 3.517A pdb=" N ARG P 566 " --> pdb=" O GLY P 562 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE P 568 " --> pdb=" O LEU P 564 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA P 573 " --> pdb=" O GLY P 569 " (cutoff:3.500A) Processing helix chain 'P' and resid 584 through 607 removed outlier: 3.624A pdb=" N ALA P 607 " --> pdb=" O ASN P 603 " (cutoff:3.500A) Processing helix chain 'P' and resid 625 through 635 Processing helix chain 'P' and resid 638 through 652 removed outlier: 3.543A pdb=" N ARG P 642 " --> pdb=" O ASN P 638 " (cutoff:3.500A) Processing helix chain 'P' and resid 655 through 670 Processing helix chain 'P' and resid 670 through 698 removed outlier: 3.972A pdb=" N PHE P 674 " --> pdb=" O GLY P 670 " (cutoff:3.500A) Processing helix chain 'P' and resid 702 through 713 Processing helix chain 'Q' and resid 418 through 430 Proline residue: Q 424 - end of helix removed outlier: 3.655A pdb=" N ILE Q 428 " --> pdb=" O PRO Q 424 " (cutoff:3.500A) Processing helix chain 'Q' and resid 435 through 449 removed outlier: 3.748A pdb=" N GLN Q 439 " --> pdb=" O GLY Q 435 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL Q 446 " --> pdb=" O ASP Q 442 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TRP Q 447 " --> pdb=" O ALA Q 443 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) Processing helix chain 'Q' and resid 451 through 478 Processing helix chain 'Q' and resid 488 through 491 Processing helix chain 'Q' and resid 492 through 513 removed outlier: 4.411A pdb=" N GLN Q 496 " --> pdb=" O PHE Q 492 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR Q 497 " --> pdb=" O GLY Q 493 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE Q 498 " --> pdb=" O LEU Q 494 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU Q 505 " --> pdb=" O ALA Q 501 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL Q 506 " --> pdb=" O ASN Q 502 " (cutoff:3.500A) Processing helix chain 'Q' and resid 518 through 545 removed outlier: 4.157A pdb=" N LEU Q 522 " --> pdb=" O ALA Q 518 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET Q 537 " --> pdb=" O VAL Q 533 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP Q 538 " --> pdb=" O GLY Q 534 " (cutoff:3.500A) Processing helix chain 'Q' and resid 549 through 561 Processing helix chain 'Q' and resid 562 through 575 removed outlier: 3.557A pdb=" N ARG Q 566 " --> pdb=" O GLY Q 562 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU Q 567 " --> pdb=" O GLY Q 563 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE Q 568 " --> pdb=" O LEU Q 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA Q 573 " --> pdb=" O GLY Q 569 " (cutoff:3.500A) Processing helix chain 'Q' and resid 584 through 607 removed outlier: 3.761A pdb=" N ALA Q 607 " --> pdb=" O ASN Q 603 " (cutoff:3.500A) Processing helix chain 'Q' and resid 625 through 635 Processing helix chain 'Q' and resid 638 through 652 Processing helix chain 'Q' and resid 655 through 670 Processing helix chain 'Q' and resid 670 through 698 removed outlier: 3.965A pdb=" N PHE Q 674 " --> pdb=" O GLY Q 670 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN Q 676 " --> pdb=" O LEU Q 672 " (cutoff:3.500A) Processing helix chain 'Q' and resid 702 through 713 Processing helix chain 'R' and resid 418 through 430 Proline residue: R 424 - end of helix removed outlier: 3.619A pdb=" N ILE R 428 " --> pdb=" O PRO R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 449 removed outlier: 3.610A pdb=" N GLN R 439 " --> pdb=" O GLY R 435 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL R 446 " --> pdb=" O ASP R 442 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP R 447 " --> pdb=" O ALA R 443 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE R 448 " --> pdb=" O LEU R 444 " (cutoff:3.500A) Processing helix chain 'R' and resid 451 through 478 Processing helix chain 'R' and resid 488 through 491 Processing helix chain 'R' and resid 493 through 513 removed outlier: 3.929A pdb=" N THR R 497 " --> pdb=" O GLY R 493 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE R 498 " --> pdb=" O LEU R 494 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU R 505 " --> pdb=" O ALA R 501 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL R 506 " --> pdb=" O ASN R 502 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN R 513 " --> pdb=" O LEU R 509 " (cutoff:3.500A) Processing helix chain 'R' and resid 519 through 545 removed outlier: 3.614A pdb=" N MET R 537 " --> pdb=" O VAL R 533 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP R 538 " --> pdb=" O GLY R 534 " (cutoff:3.500A) Processing helix chain 'R' and resid 549 through 561 Processing helix chain 'R' and resid 561 through 575 removed outlier: 4.276A pdb=" N PHE R 565 " --> pdb=" O THR R 561 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA R 573 " --> pdb=" O GLY R 569 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS R 575 " --> pdb=" O LEU R 571 " (cutoff:3.500A) Processing helix chain 'R' and resid 584 through 610 removed outlier: 3.636A pdb=" N THR R 588 " --> pdb=" O LEU R 584 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR R 610 " --> pdb=" O SER R 606 " (cutoff:3.500A) Processing helix chain 'R' and resid 625 through 635 Processing helix chain 'R' and resid 638 through 652 removed outlier: 3.656A pdb=" N ARG R 642 " --> pdb=" O ASN R 638 " (cutoff:3.500A) Processing helix chain 'R' and resid 655 through 670 Processing helix chain 'R' and resid 670 through 698 removed outlier: 3.893A pdb=" N PHE R 674 " --> pdb=" O GLY R 670 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN R 676 " --> pdb=" O LEU R 672 " (cutoff:3.500A) Processing helix chain 'R' and resid 702 through 713 removed outlier: 3.996A pdb=" N LEU R 706 " --> pdb=" O PHE R 702 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 481 through 482 Processing sheet with id=AA2, first strand: chain 'B' and resid 481 through 482 Processing sheet with id=AA3, first strand: chain 'C' and resid 481 through 482 Processing sheet with id=AA4, first strand: chain 'D' and resid 481 through 482 Processing sheet with id=AA5, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AA6, first strand: chain 'F' and resid 481 through 482 Processing sheet with id=AA7, first strand: chain 'G' and resid 481 through 482 Processing sheet with id=AA8, first strand: chain 'H' and resid 481 through 482 Processing sheet with id=AA9, first strand: chain 'I' and resid 481 through 482 Processing sheet with id=AB1, first strand: chain 'J' and resid 481 through 482 Processing sheet with id=AB2, first strand: chain 'K' and resid 481 through 482 Processing sheet with id=AB3, first strand: chain 'L' and resid 481 through 482 Processing sheet with id=AB4, first strand: chain 'M' and resid 481 through 482 Processing sheet with id=AB5, first strand: chain 'N' and resid 481 through 482 Processing sheet with id=AB6, first strand: chain 'O' and resid 481 through 482 Processing sheet with id=AB7, first strand: chain 'P' and resid 481 through 482 Processing sheet with id=AB8, first strand: chain 'Q' and resid 481 through 482 Processing sheet with id=AB9, first strand: chain 'R' and resid 481 through 482 3051 hydrogen bonds defined for protein. 9066 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: 8.41 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14292 1.34 - 1.46: 9900 1.46 - 1.58: 19404 1.58 - 1.70: 0 1.70 - 1.82: 378 Bond restraints: 43974 Sorted by residual: bond pdb=" N GLU O 608 " pdb=" CA GLU O 608 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.06e+00 bond pdb=" N GLU K 608 " pdb=" CA GLU K 608 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.73e+00 bond pdb=" CA HIS D 590 " pdb=" C HIS D 590 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.27e-02 6.20e+03 2.16e+00 bond pdb=" CA GLN M 555 " pdb=" C GLN M 555 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.28e-02 6.10e+03 1.42e+00 bond pdb=" CB GLU I 527 " pdb=" CG GLU I 527 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.38e+00 ... (remaining 43969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 59046 2.69 - 5.37: 362 5.37 - 8.06: 32 8.06 - 10.74: 10 10.74 - 13.43: 4 Bond angle restraints: 59454 Sorted by residual: angle pdb=" N VAL P 580 " pdb=" CA VAL P 580 " pdb=" C VAL P 580 " ideal model delta sigma weight residual 109.30 114.64 -5.34 1.25e+00 6.40e-01 1.82e+01 angle pdb=" N THR R 577 " pdb=" CA THR R 577 " pdb=" C THR R 577 " ideal model delta sigma weight residual 113.88 108.90 4.98 1.23e+00 6.61e-01 1.64e+01 angle pdb=" CB MET A 537 " pdb=" CG MET A 537 " pdb=" SD MET A 537 " ideal model delta sigma weight residual 112.70 124.45 -11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CA LEU R 494 " pdb=" CB LEU R 494 " pdb=" CG LEU R 494 " ideal model delta sigma weight residual 116.30 129.73 -13.43 3.50e+00 8.16e-02 1.47e+01 angle pdb=" CB MET F 537 " pdb=" CG MET F 537 " pdb=" SD MET F 537 " ideal model delta sigma weight residual 112.70 124.00 -11.30 3.00e+00 1.11e-01 1.42e+01 ... (remaining 59449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 22344 18.04 - 36.08: 3035 36.08 - 54.12: 808 54.12 - 72.16: 157 72.16 - 90.19: 80 Dihedral angle restraints: 26424 sinusoidal: 10872 harmonic: 15552 Sorted by residual: dihedral pdb=" CA PHE R 702 " pdb=" C PHE R 702 " pdb=" N GLN R 703 " pdb=" CA GLN R 703 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLU L 700 " pdb=" C GLU L 700 " pdb=" N ASN L 701 " pdb=" CA ASN L 701 " ideal model delta harmonic sigma weight residual -180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA PHE O 702 " pdb=" C PHE O 702 " pdb=" N GLN O 703 " pdb=" CA GLN O 703 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 26421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 4934 0.038 - 0.075: 1387 0.075 - 0.113: 331 0.113 - 0.150: 57 0.150 - 0.188: 5 Chirality restraints: 6714 Sorted by residual: chirality pdb=" CB VAL N 644 " pdb=" CA VAL N 644 " pdb=" CG1 VAL N 644 " pdb=" CG2 VAL N 644 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CA LEU C 465 " pdb=" N LEU C 465 " pdb=" C LEU C 465 " pdb=" CB LEU C 465 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CB VAL F 533 " pdb=" CA VAL F 533 " pdb=" CG1 VAL F 533 " pdb=" CG2 VAL F 533 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 6711 not shown) Planarity restraints: 7650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 645 " 0.022 2.00e-02 2.50e+03 1.96e-02 9.58e+00 pdb=" CG TRP I 645 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP I 645 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP I 645 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 645 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP I 645 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 645 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 645 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 645 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP I 645 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 600 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" CG ASP J 600 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP J 600 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP J 600 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 645 " -0.018 2.00e-02 2.50e+03 1.21e-02 3.67e+00 pdb=" CG TRP R 645 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP R 645 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP R 645 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 645 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 645 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 645 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 645 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 645 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 645 " -0.000 2.00e-02 2.50e+03 ... (remaining 7647 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 16866 2.92 - 3.41: 45076 3.41 - 3.91: 70708 3.91 - 4.40: 77923 4.40 - 4.90: 131799 Nonbonded interactions: 342372 Sorted by model distance: nonbonded pdb=" O LEU K 522 " pdb=" OG1 THR K 525 " model vdw 2.419 3.040 nonbonded pdb=" O HIS Q 466 " pdb=" OG SER Q 469 " model vdw 2.431 3.040 nonbonded pdb=" O HIS O 466 " pdb=" OG SER O 469 " model vdw 2.434 3.040 nonbonded pdb=" O HIS P 466 " pdb=" OG SER P 469 " model vdw 2.437 3.040 nonbonded pdb=" O GLN J 596 " pdb=" OD1 ASP J 600 " model vdw 2.440 3.040 ... (remaining 342367 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 9.580 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: 0.040 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 36.800 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 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 : 0.003 0.035 43974 Z= 0.135 Angle : 0.577 13.427 59454 Z= 0.309 Chirality : 0.037 0.188 6714 Planarity : 0.004 0.041 7650 Dihedral : 18.010 90.194 16380 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.51 % Allowed : 20.88 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.12), residues: 5292 helix: 1.74 (0.08), residues: 4104 sheet: None (None), residues: 0 loop : -1.01 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 705 TYR 0.017 0.001 TYR A 503 PHE 0.028 0.001 PHE F 568 TRP 0.053 0.002 TRP I 645 HIS 0.007 0.001 HIS J 575 Details of bonding type rmsd covalent geometry : bond 0.00266 (43974) covalent geometry : angle 0.57669 (59454) hydrogen bonds : bond 0.13988 ( 3051) hydrogen bonds : angle 5.18917 ( 9066) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 654 time to evaluate : 1.611 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: A 454 LYS cc_start: 0.4629 (mmmm) cc_final: 0.4421 (mmmm) REVERT: A 505 LEU cc_start: 0.7239 (tt) cc_final: 0.6786 (tp) REVERT: A 536 SER cc_start: 0.8032 (t) cc_final: 0.7736 (p) REVERT: B 527 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5846 (mm-30) REVERT: B 648 ARG cc_start: 0.5483 (ttm170) cc_final: 0.5109 (mtm180) REVERT: C 442 ASP cc_start: 0.7054 (t0) cc_final: 0.6777 (t0) REVERT: C 472 LEU cc_start: 0.7505 (tp) cc_final: 0.7034 (tp) REVERT: C 537 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6226 (mtp) REVERT: C 646 THR cc_start: 0.7644 (m) cc_final: 0.7367 (t) REVERT: E 472 LEU cc_start: 0.7174 (tp) cc_final: 0.6826 (tp) REVERT: E 550 MET cc_start: 0.6328 (mmt) cc_final: 0.5034 (mmt) REVERT: F 442 ASP cc_start: 0.7130 (m-30) cc_final: 0.6717 (m-30) REVERT: F 604 LEU cc_start: 0.6114 (mt) cc_final: 0.5845 (mt) REVERT: G 705 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7749 (mtt180) REVERT: I 595 PHE cc_start: 0.6662 (t80) cc_final: 0.6392 (m-80) REVERT: I 660 GLN cc_start: 0.7032 (mm110) cc_final: 0.6607 (mp10) REVERT: I 708 MET cc_start: 0.5843 (mmm) cc_final: 0.5382 (mmm) REVERT: J 556 MET cc_start: 0.7422 (tmm) cc_final: 0.7192 (ttp) REVERT: J 696 LYS cc_start: 0.6145 (mmtm) cc_final: 0.5920 (mtmt) outliers start: 24 outliers final: 13 residues processed: 670 average time/residue: 0.2515 time to fit residues: 278.6108 Evaluate side-chains 568 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 554 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 537 MET Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain F residue 433 SER Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain H residue 665 LEU Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain M residue 577 THR Chi-restraints excluded: chain N residue 567 LEU Chi-restraints excluded: chain N residue 582 VAL Chi-restraints excluded: chain O residue 689 SER Chi-restraints excluded: chain P residue 689 SER Chi-restraints excluded: chain R residue 577 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 265 optimal weight: 7.9990 chunk 497 optimal weight: 0.6980 chunk 414 optimal weight: 0.7980 chunk 310 optimal weight: 0.5980 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 chunk 516 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 GLN B 422 GLN ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 ASN D 590 HIS ** E 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 633 GLN G 703 GLN ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 638 ASN I 660 GLN J 499 ASN L 502 ASN N 603 ASN O 603 ASN P 638 ASN P 656 HIS ** Q 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 589 ASN R 603 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.246160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.208875 restraints weight = 46846.700| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 1.98 r_work: 0.4024 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 43974 Z= 0.115 Angle : 0.476 10.153 59454 Z= 0.243 Chirality : 0.036 0.152 6714 Planarity : 0.004 0.048 7650 Dihedral : 3.588 53.643 5818 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.21 % Allowed : 19.53 % Favored : 78.26 % 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: 2.45 (0.12), residues: 5292 helix: 2.37 (0.08), residues: 4086 sheet: None (None), residues: 0 loop : -1.10 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 705 TYR 0.013 0.001 TYR Q 532 PHE 0.038 0.001 PHE A 568 TRP 0.018 0.001 TRP R 645 HIS 0.004 0.001 HIS C 466 Details of bonding type rmsd covalent geometry : bond 0.00249 (43974) covalent geometry : angle 0.47563 (59454) hydrogen bonds : bond 0.03992 ( 3051) hydrogen bonds : angle 3.56017 ( 9066) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 604 time to evaluate : 1.578 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: A 505 LEU cc_start: 0.7307 (tt) cc_final: 0.7042 (tp) REVERT: A 536 SER cc_start: 0.8144 (t) cc_final: 0.7761 (p) REVERT: B 527 GLU cc_start: 0.6213 (mm-30) cc_final: 0.5757 (mm-30) REVERT: C 445 ASN cc_start: 0.7883 (t0) cc_final: 0.7592 (t0) REVERT: C 472 LEU cc_start: 0.7504 (tp) cc_final: 0.7028 (tp) REVERT: C 537 MET cc_start: 0.7811 (tpp) cc_final: 0.7464 (mmt) REVERT: C 646 THR cc_start: 0.7789 (m) cc_final: 0.7507 (t) REVERT: D 708 MET cc_start: 0.7495 (mpp) cc_final: 0.7024 (mpp) REVERT: E 428 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7015 (tt) REVERT: E 550 MET cc_start: 0.6334 (mmt) cc_final: 0.5635 (tpp) REVERT: F 442 ASP cc_start: 0.7314 (m-30) cc_final: 0.6907 (m-30) REVERT: F 474 ASP cc_start: 0.7593 (m-30) cc_final: 0.7379 (m-30) REVERT: F 604 LEU cc_start: 0.6161 (mt) cc_final: 0.5689 (mt) REVERT: G 426 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: G 465 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7500 (mm) REVERT: G 632 MET cc_start: 0.6206 (mtp) cc_final: 0.5941 (mtt) REVERT: G 705 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7953 (mtt90) REVERT: I 556 MET cc_start: 0.7410 (tmm) cc_final: 0.7107 (ttp) REVERT: I 595 PHE cc_start: 0.6772 (t80) cc_final: 0.6443 (m-80) REVERT: I 660 GLN cc_start: 0.7259 (mm-40) cc_final: 0.6730 (mp10) REVERT: J 556 MET cc_start: 0.7463 (tmm) cc_final: 0.7237 (ttp) REVERT: J 660 GLN cc_start: 0.6952 (mp10) cc_final: 0.6656 (mp10) REVERT: J 696 LYS cc_start: 0.6093 (mmtm) cc_final: 0.5881 (mtmt) REVERT: K 524 PHE cc_start: 0.5764 (t80) cc_final: 0.5447 (m-80) REVERT: K 660 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6958 (mp10) REVERT: K 708 MET cc_start: 0.5984 (mmp) cc_final: 0.5603 (mmm) REVERT: L 502 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7371 (m-40) REVERT: N 444 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8231 (mp) REVERT: N 624 PHE cc_start: 0.7023 (m-80) cc_final: 0.6791 (m-80) REVERT: R 444 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8453 (mp) outliers start: 105 outliers final: 40 residues processed: 689 average time/residue: 0.2383 time to fit residues: 275.3417 Evaluate side-chains 586 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 539 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 510 GLN Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 625 SER Chi-restraints excluded: chain H residue 625 SER Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain K residue 420 VAL Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 450 VAL Chi-restraints excluded: chain K residue 660 GLN Chi-restraints excluded: chain L residue 502 ASN Chi-restraints excluded: chain L residue 576 SER Chi-restraints excluded: chain L residue 625 SER Chi-restraints excluded: chain L residue 706 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 582 VAL Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 625 SER Chi-restraints excluded: chain O residue 420 VAL Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 582 VAL Chi-restraints excluded: chain O residue 604 LEU Chi-restraints excluded: chain O residue 706 LEU Chi-restraints excluded: chain P residue 604 LEU Chi-restraints excluded: chain P residue 638 ASN Chi-restraints excluded: chain P residue 666 MET Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 444 LEU Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 161 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 442 optimal weight: 0.2980 chunk 84 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 518 optimal weight: 1.9990 chunk 439 optimal weight: 0.5980 chunk 248 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 338 optimal weight: 0.0970 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 GLN ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 ASN D 602 GLN ** E 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 596 GLN H 513 GLN ** I 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 502 ASN L 513 GLN N 603 ASN ** P 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 638 ASN ** R 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.248518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.212619 restraints weight = 46669.236| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 1.98 r_work: 0.4039 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3975 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 43974 Z= 0.097 Angle : 0.445 8.461 59454 Z= 0.226 Chirality : 0.035 0.144 6714 Planarity : 0.003 0.045 7650 Dihedral : 3.185 24.268 5797 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.70 % Allowed : 20.71 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.12), residues: 5292 helix: 2.63 (0.08), residues: 4086 sheet: None (None), residues: 0 loop : -1.06 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 648 TYR 0.013 0.001 TYR J 532 PHE 0.030 0.001 PHE A 568 TRP 0.014 0.001 TRP P 645 HIS 0.004 0.000 HIS Q 656 Details of bonding type rmsd covalent geometry : bond 0.00206 (43974) covalent geometry : angle 0.44483 (59454) hydrogen bonds : bond 0.03370 ( 3051) hydrogen bonds : angle 3.30268 ( 9066) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 604 time to evaluate : 1.685 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: A 536 SER cc_start: 0.8041 (t) cc_final: 0.7614 (p) REVERT: B 527 GLU cc_start: 0.5951 (mm-30) cc_final: 0.5628 (mm-30) REVERT: B 697 PHE cc_start: 0.4945 (OUTLIER) cc_final: 0.4712 (t80) REVERT: B 708 MET cc_start: 0.4600 (mmp) cc_final: 0.4387 (mmm) REVERT: C 445 ASN cc_start: 0.7901 (t0) cc_final: 0.7611 (t0) REVERT: C 537 MET cc_start: 0.7727 (tpp) cc_final: 0.7322 (mmt) REVERT: C 646 THR cc_start: 0.7699 (m) cc_final: 0.7427 (t) REVERT: D 465 LEU cc_start: 0.8064 (mp) cc_final: 0.7833 (mt) REVERT: D 641 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7154 (mm) REVERT: E 428 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6903 (tt) REVERT: E 537 MET cc_start: 0.7529 (mmp) cc_final: 0.5943 (mtp) REVERT: E 550 MET cc_start: 0.6255 (mmt) cc_final: 0.5607 (tpp) REVERT: G 426 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: G 436 LEU cc_start: 0.5377 (OUTLIER) cc_final: 0.5170 (mt) REVERT: G 465 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7516 (mm) REVERT: G 705 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7982 (mtt180) REVERT: I 595 PHE cc_start: 0.6831 (t80) cc_final: 0.6418 (m-80) REVERT: I 660 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6792 (mp10) REVERT: I 708 MET cc_start: 0.5940 (mmm) cc_final: 0.5415 (mmm) REVERT: J 556 MET cc_start: 0.7423 (tmm) cc_final: 0.7189 (ttp) REVERT: J 668 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: J 696 LYS cc_start: 0.6152 (mmtm) cc_final: 0.5937 (mtpt) REVERT: K 539 LEU cc_start: 0.7951 (mm) cc_final: 0.7747 (mt) REVERT: K 660 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.7082 (mp10) REVERT: K 708 MET cc_start: 0.5942 (mmp) cc_final: 0.5540 (mmm) REVERT: N 444 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8214 (mp) REVERT: N 624 PHE cc_start: 0.6985 (m-80) cc_final: 0.6766 (m-80) REVERT: R 444 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8402 (mp) outliers start: 81 outliers final: 38 residues processed: 667 average time/residue: 0.2355 time to fit residues: 263.8000 Evaluate side-chains 600 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 552 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 510 GLN Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain F residue 536 SER Chi-restraints excluded: chain F residue 628 MET Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 625 SER Chi-restraints excluded: chain H residue 625 SER Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain J residue 668 GLU Chi-restraints excluded: chain K residue 420 VAL Chi-restraints excluded: chain K residue 450 VAL Chi-restraints excluded: chain K residue 473 ASP Chi-restraints excluded: chain K residue 660 GLN Chi-restraints excluded: chain L residue 576 SER Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 706 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 582 VAL Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 420 VAL Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 420 VAL Chi-restraints excluded: chain P residue 638 ASN Chi-restraints excluded: chain P residue 666 MET Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain Q residue 420 VAL Chi-restraints excluded: chain Q residue 580 VAL Chi-restraints excluded: chain Q residue 638 ASN Chi-restraints excluded: chain Q residue 706 LEU Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 295 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 488 optimal weight: 3.9990 chunk 515 optimal weight: 0.0670 chunk 64 optimal weight: 7.9990 chunk 258 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 349 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 GLN B 544 ASN ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 HIS D 530 ASN ** E 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 499 ASN ** I 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 502 ASN L 513 GLN M 664 ASN O 603 ASN P 638 ASN ** R 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 664 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.244339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.204584 restraints weight = 46410.603| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.02 r_work: 0.3891 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43974 Z= 0.134 Angle : 0.474 9.115 59454 Z= 0.241 Chirality : 0.036 0.158 6714 Planarity : 0.003 0.045 7650 Dihedral : 3.249 24.822 5797 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.40 % Allowed : 20.20 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.12), residues: 5292 helix: 2.55 (0.08), residues: 4104 sheet: None (None), residues: 0 loop : -1.23 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 648 TYR 0.015 0.001 TYR Q 532 PHE 0.033 0.001 PHE I 568 TRP 0.013 0.001 TRP D 645 HIS 0.004 0.001 HIS K 551 Details of bonding type rmsd covalent geometry : bond 0.00316 (43974) covalent geometry : angle 0.47405 (59454) hydrogen bonds : bond 0.04147 ( 3051) hydrogen bonds : angle 3.33920 ( 9066) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 588 time to evaluate : 1.615 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: A 536 SER cc_start: 0.8015 (t) cc_final: 0.7593 (p) REVERT: A 567 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7371 (tp) REVERT: B 527 GLU cc_start: 0.6181 (mm-30) cc_final: 0.5694 (mm-30) REVERT: B 697 PHE cc_start: 0.5165 (OUTLIER) cc_final: 0.4804 (t80) REVERT: B 708 MET cc_start: 0.4773 (mmp) cc_final: 0.4526 (mmm) REVERT: C 537 MET cc_start: 0.7916 (tpp) cc_final: 0.7537 (mmt) REVERT: C 671 THR cc_start: 0.7840 (p) cc_final: 0.7600 (p) REVERT: D 465 LEU cc_start: 0.7989 (mp) cc_final: 0.7730 (mt) REVERT: D 641 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7131 (mm) REVERT: E 428 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7056 (tt) REVERT: F 593 ARG cc_start: 0.6966 (mtt180) cc_final: 0.6684 (mtp85) REVERT: G 426 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: G 436 LEU cc_start: 0.5520 (OUTLIER) cc_final: 0.5231 (mt) REVERT: G 465 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7464 (mm) REVERT: G 660 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6658 (tt0) REVERT: G 705 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8040 (mtt180) REVERT: H 459 LYS cc_start: 0.8346 (mttm) cc_final: 0.8042 (mttt) REVERT: H 537 MET cc_start: 0.8517 (tpp) cc_final: 0.8154 (mmt) REVERT: I 527 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6175 (mm-30) REVERT: I 556 MET cc_start: 0.7394 (tmm) cc_final: 0.7140 (ttp) REVERT: I 595 PHE cc_start: 0.6930 (t80) cc_final: 0.6483 (m-80) REVERT: I 660 GLN cc_start: 0.7345 (mm-40) cc_final: 0.6868 (mp10) REVERT: J 668 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: J 696 LYS cc_start: 0.6161 (mmtm) cc_final: 0.5908 (mtpt) REVERT: K 527 GLU cc_start: 0.6292 (mp0) cc_final: 0.5967 (mp0) REVERT: K 568 PHE cc_start: 0.5268 (p90) cc_final: 0.5044 (p90) REVERT: K 660 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7140 (mp10) REVERT: K 708 MET cc_start: 0.6062 (mmp) cc_final: 0.5603 (mmm) REVERT: L 469 SER cc_start: 0.8399 (t) cc_final: 0.8060 (t) REVERT: M 436 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6597 (mt) REVERT: N 444 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8245 (mp) REVERT: N 624 PHE cc_start: 0.7143 (m-80) cc_final: 0.6903 (m-80) REVERT: O 624 PHE cc_start: 0.7069 (m-80) cc_final: 0.6832 (m-80) REVERT: P 604 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8434 (tp) REVERT: R 505 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8612 (tt) outliers start: 114 outliers final: 63 residues processed: 675 average time/residue: 0.2415 time to fit residues: 271.6449 Evaluate side-chains 627 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 550 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 695 SER Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 510 GLN Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 700 GLU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 536 SER Chi-restraints excluded: chain F residue 628 MET Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 625 SER Chi-restraints excluded: chain G residue 662 ILE Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 625 SER Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain I residue 527 GLU Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 710 LEU Chi-restraints excluded: chain J residue 668 GLU Chi-restraints excluded: chain K residue 420 VAL Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain K residue 450 VAL Chi-restraints excluded: chain K residue 473 ASP Chi-restraints excluded: chain K residue 608 GLU Chi-restraints excluded: chain K residue 660 GLN Chi-restraints excluded: chain K residue 666 MET Chi-restraints excluded: chain L residue 583 ASP Chi-restraints excluded: chain L residue 625 SER Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 706 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 582 VAL Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 625 SER Chi-restraints excluded: chain O residue 420 VAL Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 582 VAL Chi-restraints excluded: chain O residue 604 LEU Chi-restraints excluded: chain P residue 420 VAL Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 604 LEU Chi-restraints excluded: chain P residue 638 ASN Chi-restraints excluded: chain P residue 665 LEU Chi-restraints excluded: chain P residue 666 MET Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain Q residue 420 VAL Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 511 GLU Chi-restraints excluded: chain Q residue 638 ASN Chi-restraints excluded: chain Q residue 706 LEU Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 505 LEU Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 179 optimal weight: 4.9990 chunk 385 optimal weight: 0.5980 chunk 189 optimal weight: 2.9990 chunk 509 optimal weight: 0.7980 chunk 428 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 452 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 443 optimal weight: 0.6980 chunk 274 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 ASN ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN ** E 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 499 ASN ** I 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 502 ASN L 513 GLN N 603 ASN Q 581 GLN ** R 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.245433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.207115 restraints weight = 46600.351| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.10 r_work: 0.3922 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 43974 Z= 0.108 Angle : 0.447 9.366 59454 Z= 0.227 Chirality : 0.035 0.151 6714 Planarity : 0.003 0.046 7650 Dihedral : 3.163 22.480 5797 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.29 % Allowed : 20.24 % Favored : 77.46 % 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: 2.80 (0.12), residues: 5292 helix: 2.70 (0.08), residues: 4068 sheet: None (None), residues: 0 loop : -1.24 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 648 TYR 0.012 0.001 TYR Q 532 PHE 0.033 0.001 PHE I 568 TRP 0.016 0.001 TRP I 645 HIS 0.004 0.001 HIS K 551 Details of bonding type rmsd covalent geometry : bond 0.00244 (43974) covalent geometry : angle 0.44693 (59454) hydrogen bonds : bond 0.03575 ( 3051) hydrogen bonds : angle 3.22467 ( 9066) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 582 time to evaluate : 1.731 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: B 527 GLU cc_start: 0.6043 (mm-30) cc_final: 0.5630 (mm-30) REVERT: B 697 PHE cc_start: 0.5004 (OUTLIER) cc_final: 0.4674 (t80) REVERT: B 708 MET cc_start: 0.4704 (mmp) cc_final: 0.4476 (mmm) REVERT: C 465 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7794 (mm) REVERT: C 537 MET cc_start: 0.7881 (tpp) cc_final: 0.7473 (mmt) REVERT: C 671 THR cc_start: 0.7838 (p) cc_final: 0.7590 (p) REVERT: D 641 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7149 (mm) REVERT: E 428 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.6993 (tt) REVERT: E 628 MET cc_start: 0.6118 (mmp) cc_final: 0.5527 (mmm) REVERT: G 426 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: G 436 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.5222 (mt) REVERT: G 465 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7504 (mm) REVERT: G 705 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.8023 (mtt180) REVERT: I 556 MET cc_start: 0.7360 (tmm) cc_final: 0.7081 (ttp) REVERT: I 595 PHE cc_start: 0.6975 (t80) cc_final: 0.6514 (m-80) REVERT: I 660 GLN cc_start: 0.7299 (mm-40) cc_final: 0.6881 (mp10) REVERT: J 539 LEU cc_start: 0.7955 (mm) cc_final: 0.7736 (mt) REVERT: J 660 GLN cc_start: 0.7040 (mp10) cc_final: 0.6730 (mp10) REVERT: J 668 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: J 696 LYS cc_start: 0.6213 (mmtm) cc_final: 0.6009 (mtpt) REVERT: K 660 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: L 469 SER cc_start: 0.8426 (t) cc_final: 0.8093 (t) REVERT: M 436 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6669 (mt) REVERT: N 444 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8212 (mp) REVERT: N 624 PHE cc_start: 0.7103 (m-80) cc_final: 0.6779 (m-80) REVERT: O 624 PHE cc_start: 0.7004 (m-80) cc_final: 0.6767 (m-80) REVERT: P 416 LEU cc_start: 0.4240 (OUTLIER) cc_final: 0.3780 (mt) REVERT: P 436 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6682 (mt) REVERT: P 604 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8389 (tp) outliers start: 109 outliers final: 68 residues processed: 668 average time/residue: 0.2320 time to fit residues: 262.7384 Evaluate side-chains 627 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 545 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 510 GLN Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 695 SER Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain F residue 536 SER Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 628 MET Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 463 THR Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 625 SER Chi-restraints excluded: chain G residue 662 ILE Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 625 SER Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain J residue 531 LEU Chi-restraints excluded: chain J residue 668 GLU Chi-restraints excluded: chain K residue 420 VAL Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 450 VAL Chi-restraints excluded: chain K residue 473 ASP Chi-restraints excluded: chain K residue 608 GLU Chi-restraints excluded: chain K residue 660 GLN Chi-restraints excluded: chain L residue 576 SER Chi-restraints excluded: chain L residue 625 SER Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 706 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 577 THR Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 582 VAL Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 625 SER Chi-restraints excluded: chain O residue 420 VAL Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain O residue 604 LEU Chi-restraints excluded: chain O residue 706 LEU Chi-restraints excluded: chain P residue 416 LEU Chi-restraints excluded: chain P residue 420 VAL Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 436 LEU Chi-restraints excluded: chain P residue 604 LEU Chi-restraints excluded: chain P residue 665 LEU Chi-restraints excluded: chain P residue 666 MET Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain Q residue 420 VAL Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 511 GLU Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 503 optimal weight: 0.5980 chunk 326 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 405 optimal weight: 2.9990 chunk 202 optimal weight: 0.0980 chunk 322 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 363 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 GLN E 422 GLN ** E 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 513 GLN ** R 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.243076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.204973 restraints weight = 46631.218| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.09 r_work: 0.3903 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 43974 Z= 0.141 Angle : 0.482 8.654 59454 Z= 0.244 Chirality : 0.036 0.161 6714 Planarity : 0.003 0.046 7650 Dihedral : 3.252 23.465 5797 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.80 % Allowed : 20.27 % Favored : 76.94 % 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: 2.68 (0.12), residues: 5292 helix: 2.59 (0.08), residues: 4086 sheet: None (None), residues: 0 loop : -1.25 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 648 TYR 0.014 0.001 TYR P 683 PHE 0.034 0.001 PHE I 568 TRP 0.014 0.001 TRP I 645 HIS 0.004 0.001 HIS K 551 Details of bonding type rmsd covalent geometry : bond 0.00339 (43974) covalent geometry : angle 0.48160 (59454) hydrogen bonds : bond 0.04221 ( 3051) hydrogen bonds : angle 3.30796 ( 9066) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 566 time to evaluate : 1.679 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: A 567 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7510 (tp) REVERT: B 527 GLU cc_start: 0.6130 (mm-30) cc_final: 0.5715 (mm-30) REVERT: B 697 PHE cc_start: 0.5189 (OUTLIER) cc_final: 0.4759 (t80) REVERT: B 708 MET cc_start: 0.4856 (mmp) cc_final: 0.4605 (mmm) REVERT: C 465 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7851 (mm) REVERT: C 537 MET cc_start: 0.7889 (tpp) cc_final: 0.7526 (mmt) REVERT: C 641 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7259 (mt) REVERT: C 671 THR cc_start: 0.7876 (p) cc_final: 0.7655 (p) REVERT: D 641 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7144 (mm) REVERT: D 672 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7274 (mp) REVERT: E 428 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7084 (tt) REVERT: E 596 GLN cc_start: 0.7201 (tp40) cc_final: 0.6838 (mp10) REVERT: G 426 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: G 436 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.5359 (mt) REVERT: G 465 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7589 (mm) REVERT: G 660 GLN cc_start: 0.7151 (mm-40) cc_final: 0.6692 (tt0) REVERT: G 705 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8042 (mtt180) REVERT: I 537 MET cc_start: 0.6544 (mmm) cc_final: 0.6162 (mmp) REVERT: I 556 MET cc_start: 0.7314 (tmm) cc_final: 0.7051 (ttp) REVERT: I 660 GLN cc_start: 0.7308 (mm-40) cc_final: 0.6894 (mp10) REVERT: J 660 GLN cc_start: 0.7211 (mp10) cc_final: 0.6873 (mp10) REVERT: J 668 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: K 660 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7082 (mp10) REVERT: L 469 SER cc_start: 0.8438 (t) cc_final: 0.8130 (t) REVERT: L 556 MET cc_start: 0.7715 (tmm) cc_final: 0.7203 (tmm) REVERT: M 436 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6657 (mt) REVERT: M 624 PHE cc_start: 0.7125 (m-80) cc_final: 0.6902 (m-80) REVERT: M 633 GLN cc_start: 0.8052 (tp40) cc_final: 0.7188 (tt0) REVERT: N 444 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8267 (mp) REVERT: N 624 PHE cc_start: 0.7199 (m-80) cc_final: 0.6872 (m-80) REVERT: P 416 LEU cc_start: 0.4261 (OUTLIER) cc_final: 0.3805 (mt) REVERT: P 436 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6697 (mt) REVERT: P 604 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8456 (tp) outliers start: 133 outliers final: 81 residues processed: 673 average time/residue: 0.2297 time to fit residues: 262.7973 Evaluate side-chains 641 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 543 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 695 SER Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 510 GLN Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 695 SER Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 536 SER Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 628 MET Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 463 THR Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 583 ASP Chi-restraints excluded: chain G residue 625 SER Chi-restraints excluded: chain G residue 662 ILE Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain H residue 469 SER Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 542 THR Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 625 SER Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 672 LEU Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain J residue 475 VAL Chi-restraints excluded: chain J residue 668 GLU Chi-restraints excluded: chain K residue 420 VAL Chi-restraints excluded: chain K residue 450 VAL Chi-restraints excluded: chain K residue 473 ASP Chi-restraints excluded: chain K residue 608 GLU Chi-restraints excluded: chain K residue 660 GLN Chi-restraints excluded: chain L residue 576 SER Chi-restraints excluded: chain L residue 583 ASP Chi-restraints excluded: chain L residue 625 SER Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 632 MET Chi-restraints excluded: chain L residue 662 ILE Chi-restraints excluded: chain L residue 706 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 577 THR Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 582 VAL Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 625 SER Chi-restraints excluded: chain O residue 420 VAL Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 582 VAL Chi-restraints excluded: chain O residue 585 THR Chi-restraints excluded: chain O residue 604 LEU Chi-restraints excluded: chain P residue 416 LEU Chi-restraints excluded: chain P residue 420 VAL Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 436 LEU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 604 LEU Chi-restraints excluded: chain P residue 665 LEU Chi-restraints excluded: chain P residue 666 MET Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain Q residue 420 VAL Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 511 GLU Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 474 optimal weight: 0.9990 chunk 167 optimal weight: 0.0670 chunk 201 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 chunk 477 optimal weight: 3.9990 chunk 463 optimal weight: 1.9990 chunk 123 optimal weight: 0.0470 chunk 385 optimal weight: 0.9990 chunk 342 optimal weight: 6.9990 chunk 369 optimal weight: 0.1980 overall best weight: 0.4620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 HIS ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 GLN E 499 ASN ** E 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 535 GLN N 603 ASN P 603 ASN P 638 ASN Q 603 ASN ** R 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.246709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.209258 restraints weight = 46398.555| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 1.92 r_work: 0.4013 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 43974 Z= 0.095 Angle : 0.442 9.208 59454 Z= 0.223 Chirality : 0.034 0.146 6714 Planarity : 0.003 0.046 7650 Dihedral : 3.067 18.536 5797 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.19 % Allowed : 20.83 % Favored : 76.98 % 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: 2.94 (0.12), residues: 5292 helix: 2.77 (0.08), residues: 4086 sheet: None (None), residues: 0 loop : -1.14 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 483 TYR 0.011 0.001 TYR P 683 PHE 0.038 0.001 PHE K 568 TRP 0.014 0.001 TRP I 645 HIS 0.009 0.000 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00204 (43974) covalent geometry : angle 0.44206 (59454) hydrogen bonds : bond 0.03077 ( 3051) hydrogen bonds : angle 3.14227 ( 9066) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 577 time to evaluate : 2.074 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: A 567 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7543 (tp) REVERT: B 527 GLU cc_start: 0.5870 (mm-30) cc_final: 0.5558 (mm-30) REVERT: B 697 PHE cc_start: 0.4929 (OUTLIER) cc_final: 0.4590 (t80) REVERT: B 708 MET cc_start: 0.4735 (mmp) cc_final: 0.4532 (mmm) REVERT: C 465 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7751 (mm) REVERT: C 537 MET cc_start: 0.7840 (tpp) cc_final: 0.7392 (mmt) REVERT: D 641 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7190 (mm) REVERT: D 672 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6704 (mp) REVERT: E 428 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7007 (tt) REVERT: E 628 MET cc_start: 0.6044 (mmp) cc_final: 0.5188 (mmm) REVERT: G 426 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: G 436 LEU cc_start: 0.5553 (OUTLIER) cc_final: 0.5350 (mt) REVERT: G 465 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7573 (mm) REVERT: G 705 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7980 (mtt180) REVERT: I 537 MET cc_start: 0.6418 (mmm) cc_final: 0.6129 (mmt) REVERT: I 660 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6855 (mp10) REVERT: J 660 GLN cc_start: 0.7075 (mp10) cc_final: 0.6739 (mp10) REVERT: J 668 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: K 660 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: L 469 SER cc_start: 0.8396 (t) cc_final: 0.8080 (t) REVERT: L 556 MET cc_start: 0.7827 (tmm) cc_final: 0.7415 (tmm) REVERT: M 436 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6648 (mt) REVERT: M 633 GLN cc_start: 0.7935 (tp40) cc_final: 0.7234 (tt0) REVERT: N 444 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8206 (mp) REVERT: N 624 PHE cc_start: 0.7045 (m-80) cc_final: 0.6748 (m-80) REVERT: O 624 PHE cc_start: 0.6986 (m-80) cc_final: 0.6728 (m-80) REVERT: P 436 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6683 (mt) REVERT: P 604 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8352 (tp) REVERT: R 444 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8401 (mp) outliers start: 104 outliers final: 66 residues processed: 661 average time/residue: 0.2303 time to fit residues: 258.4350 Evaluate side-chains 617 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 535 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 695 SER Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 510 GLN Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain F residue 667 LYS Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 625 SER Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 625 SER Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain J residue 668 GLU Chi-restraints excluded: chain K residue 420 VAL Chi-restraints excluded: chain K residue 450 VAL Chi-restraints excluded: chain K residue 473 ASP Chi-restraints excluded: chain K residue 608 GLU Chi-restraints excluded: chain K residue 660 GLN Chi-restraints excluded: chain L residue 583 ASP Chi-restraints excluded: chain L residue 625 SER Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 706 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 577 THR Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 420 VAL Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain O residue 585 THR Chi-restraints excluded: chain O residue 604 LEU Chi-restraints excluded: chain O residue 710 LEU Chi-restraints excluded: chain P residue 420 VAL Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 436 LEU Chi-restraints excluded: chain P residue 603 ASN Chi-restraints excluded: chain P residue 604 LEU Chi-restraints excluded: chain P residue 665 LEU Chi-restraints excluded: chain P residue 666 MET Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain Q residue 420 VAL Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 511 GLU Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain R residue 444 LEU Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 511 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 312 optimal weight: 7.9990 chunk 408 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 473 optimal weight: 0.8980 chunk 300 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 455 optimal weight: 0.3980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 GLN ** E 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 603 ASN P 589 ASN P 603 ASN P 638 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.242831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.203493 restraints weight = 46487.541| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.04 r_work: 0.3860 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43974 Z= 0.136 Angle : 0.483 9.099 59454 Z= 0.245 Chirality : 0.036 0.161 6714 Planarity : 0.003 0.047 7650 Dihedral : 3.196 19.670 5796 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.23 % Allowed : 21.04 % Favored : 76.73 % 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: 2.78 (0.12), residues: 5292 helix: 2.66 (0.08), residues: 4086 sheet: None (None), residues: 0 loop : -1.20 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 483 TYR 0.015 0.001 TYR Q 532 PHE 0.038 0.001 PHE I 568 TRP 0.014 0.001 TRP I 645 HIS 0.007 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00322 (43974) covalent geometry : angle 0.48288 (59454) hydrogen bonds : bond 0.04137 ( 3051) hydrogen bonds : angle 3.28200 ( 9066) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 551 time to evaluate : 1.487 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: A 567 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7491 (tp) REVERT: B 527 GLU cc_start: 0.5966 (mm-30) cc_final: 0.5585 (mm-30) REVERT: B 697 PHE cc_start: 0.5141 (OUTLIER) cc_final: 0.4701 (t80) REVERT: B 708 MET cc_start: 0.4783 (mmp) cc_final: 0.4537 (mmm) REVERT: C 465 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7781 (mm) REVERT: C 537 MET cc_start: 0.7576 (tpp) cc_final: 0.7329 (mmt) REVERT: C 641 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7288 (mt) REVERT: D 641 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7143 (mm) REVERT: D 672 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6822 (mp) REVERT: D 708 MET cc_start: 0.8035 (mmm) cc_final: 0.7344 (mpp) REVERT: E 428 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6888 (tt) REVERT: E 628 MET cc_start: 0.6219 (mmp) cc_final: 0.5428 (mmm) REVERT: G 426 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: G 436 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.5282 (mt) REVERT: G 465 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7545 (mm) REVERT: G 705 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7991 (mtt180) REVERT: I 537 MET cc_start: 0.6354 (mmm) cc_final: 0.6123 (mmt) REVERT: I 660 GLN cc_start: 0.7268 (mm-40) cc_final: 0.6869 (mp10) REVERT: J 660 GLN cc_start: 0.7287 (mp10) cc_final: 0.6900 (mp10) REVERT: J 668 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: K 660 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: L 469 SER cc_start: 0.8355 (t) cc_final: 0.8058 (t) REVERT: L 556 MET cc_start: 0.7928 (tmm) cc_final: 0.7468 (tmm) REVERT: M 436 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6478 (mt) REVERT: N 444 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8270 (mp) REVERT: N 624 PHE cc_start: 0.7008 (m-80) cc_final: 0.6748 (m-80) REVERT: P 416 LEU cc_start: 0.4219 (OUTLIER) cc_final: 0.3945 (mp) REVERT: P 436 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6550 (mt) outliers start: 106 outliers final: 78 residues processed: 641 average time/residue: 0.2243 time to fit residues: 246.1481 Evaluate side-chains 620 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 526 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 695 SER Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 510 GLN Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 695 SER Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 536 SER Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 628 MET Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 625 SER Chi-restraints excluded: chain G residue 662 ILE Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 625 SER Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain J residue 475 VAL Chi-restraints excluded: chain J residue 531 LEU Chi-restraints excluded: chain J residue 668 GLU Chi-restraints excluded: chain K residue 420 VAL Chi-restraints excluded: chain K residue 450 VAL Chi-restraints excluded: chain K residue 473 ASP Chi-restraints excluded: chain K residue 608 GLU Chi-restraints excluded: chain K residue 660 GLN Chi-restraints excluded: chain L residue 583 ASP Chi-restraints excluded: chain L residue 625 SER Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 632 MET Chi-restraints excluded: chain L residue 706 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 577 THR Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 582 VAL Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 625 SER Chi-restraints excluded: chain O residue 420 VAL Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 582 VAL Chi-restraints excluded: chain O residue 585 THR Chi-restraints excluded: chain O residue 604 LEU Chi-restraints excluded: chain P residue 416 LEU Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 436 LEU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 638 ASN Chi-restraints excluded: chain P residue 665 LEU Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain Q residue 420 VAL Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 511 GLU Chi-restraints excluded: chain Q residue 638 ASN Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 390 optimal weight: 0.7980 chunk 284 optimal weight: 20.0000 chunk 325 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 369 optimal weight: 0.7980 chunk 354 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 282 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 389 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 GLN ** E 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 676 GLN M 603 ASN P 603 ASN P 638 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.244392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.203887 restraints weight = 46352.010| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.04 r_work: 0.3852 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 43974 Z= 0.126 Angle : 0.479 11.322 59454 Z= 0.241 Chirality : 0.036 0.157 6714 Planarity : 0.003 0.046 7650 Dihedral : 3.176 19.300 5796 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.29 % Allowed : 21.21 % Favored : 76.49 % 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: 2.75 (0.12), residues: 5292 helix: 2.64 (0.08), residues: 4086 sheet: None (None), residues: 0 loop : -1.20 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 483 TYR 0.012 0.001 TYR N 540 PHE 0.038 0.001 PHE K 568 TRP 0.014 0.001 TRP I 645 HIS 0.006 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00296 (43974) covalent geometry : angle 0.47934 (59454) hydrogen bonds : bond 0.03838 ( 3051) hydrogen bonds : angle 3.24651 ( 9066) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 546 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7486 (tp) REVERT: B 581 GLN cc_start: 0.4422 (mm-40) cc_final: 0.4202 (mm-40) REVERT: B 697 PHE cc_start: 0.5208 (OUTLIER) cc_final: 0.4740 (t80) REVERT: B 708 MET cc_start: 0.4828 (mmp) cc_final: 0.4594 (mmm) REVERT: C 465 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7757 (mm) REVERT: C 537 MET cc_start: 0.7676 (tpp) cc_final: 0.7338 (mmt) REVERT: C 641 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7233 (mt) REVERT: D 641 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7180 (mm) REVERT: D 672 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6839 (mp) REVERT: D 708 MET cc_start: 0.7965 (mmm) cc_final: 0.7549 (mpp) REVERT: E 428 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6850 (tt) REVERT: E 628 MET cc_start: 0.6159 (mmp) cc_final: 0.5454 (mmm) REVERT: F 550 MET cc_start: 0.7395 (mmt) cc_final: 0.6955 (tpp) REVERT: G 436 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5218 (mt) REVERT: G 465 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7519 (mm) REVERT: G 705 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.8007 (mtt180) REVERT: I 537 MET cc_start: 0.6380 (mmm) cc_final: 0.6123 (mmt) REVERT: I 660 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6872 (mp10) REVERT: J 660 GLN cc_start: 0.7336 (mp10) cc_final: 0.6994 (mp10) REVERT: J 668 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: K 660 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: L 469 SER cc_start: 0.8344 (t) cc_final: 0.8047 (t) REVERT: L 556 MET cc_start: 0.7928 (tmm) cc_final: 0.7576 (tmm) REVERT: M 436 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6489 (mt) REVERT: M 633 GLN cc_start: 0.7753 (tp40) cc_final: 0.7060 (tt0) REVERT: N 444 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8238 (mp) REVERT: N 624 PHE cc_start: 0.6969 (m-80) cc_final: 0.6769 (m-80) REVERT: O 624 PHE cc_start: 0.6884 (m-80) cc_final: 0.6642 (m-80) REVERT: P 416 LEU cc_start: 0.4132 (OUTLIER) cc_final: 0.3750 (mt) REVERT: P 436 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6552 (mt) outliers start: 109 outliers final: 78 residues processed: 638 average time/residue: 0.2263 time to fit residues: 247.8911 Evaluate side-chains 620 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 527 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 695 SER Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 510 GLN Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 695 SER Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain F residue 667 LYS Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 625 SER Chi-restraints excluded: chain G residue 662 ILE Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 625 SER Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 672 LEU Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain J residue 475 VAL Chi-restraints excluded: chain J residue 531 LEU Chi-restraints excluded: chain J residue 668 GLU Chi-restraints excluded: chain K residue 420 VAL Chi-restraints excluded: chain K residue 450 VAL Chi-restraints excluded: chain K residue 473 ASP Chi-restraints excluded: chain K residue 608 GLU Chi-restraints excluded: chain K residue 660 GLN Chi-restraints excluded: chain L residue 583 ASP Chi-restraints excluded: chain L residue 625 SER Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 632 MET Chi-restraints excluded: chain L residue 706 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 577 THR Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 582 VAL Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 625 SER Chi-restraints excluded: chain O residue 420 VAL Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 582 VAL Chi-restraints excluded: chain O residue 585 THR Chi-restraints excluded: chain O residue 604 LEU Chi-restraints excluded: chain P residue 416 LEU Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 436 LEU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 638 ASN Chi-restraints excluded: chain P residue 665 LEU Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain Q residue 420 VAL Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 511 GLU Chi-restraints excluded: chain Q residue 638 ASN Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 428 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 227 optimal weight: 7.9990 chunk 453 optimal weight: 0.8980 chunk 452 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 GLN ** E 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 555 GLN M 603 ASN N 603 ASN P 603 ASN P 638 ASN Q 581 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.243700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.205701 restraints weight = 46520.539| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.95 r_work: 0.3943 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43974 Z= 0.119 Angle : 0.478 9.811 59454 Z= 0.240 Chirality : 0.036 0.154 6714 Planarity : 0.003 0.046 7650 Dihedral : 3.154 18.367 5796 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.19 % Allowed : 21.55 % Favored : 76.26 % 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: 2.79 (0.12), residues: 5292 helix: 2.66 (0.08), residues: 4086 sheet: None (None), residues: 0 loop : -1.17 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 483 TYR 0.012 0.001 TYR Q 532 PHE 0.039 0.001 PHE K 568 TRP 0.015 0.001 TRP I 645 HIS 0.005 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00277 (43974) covalent geometry : angle 0.47781 (59454) hydrogen bonds : bond 0.03742 ( 3051) hydrogen bonds : angle 3.22681 ( 9066) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 540 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7624 (tp) REVERT: B 697 PHE cc_start: 0.5193 (OUTLIER) cc_final: 0.4743 (t80) REVERT: B 708 MET cc_start: 0.4835 (mmp) cc_final: 0.4634 (mmm) REVERT: C 465 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7832 (mm) REVERT: C 537 MET cc_start: 0.7828 (tpp) cc_final: 0.7427 (mmt) REVERT: C 641 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7201 (mt) REVERT: D 602 GLN cc_start: 0.6853 (mt0) cc_final: 0.6623 (mt0) REVERT: D 672 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6956 (mp) REVERT: E 428 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.7011 (tt) REVERT: E 628 MET cc_start: 0.6324 (mmp) cc_final: 0.5593 (mmm) REVERT: E 634 THR cc_start: 0.7177 (m) cc_final: 0.6948 (m) REVERT: F 550 MET cc_start: 0.7364 (mmt) cc_final: 0.6945 (tpp) REVERT: G 436 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.5340 (mt) REVERT: G 465 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7651 (mm) REVERT: G 705 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.8020 (mtt180) REVERT: I 660 GLN cc_start: 0.7165 (mm-40) cc_final: 0.6889 (mp10) REVERT: J 660 GLN cc_start: 0.7143 (mp10) cc_final: 0.6873 (mp10) REVERT: J 668 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6136 (mp0) REVERT: K 660 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: L 469 SER cc_start: 0.8405 (t) cc_final: 0.8126 (t) REVERT: L 556 MET cc_start: 0.7936 (tmm) cc_final: 0.7595 (tmm) REVERT: M 436 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6632 (mt) REVERT: M 633 GLN cc_start: 0.7820 (tp40) cc_final: 0.7179 (tt0) REVERT: N 444 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8240 (mp) REVERT: N 624 PHE cc_start: 0.7087 (m-80) cc_final: 0.6785 (m-80) REVERT: O 624 PHE cc_start: 0.7058 (m-80) cc_final: 0.6786 (m-80) REVERT: P 416 LEU cc_start: 0.4241 (OUTLIER) cc_final: 0.3842 (mt) REVERT: P 436 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6670 (mt) outliers start: 104 outliers final: 80 residues processed: 626 average time/residue: 0.2240 time to fit residues: 240.1331 Evaluate side-chains 625 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 531 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 695 SER Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 510 GLN Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain F residue 667 LYS Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 625 SER Chi-restraints excluded: chain G residue 662 ILE Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 625 SER Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 662 ILE Chi-restraints excluded: chain H residue 672 LEU Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain J residue 475 VAL Chi-restraints excluded: chain J residue 531 LEU Chi-restraints excluded: chain J residue 668 GLU Chi-restraints excluded: chain K residue 420 VAL Chi-restraints excluded: chain K residue 450 VAL Chi-restraints excluded: chain K residue 473 ASP Chi-restraints excluded: chain K residue 660 GLN Chi-restraints excluded: chain L residue 554 PHE Chi-restraints excluded: chain L residue 583 ASP Chi-restraints excluded: chain L residue 625 SER Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 706 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 577 THR Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 582 VAL Chi-restraints excluded: chain M residue 603 ASN Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 420 VAL Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 625 SER Chi-restraints excluded: chain O residue 420 VAL Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 582 VAL Chi-restraints excluded: chain O residue 585 THR Chi-restraints excluded: chain O residue 604 LEU Chi-restraints excluded: chain P residue 416 LEU Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 436 LEU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 638 ASN Chi-restraints excluded: chain P residue 665 LEU Chi-restraints excluded: chain P residue 672 LEU Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain Q residue 420 VAL Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 511 GLU Chi-restraints excluded: chain Q residue 638 ASN Chi-restraints excluded: chain Q residue 694 GLU Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 381 optimal weight: 0.6980 chunk 275 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 308 optimal weight: 10.0000 chunk 458 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 482 optimal weight: 0.5980 chunk 200 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 249 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 603 ASN P 603 ASN Q 581 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.242319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.207387 restraints weight = 46857.562| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.82 r_work: 0.4019 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3970 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43974 Z= 0.117 Angle : 0.475 9.646 59454 Z= 0.239 Chirality : 0.036 0.159 6714 Planarity : 0.003 0.046 7650 Dihedral : 3.140 17.594 5796 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.19 % Allowed : 21.51 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.12), residues: 5292 helix: 2.68 (0.08), residues: 4086 sheet: None (None), residues: 0 loop : -1.14 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 483 TYR 0.012 0.001 TYR Q 532 PHE 0.038 0.001 PHE K 568 TRP 0.015 0.001 TRP G 645 HIS 0.005 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00270 (43974) covalent geometry : angle 0.47490 (59454) hydrogen bonds : bond 0.03683 ( 3051) hydrogen bonds : angle 3.20885 ( 9066) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10640.74 seconds wall clock time: 182 minutes 47.81 seconds (10967.81 seconds total)