Starting phenix.real_space_refine on Sat Feb 7 16:35:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hpl_52333/02_2026/9hpl_52333.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hpl_52333/02_2026/9hpl_52333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hpl_52333/02_2026/9hpl_52333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hpl_52333/02_2026/9hpl_52333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hpl_52333/02_2026/9hpl_52333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hpl_52333/02_2026/9hpl_52333.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.078 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 140 5.16 5 C 19848 2.51 5 N 5576 2.21 5 O 8622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34186 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7840 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 59, 'TRANS': 918} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7840 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 59, 'TRANS': 918} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7840 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 59, 'TRANS': 918} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7840 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 59, 'TRANS': 918} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 715 Classifications: {'water': 715} Link IDs: {None: 714} Chain: "B" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 699 Classifications: {'water': 699} Link IDs: {None: 698} Chain: "C" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 709 Classifications: {'water': 709} Link IDs: {None: 708} Chain: "D" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 703 Classifications: {'water': 703} Link IDs: {None: 702} Time building chain proxies: 8.35, per 1000 atoms: 0.24 Number of scatterers: 34186 At special positions: 0 Unit cell: (152.29, 107.67, 196.91, 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 140 16.00 O 8622 8.00 N 5576 7.00 C 19848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 44 sheets defined 18.8% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 12 through 13 No H-bonds generated for 'chain 'A' and resid 12 through 13' Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.625A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.676A pdb=" N VAL A 69 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.725A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.951A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.758A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.596A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.751A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.518A pdb=" N TYR A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 606 through 607 No H-bonds generated for 'chain 'A' and resid 606 through 607' Processing helix chain 'A' and resid 614 through 624 removed outlier: 4.067A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 814 Processing helix chain 'A' and resid 923 through 926 Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 12 through 13 No H-bonds generated for 'chain 'B' and resid 12 through 13' Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.636A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.675A pdb=" N VAL B 69 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 130 through 136 removed outlier: 3.731A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.949A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 448 removed outlier: 3.758A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.596A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 removed outlier: 3.751A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.517A pdb=" N TYR B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 606 through 607 No H-bonds generated for 'chain 'B' and resid 606 through 607' Processing helix chain 'B' and resid 614 through 624 removed outlier: 4.068A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 814 Processing helix chain 'B' and resid 923 through 926 Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1004 through 1008 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 12 through 13 No H-bonds generated for 'chain 'C' and resid 12 through 13' Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.610A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 removed outlier: 3.675A pdb=" N VAL C 69 " --> pdb=" O PRO C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.725A pdb=" N LEU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.934A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 448 removed outlier: 3.759A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.596A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 removed outlier: 3.751A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.517A pdb=" N TYR C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 606 through 607 No H-bonds generated for 'chain 'C' and resid 606 through 607' Processing helix chain 'C' and resid 614 through 624 removed outlier: 4.067A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 814 Processing helix chain 'C' and resid 923 through 926 Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 972 through 976 Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 13 No H-bonds generated for 'chain 'D' and resid 12 through 13' Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.607A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.674A pdb=" N VAL D 69 " --> pdb=" O PRO D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.725A pdb=" N LEU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.950A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.759A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.596A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 removed outlier: 3.751A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.518A pdb=" N TYR D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 571 No H-bonds generated for 'chain 'D' and resid 569 through 571' Processing helix chain 'D' and resid 606 through 607 No H-bonds generated for 'chain 'D' and resid 606 through 607' Processing helix chain 'D' and resid 614 through 624 removed outlier: 4.068A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 923 through 926 Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 972 through 976 Processing helix chain 'D' and resid 1004 through 1008 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.650A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 149 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.458A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 273 removed outlier: 6.696A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU A 254 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 487 removed outlier: 7.907A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLU A 487 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 458 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 409 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N SER A 457 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP A 411 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY A 459 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG A 352 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ARG A 388 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 354 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AA8, first strand: chain 'A' and resid 661 through 669 removed outlier: 6.001A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.072A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.495A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.007A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.407A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.372A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.347A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA A 833 " --> pdb=" O THR A 829 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR A 829 " --> pdb=" O ALA A 833 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 835 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 827 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR A 837 " --> pdb=" O CYS A 825 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS A 825 " --> pdb=" O THR A 837 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA A 839 " --> pdb=" O LEU A 823 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.495A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.007A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A 941 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU A 900 " --> pdb=" O THR A 941 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 23 through 24 removed outlier: 6.649A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 149 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB5, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.458A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 265 through 273 removed outlier: 6.696A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU B 254 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AB8, first strand: chain 'B' and resid 484 through 487 removed outlier: 7.907A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLU B 487 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU B 458 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 409 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER B 457 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP B 411 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY B 459 " --> pdb=" O ASP B 411 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG B 352 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ARG B 388 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 354 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B 533 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY B 565 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B 535 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL B 567 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU B 537 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC1, first strand: chain 'B' and resid 661 through 669 removed outlier: 6.001A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 723 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU B 696 " --> pdb=" O ARG B 721 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ARG B 721 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 698 " --> pdb=" O GLN B 719 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLN B 719 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B 700 " --> pdb=" O TRP B 717 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TRP B 717 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N GLN B 702 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N SER B 715 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.059A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.500A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.406A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.372A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.348A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 833 " --> pdb=" O THR B 829 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR B 829 " --> pdb=" O ALA B 833 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 835 " --> pdb=" O ALA B 827 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA B 827 " --> pdb=" O LEU B 835 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR B 837 " --> pdb=" O CYS B 825 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N CYS B 825 " --> pdb=" O THR B 837 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 839 " --> pdb=" O LEU B 823 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.500A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR B 941 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 900 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.649A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 149 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AC7, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.457A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 265 through 273 removed outlier: 6.696A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU C 254 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD1, first strand: chain 'C' and resid 484 through 487 removed outlier: 7.907A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLU C 487 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU C 458 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 409 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER C 457 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP C 411 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY C 459 " --> pdb=" O ASP C 411 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG C 352 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ARG C 388 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 354 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AD3, first strand: chain 'C' and resid 661 through 669 removed outlier: 6.002A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.069A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.497A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.009A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.406A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.370A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.346A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA C 833 " --> pdb=" O THR C 829 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR C 829 " --> pdb=" O ALA C 833 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 835 " --> pdb=" O ALA C 827 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA C 827 " --> pdb=" O LEU C 835 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR C 837 " --> pdb=" O CYS C 825 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N CYS C 825 " --> pdb=" O THR C 837 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA C 839 " --> pdb=" O LEU C 823 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.497A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.009A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C 941 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU C 900 " --> pdb=" O THR C 941 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 23 through 24 removed outlier: 6.649A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 149 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AD9, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.457A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 265 through 273 removed outlier: 6.695A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU D 254 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AE3, first strand: chain 'D' and resid 484 through 487 removed outlier: 7.921A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU D 487 " --> pdb=" O TRP D 456 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU D 458 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL D 409 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER D 457 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP D 411 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY D 459 " --> pdb=" O ASP D 411 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG D 352 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ARG D 388 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D 354 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU D 533 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY D 565 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU D 535 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL D 567 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU D 537 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AE5, first strand: chain 'D' and resid 661 through 669 removed outlier: 6.001A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 723 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU D 696 " --> pdb=" O ARG D 721 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ARG D 721 " --> pdb=" O LEU D 696 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL D 698 " --> pdb=" O GLN D 719 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLN D 719 " --> pdb=" O VAL D 698 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 700 " --> pdb=" O TRP D 717 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TRP D 717 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLN D 702 " --> pdb=" O SER D 715 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N SER D 715 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.068A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.495A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.406A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.372A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.348A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA D 833 " --> pdb=" O THR D 829 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR D 829 " --> pdb=" O ALA D 833 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU D 835 " --> pdb=" O ALA D 827 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA D 827 " --> pdb=" O LEU D 835 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR D 837 " --> pdb=" O CYS D 825 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N CYS D 825 " --> pdb=" O THR D 837 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA D 839 " --> pdb=" O LEU D 823 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.495A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR D 941 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU D 900 " --> pdb=" O THR D 941 " (cutoff:3.500A) 1202 hydrogen bonds defined for protein. 3156 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: 10.74 Time building geometry restraints manager: 3.80 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: 10566 1.34 - 1.46: 7373 1.46 - 1.58: 14109 1.58 - 1.69: 0 1.69 - 1.81: 220 Bond restraints: 32268 Sorted by residual: bond pdb=" C VAL A 86 " pdb=" N PRO A 87 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.14e+00 bond pdb=" C VAL C 86 " pdb=" N PRO C 87 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.13e+00 bond pdb=" C VAL D 86 " pdb=" N PRO D 87 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.13e+00 bond pdb=" C VAL B 86 " pdb=" N PRO B 87 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.13e+00 bond pdb=" C GLU C 681 " pdb=" N LEU C 682 " ideal model delta sigma weight residual 1.331 1.302 0.029 2.83e-02 1.25e+03 1.04e+00 ... (remaining 32263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 42332 1.46 - 2.93: 1400 2.93 - 4.39: 226 4.39 - 5.86: 30 5.86 - 7.32: 16 Bond angle restraints: 44004 Sorted by residual: angle pdb=" CA TRP C 553 " pdb=" CB TRP C 553 " pdb=" CG TRP C 553 " ideal model delta sigma weight residual 113.60 106.32 7.28 1.90e+00 2.77e-01 1.47e+01 angle pdb=" CA TRP D 553 " pdb=" CB TRP D 553 " pdb=" CG TRP D 553 " ideal model delta sigma weight residual 113.60 106.33 7.27 1.90e+00 2.77e-01 1.46e+01 angle pdb=" CA TRP B 553 " pdb=" CB TRP B 553 " pdb=" CG TRP B 553 " ideal model delta sigma weight residual 113.60 106.38 7.22 1.90e+00 2.77e-01 1.44e+01 angle pdb=" CA TRP A 553 " pdb=" CB TRP A 553 " pdb=" CG TRP A 553 " ideal model delta sigma weight residual 113.60 106.38 7.22 1.90e+00 2.77e-01 1.44e+01 angle pdb=" C ASN D 147 " pdb=" N SER D 148 " pdb=" CA SER D 148 " ideal model delta sigma weight residual 121.54 127.35 -5.81 1.91e+00 2.74e-01 9.25e+00 ... (remaining 43999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 16649 17.73 - 35.46: 1595 35.46 - 53.19: 422 53.19 - 70.92: 179 70.92 - 88.65: 63 Dihedral angle restraints: 18908 sinusoidal: 7620 harmonic: 11288 Sorted by residual: dihedral pdb=" CA PHE C 957 " pdb=" C PHE C 957 " pdb=" N ASN C 958 " pdb=" CA ASN C 958 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PHE A 957 " pdb=" C PHE A 957 " pdb=" N ASN A 958 " pdb=" CA ASN A 958 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA PHE D 957 " pdb=" C PHE D 957 " pdb=" N ASN D 958 " pdb=" CA ASN D 958 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 18905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2729 0.032 - 0.063: 1212 0.063 - 0.095: 400 0.095 - 0.127: 236 0.127 - 0.158: 51 Chirality restraints: 4628 Sorted by residual: chirality pdb=" CA TRP C 553 " pdb=" N TRP C 553 " pdb=" C TRP C 553 " pdb=" CB TRP C 553 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA TRP A 553 " pdb=" N TRP A 553 " pdb=" C TRP A 553 " pdb=" CB TRP A 553 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA TRP B 553 " pdb=" N TRP B 553 " pdb=" C TRP B 553 " pdb=" CB TRP B 553 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.26e-01 ... (remaining 4625 not shown) Planarity restraints: 5792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 553 " -0.027 2.00e-02 2.50e+03 1.48e-02 5.48e+00 pdb=" CG TRP B 553 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 553 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP B 553 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 553 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 553 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 553 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 553 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 553 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 553 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 553 " 0.027 2.00e-02 2.50e+03 1.48e-02 5.47e+00 pdb=" CG TRP D 553 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP D 553 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 553 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 553 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 553 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 553 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 553 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 553 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 553 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 553 " 0.027 2.00e-02 2.50e+03 1.48e-02 5.47e+00 pdb=" CG TRP A 553 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 553 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 553 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 553 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 553 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 553 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 553 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 553 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 553 " 0.005 2.00e-02 2.50e+03 ... (remaining 5789 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1138 2.63 - 3.20: 29182 3.20 - 3.76: 60874 3.76 - 4.33: 91818 4.33 - 4.90: 136028 Nonbonded interactions: 319040 Sorted by model distance: nonbonded pdb=" OG1 THR A 855 " pdb=" OG1 THR A 867 " model vdw 2.062 3.040 nonbonded pdb=" OG1 THR B 855 " pdb=" OG1 THR B 867 " model vdw 2.062 3.040 nonbonded pdb=" OG1 THR C 855 " pdb=" OG1 THR C 867 " model vdw 2.062 3.040 nonbonded pdb=" OG1 THR D 855 " pdb=" OG1 THR D 867 " model vdw 2.064 3.040 nonbonded pdb=" OG1 THR B 317 " pdb=" OD1 ASP B 319 " model vdw 2.111 3.040 ... (remaining 319035 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 37.130 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 0.033 32268 Z= 0.155 Angle : 0.644 7.319 44004 Z= 0.360 Chirality : 0.046 0.158 4628 Planarity : 0.005 0.054 5792 Dihedral : 16.944 88.652 11628 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 1.65 % Allowed : 13.99 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.13), residues: 3880 helix: 0.04 (0.23), residues: 468 sheet: 0.95 (0.14), residues: 1288 loop : -0.37 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 292 TYR 0.014 0.002 TYR B 486 PHE 0.012 0.001 PHE A 747 TRP 0.037 0.002 TRP D 553 HIS 0.008 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00314 (32268) covalent geometry : angle 0.64434 (44004) hydrogen bonds : bond 0.13730 ( 1146) hydrogen bonds : angle 6.51082 ( 3156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 434 time to evaluate : 1.350 Fit side-chains REVERT: A 745 MET cc_start: 0.6650 (mpp) cc_final: 0.6234 (ttm) outliers start: 55 outliers final: 49 residues processed: 476 average time/residue: 0.9607 time to fit residues: 527.9984 Evaluate side-chains 477 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 428 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 38 ASN A 245 GLN A 359 HIS A 365 GLN A 374 GLN A 540 HIS A 614 HIS A 624 GLN A 693 GLN A 735 HIS A 890 GLN A 974 HIS A1022 GLN B 38 ASN B 93 HIS B 245 GLN B 359 HIS B 365 GLN B 374 GLN B 614 HIS B 735 HIS B 890 GLN B 974 HIS C 12 GLN C 38 ASN C 245 GLN C 359 HIS C 365 GLN C 374 GLN C 614 HIS C 624 GLN C 693 GLN C 735 HIS C 890 GLN C 974 HIS C1022 GLN D 12 GLN D 38 ASN D 245 GLN D 359 HIS D 365 GLN D 374 GLN D 614 HIS D 693 GLN D 735 HIS D 890 GLN D 974 HIS D1022 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116590 restraints weight = 30379.086| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.08 r_work: 0.3107 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 32268 Z= 0.172 Angle : 0.630 7.708 44004 Z= 0.339 Chirality : 0.047 0.161 4628 Planarity : 0.005 0.046 5792 Dihedral : 7.297 56.937 4355 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 2.49 % Allowed : 12.58 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.13), residues: 3880 helix: 0.38 (0.23), residues: 480 sheet: 0.92 (0.14), residues: 1324 loop : -0.30 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 352 TYR 0.013 0.002 TYR D 486 PHE 0.015 0.002 PHE A 989 TRP 0.037 0.002 TRP B 553 HIS 0.008 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00373 (32268) covalent geometry : angle 0.62997 (44004) hydrogen bonds : bond 0.04729 ( 1146) hydrogen bonds : angle 5.58104 ( 3156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 445 time to evaluate : 1.342 Fit side-chains REVERT: A 131 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6580 (tp30) REVERT: A 630 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8124 (mtp180) REVERT: A 745 MET cc_start: 0.7020 (mpp) cc_final: 0.6796 (mmt) REVERT: A 863 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6763 (mt0) REVERT: B 630 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8136 (mtp180) REVERT: B 863 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6784 (mt0) REVERT: C 74 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.6784 (tp) REVERT: C 131 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6617 (tp30) REVERT: C 630 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8125 (mtp180) REVERT: C 863 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6766 (mt0) REVERT: D 57 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7599 (mm-30) REVERT: D 74 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.6791 (tp) REVERT: D 131 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6582 (tp30) REVERT: D 219 THR cc_start: 0.8533 (p) cc_final: 0.8313 (t) REVERT: D 630 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8120 (mtp180) REVERT: D 819 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7186 (mp0) REVERT: D 863 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6787 (mt0) outliers start: 83 outliers final: 32 residues processed: 493 average time/residue: 0.9097 time to fit residues: 518.6481 Evaluate side-chains 474 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 436 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 863 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 207 optimal weight: 7.9990 chunk 258 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 95 optimal weight: 0.0070 chunk 194 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 326 optimal weight: 9.9990 chunk 361 optimal weight: 20.0000 chunk 322 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 38 ASN A 128 ASN A 245 GLN A 365 GLN A 374 GLN A 614 HIS A 693 GLN A 890 GLN A 974 HIS A1022 GLN B 12 GLN B 38 ASN B 128 ASN B 245 GLN B 365 GLN B 374 GLN B 614 HIS B 693 GLN B 890 GLN B 974 HIS C 12 GLN C 38 ASN C 128 ASN C 245 GLN C 365 GLN C 374 GLN C 614 HIS C 653 HIS C 693 GLN C 890 GLN C 974 HIS C1022 GLN D 12 GLN D 38 ASN D 128 ASN D 245 GLN D 365 GLN D 374 GLN D 614 HIS D 693 GLN D 890 GLN D 974 HIS D1022 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.114028 restraints weight = 30222.206| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.13 r_work: 0.3070 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 32268 Z= 0.269 Angle : 0.723 8.808 44004 Z= 0.391 Chirality : 0.052 0.214 4628 Planarity : 0.006 0.047 5792 Dihedral : 7.289 57.963 4320 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 3.33 % Allowed : 12.48 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 3880 helix: 0.23 (0.23), residues: 480 sheet: 0.81 (0.14), residues: 1336 loop : -0.39 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 352 TYR 0.016 0.003 TYR B 906 PHE 0.024 0.002 PHE D 989 TRP 0.040 0.003 TRP C 553 HIS 0.008 0.002 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00599 (32268) covalent geometry : angle 0.72345 (44004) hydrogen bonds : bond 0.05465 ( 1146) hydrogen bonds : angle 5.75452 ( 3156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 429 time to evaluate : 1.284 Fit side-chains REVERT: A 630 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8050 (mtp180) REVERT: A 681 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7707 (tm-30) REVERT: A 745 MET cc_start: 0.7045 (mpp) cc_final: 0.6752 (mmm) REVERT: A 863 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6630 (mt0) REVERT: B 74 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.6839 (tp) REVERT: B 630 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8135 (mtp180) REVERT: B 681 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7718 (tm-30) REVERT: B 863 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6658 (mt0) REVERT: C 74 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.6820 (tp) REVERT: C 630 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8137 (mtp180) REVERT: C 681 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7730 (tm-30) REVERT: C 863 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6645 (mt0) REVERT: D 74 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.6828 (tp) REVERT: D 630 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8043 (mtp180) REVERT: D 681 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7728 (tm-30) REVERT: D 863 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6659 (mt0) outliers start: 111 outliers final: 58 residues processed: 495 average time/residue: 0.9059 time to fit residues: 520.0846 Evaluate side-chains 489 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 420 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 630 ARG Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 630 ARG Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 169 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 0.0470 chunk 1 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 255 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 193 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 128 ASN A 245 GLN A 357 HIS A 365 GLN A 374 GLN A 614 HIS A 693 GLN A 890 GLN A 974 HIS A1022 GLN B 38 ASN B 128 ASN B 245 GLN B 357 HIS B 365 GLN B 374 GLN B 614 HIS B 693 GLN B 890 GLN B 974 HIS C 38 ASN C 128 ASN C 245 GLN C 365 GLN C 374 GLN C 614 HIS C 693 GLN C 890 GLN C 974 HIS C1022 GLN D 38 ASN D 128 ASN D 245 GLN D 357 HIS D 365 GLN D 374 GLN D 614 HIS D 693 GLN D 890 GLN D 974 HIS D1022 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118705 restraints weight = 30193.758| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.05 r_work: 0.3136 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32268 Z= 0.122 Angle : 0.565 7.088 44004 Z= 0.302 Chirality : 0.045 0.150 4628 Planarity : 0.005 0.048 5792 Dihedral : 6.606 56.938 4320 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 2.43 % Allowed : 13.21 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 3880 helix: 0.61 (0.23), residues: 484 sheet: 0.92 (0.14), residues: 1296 loop : -0.34 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 352 TYR 0.013 0.001 TYR A 196 PHE 0.010 0.001 PHE C 989 TRP 0.035 0.002 TRP B 553 HIS 0.011 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00262 (32268) covalent geometry : angle 0.56532 (44004) hydrogen bonds : bond 0.03971 ( 1146) hydrogen bonds : angle 5.35081 ( 3156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 439 time to evaluate : 1.342 Fit side-chains REVERT: A 74 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7263 (mp) REVERT: A 131 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6650 (tp30) REVERT: A 378 LEU cc_start: 0.8853 (mt) cc_final: 0.8644 (mt) REVERT: A 630 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8113 (mtp180) REVERT: A 681 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7712 (tm-30) REVERT: A 745 MET cc_start: 0.7042 (mpp) cc_final: 0.6756 (mmm) REVERT: A 819 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7112 (mp0) REVERT: B 74 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7287 (mp) REVERT: B 131 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6342 (tp30) REVERT: B 378 LEU cc_start: 0.8860 (mt) cc_final: 0.8651 (mt) REVERT: B 630 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8125 (mtp180) REVERT: B 681 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7728 (tm-30) REVERT: B 819 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7240 (mp0) REVERT: B 863 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6605 (mt0) REVERT: C 74 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7245 (mp) REVERT: C 131 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6677 (tp30) REVERT: C 338 GLU cc_start: 0.8193 (tt0) cc_final: 0.7990 (tm-30) REVERT: C 378 LEU cc_start: 0.8846 (mt) cc_final: 0.8637 (mt) REVERT: C 630 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8119 (mtp180) REVERT: C 681 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7741 (tm-30) REVERT: C 819 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7239 (mp0) REVERT: D 74 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7250 (mp) REVERT: D 131 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6620 (tp30) REVERT: D 378 LEU cc_start: 0.8855 (mt) cc_final: 0.8652 (mt) REVERT: D 630 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8111 (mtp180) REVERT: D 681 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7739 (tm-30) REVERT: D 819 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7086 (mp0) outliers start: 81 outliers final: 34 residues processed: 504 average time/residue: 0.8837 time to fit residues: 516.9560 Evaluate side-chains 470 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 431 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 307 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 8 optimal weight: 0.0000 chunk 120 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 245 GLN A 365 GLN A 374 GLN A 614 HIS A 693 GLN A 890 GLN A 974 HIS A1022 GLN B 38 ASN B 245 GLN B 365 GLN B 374 GLN B 614 HIS B 693 GLN B 890 GLN B 974 HIS C 38 ASN C 245 GLN C 365 GLN C 374 GLN C 614 HIS C 693 GLN C 885 ASN C 890 GLN C 974 HIS C1022 GLN D 38 ASN D 245 GLN D 365 GLN D 374 GLN D 614 HIS D 693 GLN D 890 GLN D 974 HIS D1022 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.145222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116472 restraints weight = 30141.162| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.09 r_work: 0.3106 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 32268 Z= 0.175 Angle : 0.624 7.966 44004 Z= 0.334 Chirality : 0.047 0.163 4628 Planarity : 0.005 0.048 5792 Dihedral : 6.280 57.920 4292 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.19 % Allowed : 13.69 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 3880 helix: 0.58 (0.23), residues: 480 sheet: 0.84 (0.14), residues: 1324 loop : -0.30 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 352 TYR 0.013 0.002 TYR D 486 PHE 0.016 0.002 PHE B 989 TRP 0.034 0.002 TRP B 553 HIS 0.010 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00386 (32268) covalent geometry : angle 0.62359 (44004) hydrogen bonds : bond 0.04501 ( 1146) hydrogen bonds : angle 5.45809 ( 3156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 438 time to evaluate : 1.375 Fit side-chains REVERT: A 74 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7312 (mp) REVERT: A 131 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6520 (tp30) REVERT: A 378 LEU cc_start: 0.8866 (mt) cc_final: 0.8654 (mt) REVERT: A 630 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8138 (mtp180) REVERT: A 681 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7711 (tm-30) REVERT: A 745 MET cc_start: 0.7049 (mpp) cc_final: 0.6773 (mmm) REVERT: A 819 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7111 (mp0) REVERT: A 863 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6615 (mt0) REVERT: B 74 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7339 (mp) REVERT: B 92 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7813 (mmm) REVERT: B 131 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6398 (tp30) REVERT: B 378 LEU cc_start: 0.8875 (mt) cc_final: 0.8657 (mt) REVERT: B 630 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8154 (mtp180) REVERT: B 681 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7721 (tm-30) REVERT: B 819 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7294 (mp0) REVERT: B 863 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6662 (mt0) REVERT: C 74 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7291 (mp) REVERT: C 131 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6551 (tp30) REVERT: C 370 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7379 (mm110) REVERT: C 630 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8144 (mtp180) REVERT: C 681 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7713 (tm-30) REVERT: C 819 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7292 (mp0) REVERT: C 863 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6631 (mt0) REVERT: D 74 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7295 (mp) REVERT: D 131 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6652 (tp30) REVERT: D 378 LEU cc_start: 0.8871 (mt) cc_final: 0.8657 (mt) REVERT: D 630 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8138 (mtp180) REVERT: D 681 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7718 (tm-30) REVERT: D 819 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7105 (mp0) REVERT: D 863 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6648 (mt0) outliers start: 73 outliers final: 42 residues processed: 479 average time/residue: 0.9424 time to fit residues: 521.6129 Evaluate side-chains 483 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 431 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 chunk 380 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 291 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 386 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 128 ASN A 245 GLN A 357 HIS A 365 GLN A 374 GLN A 614 HIS A 693 GLN A 890 GLN A 974 HIS A1022 GLN B 38 ASN B 128 ASN B 245 GLN B 357 HIS B 365 GLN B 374 GLN B 614 HIS B 693 GLN B 890 GLN B 974 HIS C 38 ASN C 128 ASN C 245 GLN C 365 GLN C 374 GLN C 614 HIS C 693 GLN C 885 ASN C 890 GLN C 974 HIS C1022 GLN D 38 ASN D 128 ASN D 245 GLN D 357 HIS D 365 GLN D 374 GLN D 614 HIS D 693 GLN D 890 GLN D 974 HIS D1022 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119997 restraints weight = 30177.694| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.06 r_work: 0.3161 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32268 Z= 0.108 Angle : 0.542 7.181 44004 Z= 0.288 Chirality : 0.044 0.154 4628 Planarity : 0.004 0.049 5792 Dihedral : 5.808 56.638 4290 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.07 % Allowed : 14.11 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 3880 helix: 0.81 (0.23), residues: 484 sheet: 0.99 (0.14), residues: 1296 loop : -0.30 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 439 TYR 0.011 0.001 TYR C 196 PHE 0.009 0.001 PHE A 758 TRP 0.035 0.002 TRP C 553 HIS 0.010 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00232 (32268) covalent geometry : angle 0.54204 (44004) hydrogen bonds : bond 0.03675 ( 1146) hydrogen bonds : angle 5.19230 ( 3156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 455 time to evaluate : 1.235 Fit side-chains REVERT: A 74 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7307 (mp) REVERT: A 92 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7574 (mmm) REVERT: A 131 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6531 (tp30) REVERT: A 378 LEU cc_start: 0.8845 (mt) cc_final: 0.8636 (mt) REVERT: A 630 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8136 (mtp180) REVERT: A 665 SER cc_start: 0.8834 (p) cc_final: 0.8522 (m) REVERT: A 681 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7700 (tm-30) REVERT: A 745 MET cc_start: 0.7035 (mpp) cc_final: 0.6684 (mmt) REVERT: A 819 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7090 (mp0) REVERT: B 74 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7326 (mp) REVERT: B 131 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6411 (tp30) REVERT: B 378 LEU cc_start: 0.8855 (mt) cc_final: 0.8644 (mt) REVERT: B 420 MET cc_start: 0.8473 (mmm) cc_final: 0.8244 (mmp) REVERT: B 630 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8140 (mtp180) REVERT: B 665 SER cc_start: 0.8843 (p) cc_final: 0.8523 (m) REVERT: B 681 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7709 (tm-30) REVERT: B 819 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7233 (mp0) REVERT: C 74 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7354 (mp) REVERT: C 131 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6551 (tp30) REVERT: C 338 GLU cc_start: 0.8139 (tt0) cc_final: 0.7858 (tm-30) REVERT: C 378 LEU cc_start: 0.8837 (mt) cc_final: 0.8627 (mt) REVERT: C 630 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8136 (mtp180) REVERT: C 665 SER cc_start: 0.8853 (p) cc_final: 0.8534 (m) REVERT: C 681 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7717 (tm-30) REVERT: C 819 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7233 (mp0) REVERT: D 74 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7320 (mp) REVERT: D 92 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7703 (mmm) REVERT: D 131 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6688 (tp30) REVERT: D 378 LEU cc_start: 0.8851 (mt) cc_final: 0.8646 (mt) REVERT: D 630 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8131 (mtp180) REVERT: D 665 SER cc_start: 0.8859 (p) cc_final: 0.8528 (m) REVERT: D 681 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7706 (tm-30) REVERT: D 819 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7114 (mp0) outliers start: 69 outliers final: 37 residues processed: 505 average time/residue: 0.8964 time to fit residues: 524.6352 Evaluate side-chains 489 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 446 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 223 optimal weight: 9.9990 chunk 273 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 275 optimal weight: 6.9990 chunk 363 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 302 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 128 ASN A 245 GLN A 365 GLN A 374 GLN A 614 HIS A 693 GLN A 890 GLN A 974 HIS A1022 GLN B 38 ASN B 128 ASN B 245 GLN B 365 GLN B 374 GLN B 614 HIS B 693 GLN B 890 GLN B 974 HIS C 38 ASN C 128 ASN C 245 GLN C 365 GLN C 374 GLN C 614 HIS C 693 GLN C 885 ASN C 890 GLN C 974 HIS C1022 GLN D 38 ASN D 128 ASN D 245 GLN D 365 GLN D 374 GLN D 614 HIS D 890 GLN D 974 HIS D1022 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116056 restraints weight = 30188.669| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.02 r_work: 0.3095 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 32268 Z= 0.250 Angle : 0.700 8.824 44004 Z= 0.377 Chirality : 0.051 0.205 4628 Planarity : 0.006 0.049 5792 Dihedral : 6.424 57.962 4290 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.09 % Allowed : 13.48 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 3880 helix: 0.43 (0.23), residues: 480 sheet: 0.83 (0.14), residues: 1324 loop : -0.30 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 352 TYR 0.015 0.002 TYR D 906 PHE 0.023 0.002 PHE B 989 TRP 0.033 0.003 TRP A 553 HIS 0.009 0.002 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00557 (32268) covalent geometry : angle 0.69952 (44004) hydrogen bonds : bond 0.05163 ( 1146) hydrogen bonds : angle 5.61261 ( 3156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 442 time to evaluate : 1.224 Fit side-chains REVERT: A 74 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7385 (mp) REVERT: A 92 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7646 (mmm) REVERT: A 131 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6663 (tp30) REVERT: A 344 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8962 (tt) REVERT: A 370 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7461 (mm110) REVERT: A 630 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8148 (mtp180) REVERT: A 681 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7710 (tm-30) REVERT: A 745 MET cc_start: 0.7112 (mpp) cc_final: 0.6832 (mmm) REVERT: A 819 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7251 (mp0) REVERT: A 863 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6935 (mt0) REVERT: B 74 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7406 (mp) REVERT: B 344 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8963 (tt) REVERT: B 370 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7454 (mm110) REVERT: B 630 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8147 (mtp180) REVERT: B 681 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7720 (tm-30) REVERT: B 863 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6942 (mt0) REVERT: C 74 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7311 (mp) REVERT: C 131 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6761 (tp30) REVERT: C 344 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8955 (tt) REVERT: C 630 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8196 (mtp180) REVERT: C 681 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7737 (tm-30) REVERT: C 863 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6714 (mt0) REVERT: D 74 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7350 (mp) REVERT: D 131 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6776 (tp30) REVERT: D 344 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8955 (tt) REVERT: D 370 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7457 (mm110) REVERT: D 630 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8138 (mtp180) REVERT: D 681 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7724 (tm-30) REVERT: D 819 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7214 (mp0) REVERT: D 863 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6709 (mt0) outliers start: 103 outliers final: 48 residues processed: 506 average time/residue: 0.9007 time to fit residues: 529.9281 Evaluate side-chains 500 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 432 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 630 ARG Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 630 ARG Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 194 optimal weight: 0.2980 chunk 107 optimal weight: 0.0970 chunk 167 optimal weight: 10.0000 chunk 343 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 337 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 273 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 128 ASN A 245 GLN A 357 HIS A 374 GLN A 614 HIS A 693 GLN A 890 GLN A 974 HIS A1022 GLN B 38 ASN B 128 ASN B 245 GLN B 357 HIS B 365 GLN B 374 GLN B 614 HIS B 693 GLN B 890 GLN B 974 HIS C 38 ASN C 128 ASN C 245 GLN C 365 GLN C 374 GLN C 614 HIS C 693 GLN C 885 ASN C 890 GLN C 974 HIS C1022 GLN D 38 ASN D 128 ASN D 245 GLN D 357 HIS D 365 GLN D 374 GLN D 614 HIS D 693 GLN D 890 GLN D 974 HIS D1022 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119187 restraints weight = 30235.536| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.09 r_work: 0.3148 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32268 Z= 0.107 Angle : 0.548 7.122 44004 Z= 0.292 Chirality : 0.044 0.155 4628 Planarity : 0.004 0.049 5792 Dihedral : 5.714 56.951 4284 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.25 % Allowed : 14.14 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.13), residues: 3880 helix: 0.71 (0.23), residues: 484 sheet: 0.98 (0.14), residues: 1296 loop : -0.29 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 352 TYR 0.013 0.001 TYR C 196 PHE 0.009 0.001 PHE D 758 TRP 0.037 0.002 TRP D 553 HIS 0.010 0.001 HIS D 614 Details of bonding type rmsd covalent geometry : bond 0.00232 (32268) covalent geometry : angle 0.54810 (44004) hydrogen bonds : bond 0.03704 ( 1146) hydrogen bonds : angle 5.20112 ( 3156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 447 time to evaluate : 1.409 Fit side-chains REVERT: A 74 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7276 (mp) REVERT: A 131 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6628 (tp30) REVERT: A 378 LEU cc_start: 0.8843 (mt) cc_final: 0.8633 (mt) REVERT: A 630 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8143 (mtp180) REVERT: A 681 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7633 (tm-30) REVERT: A 745 MET cc_start: 0.7026 (mpp) cc_final: 0.6615 (mmt) REVERT: A 819 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7079 (mp0) REVERT: A 863 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6529 (mt0) REVERT: B 74 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7319 (mp) REVERT: B 131 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6298 (tp30) REVERT: B 378 LEU cc_start: 0.8848 (mt) cc_final: 0.8637 (mt) REVERT: B 420 MET cc_start: 0.8497 (mmm) cc_final: 0.8253 (mmp) REVERT: B 630 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8149 (mtp180) REVERT: B 681 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7635 (tm-30) REVERT: B 819 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7213 (mp0) REVERT: B 863 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6702 (mt0) REVERT: C 74 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7294 (mp) REVERT: C 131 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6598 (tp30) REVERT: C 338 GLU cc_start: 0.8295 (tt0) cc_final: 0.8042 (tm-30) REVERT: C 378 LEU cc_start: 0.8836 (mt) cc_final: 0.8627 (mt) REVERT: C 630 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8154 (mtp180) REVERT: C 681 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7645 (tm-30) REVERT: C 819 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7208 (mp0) REVERT: C 863 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6803 (mt0) REVERT: D 74 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7325 (mp) REVERT: D 131 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6653 (tp30) REVERT: D 378 LEU cc_start: 0.8843 (mt) cc_final: 0.8638 (mt) REVERT: D 420 MET cc_start: 0.8452 (mmm) cc_final: 0.8251 (mmp) REVERT: D 630 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8146 (mtp180) REVERT: D 681 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7637 (tm-30) REVERT: D 819 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7079 (mp0) REVERT: D 863 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6564 (mt0) outliers start: 75 outliers final: 41 residues processed: 503 average time/residue: 0.8995 time to fit residues: 524.4989 Evaluate side-chains 485 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 436 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 24 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 341 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 289 optimal weight: 0.5980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 128 ASN A 245 GLN A 374 GLN A 614 HIS A 693 GLN A 885 ASN A 890 GLN A 974 HIS A1022 GLN B 38 ASN B 128 ASN B 245 GLN B 374 GLN B 614 HIS B 693 GLN B 890 GLN B 974 HIS C 38 ASN C 128 ASN C 245 GLN C 365 GLN C 374 GLN C 614 HIS C 693 GLN C 885 ASN C 890 GLN C 974 HIS C1022 GLN D 38 ASN D 128 ASN D 245 GLN D 374 GLN D 614 HIS D 693 GLN D 885 ASN D 890 GLN D 974 HIS D1022 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116618 restraints weight = 30038.585| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.04 r_work: 0.3122 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32268 Z= 0.173 Angle : 0.621 9.574 44004 Z= 0.332 Chirality : 0.047 0.161 4628 Planarity : 0.005 0.049 5792 Dihedral : 5.940 57.304 4284 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.07 % Allowed : 14.62 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.13), residues: 3880 helix: 0.61 (0.23), residues: 480 sheet: 0.87 (0.14), residues: 1324 loop : -0.26 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 352 TYR 0.013 0.002 TYR D 486 PHE 0.015 0.002 PHE B 989 TRP 0.031 0.002 TRP D 553 HIS 0.009 0.001 HIS D 614 Details of bonding type rmsd covalent geometry : bond 0.00383 (32268) covalent geometry : angle 0.62120 (44004) hydrogen bonds : bond 0.04370 ( 1146) hydrogen bonds : angle 5.35555 ( 3156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 436 time to evaluate : 1.157 Fit side-chains REVERT: A 74 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7313 (mp) REVERT: A 131 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6684 (tp30) REVERT: A 630 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8146 (mtp180) REVERT: A 681 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7619 (tm-30) REVERT: A 745 MET cc_start: 0.7055 (mpp) cc_final: 0.6671 (mmt) REVERT: A 819 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7160 (mp0) REVERT: A 863 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6734 (mt0) REVERT: B 74 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7360 (mp) REVERT: B 131 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6445 (tp30) REVERT: B 630 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8149 (mtp180) REVERT: B 681 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7629 (tm-30) REVERT: B 819 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7306 (mp0) REVERT: B 863 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6915 (mt0) REVERT: C 74 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7341 (mp) REVERT: C 131 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6688 (tp30) REVERT: C 338 GLU cc_start: 0.8178 (tt0) cc_final: 0.7915 (tm-30) REVERT: C 630 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8157 (mtp180) REVERT: C 681 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7641 (tm-30) REVERT: C 819 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7303 (mp0) REVERT: C 863 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6559 (mt0) REVERT: D 74 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7336 (mp) REVERT: D 131 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6732 (tp30) REVERT: D 630 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8140 (mtp180) REVERT: D 681 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7621 (tm-30) REVERT: D 745 MET cc_start: 0.7045 (mmm) cc_final: 0.6333 (pmm) REVERT: D 819 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7169 (mp0) REVERT: D 863 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6669 (mt0) outliers start: 69 outliers final: 39 residues processed: 485 average time/residue: 0.8828 time to fit residues: 495.7902 Evaluate side-chains 488 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 439 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 630 ARG Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 72 optimal weight: 9.9990 chunk 58 optimal weight: 0.0770 chunk 372 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 282 optimal weight: 0.2980 chunk 181 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.8744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 128 ASN A 245 GLN A 374 GLN A 614 HIS A 885 ASN A 890 GLN A1022 GLN B 38 ASN B 128 ASN B 245 GLN B 374 GLN B 614 HIS B 693 GLN B 890 GLN C 38 ASN C 128 ASN C 245 GLN C 365 GLN C 374 GLN C 614 HIS C 693 GLN C 885 ASN C 890 GLN C 974 HIS C1022 GLN D 38 ASN D 128 ASN D 245 GLN D 374 GLN D 614 HIS D 693 GLN D 885 ASN D 890 GLN D1022 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.146921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.118056 restraints weight = 30256.014| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.08 r_work: 0.3127 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32268 Z= 0.139 Angle : 0.589 9.611 44004 Z= 0.314 Chirality : 0.046 0.155 4628 Planarity : 0.005 0.048 5792 Dihedral : 5.801 57.180 4284 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.01 % Allowed : 14.68 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 3880 helix: 0.68 (0.23), residues: 480 sheet: 0.95 (0.14), residues: 1296 loop : -0.28 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 352 TYR 0.013 0.002 TYR D 486 PHE 0.012 0.001 PHE B 989 TRP 0.032 0.002 TRP D 553 HIS 0.010 0.001 HIS D 614 Details of bonding type rmsd covalent geometry : bond 0.00306 (32268) covalent geometry : angle 0.58865 (44004) hydrogen bonds : bond 0.04058 ( 1146) hydrogen bonds : angle 5.27529 ( 3156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 436 time to evaluate : 1.440 Fit side-chains REVERT: A 74 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7304 (mp) REVERT: A 131 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6734 (tp30) REVERT: A 378 LEU cc_start: 0.8848 (mt) cc_final: 0.8633 (mt) REVERT: A 630 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8135 (mtp180) REVERT: A 681 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7601 (tm-30) REVERT: A 745 MET cc_start: 0.7014 (mpp) cc_final: 0.6619 (mmt) REVERT: A 819 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7110 (mp0) REVERT: A 863 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6571 (mt0) REVERT: A 968 MET cc_start: 0.8507 (ttt) cc_final: 0.8217 (mtm) REVERT: B 74 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7345 (mp) REVERT: B 131 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6392 (tp30) REVERT: B 630 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8144 (mtp180) REVERT: B 681 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7598 (tm-30) REVERT: B 819 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7257 (mp0) REVERT: B 863 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6757 (mt0) REVERT: B 968 MET cc_start: 0.8498 (ttt) cc_final: 0.8204 (mtm) REVERT: C 74 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7329 (mp) REVERT: C 131 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6634 (tp30) REVERT: C 338 GLU cc_start: 0.8161 (tt0) cc_final: 0.7875 (tm-30) REVERT: C 630 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8147 (mtp180) REVERT: C 681 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7615 (tm-30) REVERT: C 819 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7252 (mp0) REVERT: C 863 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6753 (mt0) REVERT: C 968 MET cc_start: 0.8494 (ttt) cc_final: 0.8199 (mtm) REVERT: D 74 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7326 (mp) REVERT: D 131 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6711 (tp30) REVERT: D 630 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8139 (mtp180) REVERT: D 681 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7600 (tm-30) REVERT: D 745 MET cc_start: 0.7039 (mmm) cc_final: 0.6303 (pmm) REVERT: D 819 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7124 (mp0) REVERT: D 863 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6572 (mt0) REVERT: D 968 MET cc_start: 0.8511 (ttt) cc_final: 0.8216 (mtm) outliers start: 67 outliers final: 46 residues processed: 487 average time/residue: 0.9056 time to fit residues: 510.7931 Evaluate side-chains 492 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 437 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 373 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 252 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 345 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 341 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 320 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 overall best weight: 1.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 128 ASN A 245 GLN A 374 GLN A 614 HIS A 693 GLN A 885 ASN A 890 GLN A 974 HIS A1022 GLN B 38 ASN B 128 ASN B 245 GLN B 374 GLN B 614 HIS B 890 GLN B 974 HIS C 38 ASN C 128 ASN C 245 GLN C 365 GLN C 374 GLN C 614 HIS C 885 ASN C 890 GLN C1022 GLN D 38 ASN D 128 ASN D 245 GLN D 374 GLN D 614 HIS D 885 ASN D 890 GLN D 974 HIS D1022 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118040 restraints weight = 30181.941| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.08 r_work: 0.3128 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32268 Z= 0.139 Angle : 0.590 9.326 44004 Z= 0.315 Chirality : 0.046 0.153 4628 Planarity : 0.005 0.048 5792 Dihedral : 5.780 57.278 4284 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.13 % Allowed : 14.41 % Favored : 83.46 % 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: 0.36 (0.13), residues: 3880 helix: 0.68 (0.23), residues: 480 sheet: 0.88 (0.14), residues: 1324 loop : -0.24 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1013 TYR 0.013 0.002 TYR D 486 PHE 0.013 0.001 PHE D 989 TRP 0.032 0.002 TRP C 553 HIS 0.010 0.001 HIS D 614 Details of bonding type rmsd covalent geometry : bond 0.00305 (32268) covalent geometry : angle 0.59038 (44004) hydrogen bonds : bond 0.04056 ( 1146) hydrogen bonds : angle 5.25887 ( 3156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15332.28 seconds wall clock time: 260 minutes 58.86 seconds (15658.86 seconds total)