Starting phenix.real_space_refine on Mon Jul 6 06:21:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ri6_19181/07_2026/8ri6_19181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ri6_19181/07_2026/8ri6_19181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ri6_19181/07_2026/8ri6_19181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ri6_19181/07_2026/8ri6_19181.map" model { file = "/net/cci-nas-00/data/ceres_data/8ri6_19181/07_2026/8ri6_19181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ri6_19181/07_2026/8ri6_19181.cif" } resolution = 2.06 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 8 5.21 5 S 156 5.16 5 Na 8 4.78 5 C 20643 2.51 5 N 5768 2.21 5 O 7067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33650 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 8159 Classifications: {'peptide': 1016} Link IDs: {'CIS': 4, 'PCIS': 4, 'PTRANS': 58, 'TRANS': 949} Chain breaks: 1 Chain: "B" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 8159 Classifications: {'peptide': 1016} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 951} Chain breaks: 1 Chain: "C" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 8159 Classifications: {'peptide': 1016} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 58, 'TRANS': 952} Chain breaks: 1 Chain: "D" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 8159 Classifications: {'peptide': 1016} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 951} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 2 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 2 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 2 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 2 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "A" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 247 Classifications: {'water': 247} Link IDs: {None: 246} Chain: "B" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 249 Classifications: {'water': 249} Link IDs: {None: 248} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 251 Classifications: {'water': 251} Link IDs: {None: 250} Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 251 Classifications: {'water': 251} Link IDs: {None: 250} Time building chain proxies: 6.45, per 1000 atoms: 0.19 Number of scatterers: 33650 At special positions: 0 Unit cell: (150.411, 195.285, 102.213, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 156 16.00 Mg 8 11.99 Na 8 11.00 O 7067 8.00 N 5768 7.00 C 20643 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: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7560 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 53 sheets defined 18.8% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 3 through 6 Processing helix chain 'A' and resid 7 through 12 Processing helix chain 'A' and resid 15 through 19 removed outlier: 3.555A pdb=" N ASN A 19 " --> pdb=" O ASP A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.578A pdb=" N GLY A 95 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.580A pdb=" N LEU A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 396 through 407 removed outlier: 4.173A pdb=" N TYR A 400 " --> pdb=" O HIS A 396 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 433 through 449 removed outlier: 3.817A pdb=" N MET A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.527A pdb=" N ASP A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.869A pdb=" N SER A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.576A pdb=" N TYR A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.990A pdb=" N CYS A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 625 removed outlier: 3.920A pdb=" N GLU A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 806 through 815 Processing helix chain 'A' and resid 924 through 927 Processing helix chain 'A' and resid 964 through 971 Processing helix chain 'A' and resid 973 through 977 Processing helix chain 'A' and resid 1005 through 1009 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 15 through 19 removed outlier: 3.526A pdb=" N ASN B 19 " --> pdb=" O ASP B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.600A pdb=" N GLY B 95 " --> pdb=" O GLN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.649A pdb=" N LEU B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 137 " --> pdb=" O SER B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 396 through 407 removed outlier: 4.172A pdb=" N TYR B 400 " --> pdb=" O HIS B 396 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 401 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 433 through 449 removed outlier: 3.819A pdb=" N MET B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 480 removed outlier: 3.526A pdb=" N ASP B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.903A pdb=" N SER B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.576A pdb=" N TYR B 553 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 594 removed outlier: 4.382A pdb=" N PHE B 593 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 594 " --> pdb=" O GLY B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 604 removed outlier: 3.971A pdb=" N CYS B 603 " --> pdb=" O ARG B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 625 removed outlier: 3.920A pdb=" N GLU B 620 " --> pdb=" O PRO B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 806 through 815 Processing helix chain 'B' and resid 924 through 927 Processing helix chain 'B' and resid 964 through 971 Processing helix chain 'B' and resid 973 through 977 Processing helix chain 'B' and resid 1005 through 1009 Processing helix chain 'C' and resid 3 through 6 Processing helix chain 'C' and resid 7 through 14 removed outlier: 3.887A pdb=" N ARG C 14 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 19 removed outlier: 3.511A pdb=" N ASN C 19 " --> pdb=" O ASP C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 46 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.573A pdb=" N GLY C 95 " --> pdb=" O GLN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 137 removed outlier: 3.572A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 369 through 383 Processing helix chain 'C' and resid 396 through 407 removed outlier: 4.172A pdb=" N TYR C 400 " --> pdb=" O HIS C 396 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR C 401 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 432 No H-bonds generated for 'chain 'C' and resid 430 through 432' Processing helix chain 'C' and resid 433 through 449 removed outlier: 3.819A pdb=" N MET C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 480 removed outlier: 3.525A pdb=" N ASP C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 526 removed outlier: 3.864A pdb=" N SER C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 removed outlier: 3.576A pdb=" N TYR C 553 " --> pdb=" O GLY C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 604 removed outlier: 4.003A pdb=" N CYS C 603 " --> pdb=" O ARG C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 625 removed outlier: 3.891A pdb=" N GLU C 620 " --> pdb=" O PRO C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 795 Processing helix chain 'C' and resid 806 through 815 Processing helix chain 'C' and resid 924 through 927 Processing helix chain 'C' and resid 964 through 971 Processing helix chain 'C' and resid 973 through 977 Processing helix chain 'C' and resid 1005 through 1009 Processing helix chain 'D' and resid 3 through 6 Processing helix chain 'D' and resid 7 through 12 Processing helix chain 'D' and resid 15 through 19 removed outlier: 3.510A pdb=" N ASN D 19 " --> pdb=" O ASP D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.577A pdb=" N GLY D 95 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 137 removed outlier: 3.642A pdb=" N LEU D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 199 Processing helix chain 'D' and resid 369 through 383 Processing helix chain 'D' and resid 396 through 407 removed outlier: 4.181A pdb=" N TYR D 400 " --> pdb=" O HIS D 396 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR D 401 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 433 through 449 removed outlier: 3.852A pdb=" N MET D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 480 removed outlier: 3.513A pdb=" N ASP D 470 " --> pdb=" O GLY D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 526 removed outlier: 3.503A pdb=" N LEU D 525 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 526 " --> pdb=" O LYS D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 removed outlier: 3.829A pdb=" N TYR D 553 " --> pdb=" O GLY D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 594 removed outlier: 4.429A pdb=" N PHE D 593 " --> pdb=" O GLY D 590 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 594 " --> pdb=" O GLY D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 removed outlier: 3.968A pdb=" N CYS D 603 " --> pdb=" O ARG D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 625 removed outlier: 3.957A pdb=" N GLU D 620 " --> pdb=" O PRO D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 795 Processing helix chain 'D' and resid 806 through 815 Processing helix chain 'D' and resid 924 through 927 Processing helix chain 'D' and resid 964 through 971 Processing helix chain 'D' and resid 973 through 977 Processing helix chain 'D' and resid 1005 through 1009 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 87 removed outlier: 8.646A pdb=" N GLU A 58 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR A 127 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 181 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 150 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 153 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 4.197A pdb=" N THR A 102 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET A 203 " --> pdb=" O THR A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 232 removed outlier: 5.429A pdb=" N ILE A 223 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N CYS A 248 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 274 removed outlier: 5.839A pdb=" N GLN A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN A 263 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 269 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR A 318 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 323 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 339 Processing sheet with id=AA7, first strand: chain 'A' and resid 485 through 486 removed outlier: 8.181A pdb=" N GLN A 486 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP A 457 " --> pdb=" O GLN A 486 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 410 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER A 458 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP A 412 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU A 413 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG A 353 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ARG A 389 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 355 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 534 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N PHE A 567 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 536 " --> pdb=" O PHE A 567 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 579 Processing sheet with id=AA9, first strand: chain 'A' and resid 628 through 633 Processing sheet with id=AB1, first strand: chain 'A' and resid 663 through 670 removed outlier: 6.594A pdb=" N GLY A 693 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU A 725 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 695 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 717 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLN A 703 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 715 " --> pdb=" O GLN A 703 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 740 through 743 removed outlier: 6.385A pdb=" N ASN A 760 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A 766 " --> pdb=" O ASN A 760 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 777 through 784 removed outlier: 6.488A pdb=" N GLN A 888 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN A 886 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A 782 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY A 884 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN A 784 " --> pdb=" O ARG A 882 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ARG A 882 " --> pdb=" O GLN A 784 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 883 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE A 990 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 11.807A pdb=" N ASP A 955 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP A 955 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN A1018 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 10.559A pdb=" N GLN A 957 " --> pdb=" O HIS A1016 " (cutoff:3.500A) removed outlier: 13.522A pdb=" N HIS A1016 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 20.599A pdb=" N ASN A 959 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 23.815A pdb=" N ARG A1014 " --> pdb=" O ASN A 959 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP A 843 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 852 " --> pdb=" O HIS A 841 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS A 841 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG A 854 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 839 " --> pdb=" O ARG A 854 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 856 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 837 " --> pdb=" O THR A 856 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG A 858 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 835 " --> pdb=" O ARG A 858 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA A 842 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU A 823 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN A 844 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA A 821 " --> pdb=" O GLN A 844 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 777 through 784 removed outlier: 6.488A pdb=" N GLN A 888 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN A 886 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A 782 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY A 884 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN A 784 " --> pdb=" O ARG A 882 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ARG A 882 " --> pdb=" O GLN A 784 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 883 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE A 990 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 11.807A pdb=" N ASP A 955 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG A 943 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE A 956 " --> pdb=" O GLY A 941 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 941 " --> pdb=" O PHE A 956 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A 942 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU A 901 " --> pdb=" O THR A 942 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 24 through 25 removed outlier: 6.763A pdb=" N LEU B 153 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR B 162 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE B 151 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 150 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 181 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR B 127 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU B 58 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AB7, first strand: chain 'B' and resid 100 through 102 removed outlier: 4.197A pdb=" N THR B 102 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET B 203 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 147 through 148 Processing sheet with id=AB9, first strand: chain 'B' and resid 222 through 232 removed outlier: 5.424A pdb=" N ILE B 223 " --> pdb=" O CYS B 248 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N CYS B 248 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 266 through 274 removed outlier: 5.860A pdb=" N GLN B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN B 263 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 269 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR B 318 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 323 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AC3, first strand: chain 'B' and resid 485 through 486 removed outlier: 8.163A pdb=" N GLN B 486 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TRP B 457 " --> pdb=" O GLN B 486 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 410 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N SER B 458 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 412 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU B 413 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG B 353 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ARG B 389 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 355 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 534 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N PHE B 567 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 536 " --> pdb=" O PHE B 567 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 576 through 579 Processing sheet with id=AC5, first strand: chain 'B' and resid 628 through 632 Processing sheet with id=AC6, first strand: chain 'B' and resid 662 through 670 removed outlier: 5.862A pdb=" N LEU B 659 " --> pdb=" O PRO B 663 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY B 693 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU B 725 " --> pdb=" O GLY B 693 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 695 " --> pdb=" O LEU B 723 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B 717 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLN B 703 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE B 715 " --> pdb=" O GLN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 740 through 743 removed outlier: 6.370A pdb=" N ASN B 760 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU B 766 " --> pdb=" O ASN B 760 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 777 through 784 removed outlier: 6.488A pdb=" N GLN B 888 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN B 886 " --> pdb=" O PRO B 780 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG B 782 " --> pdb=" O GLY B 884 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY B 884 " --> pdb=" O ARG B 782 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN B 784 " --> pdb=" O ARG B 882 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ARG B 882 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 883 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B 990 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 11.834A pdb=" N ASP B 955 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP B 955 " --> pdb=" O GLN B1018 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN B1018 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N GLN B 957 " --> pdb=" O HIS B1016 " (cutoff:3.500A) removed outlier: 13.529A pdb=" N HIS B1016 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 20.610A pdb=" N ASN B 959 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 23.682A pdb=" N ARG B1014 " --> pdb=" O ASN B 959 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS B 845 " --> pdb=" O THR B 849 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 851 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA B 842 " --> pdb=" O LEU B 823 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU B 823 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN B 844 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA B 821 " --> pdb=" O GLN B 844 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 777 through 784 removed outlier: 6.488A pdb=" N GLN B 888 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN B 886 " --> pdb=" O PRO B 780 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG B 782 " --> pdb=" O GLY B 884 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY B 884 " --> pdb=" O ARG B 782 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN B 784 " --> pdb=" O ARG B 882 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ARG B 882 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 883 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B 990 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 11.834A pdb=" N ASP B 955 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG B 943 " --> pdb=" O GLY B 954 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE B 956 " --> pdb=" O GLY B 941 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 941 " --> pdb=" O PHE B 956 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR B 942 " --> pdb=" O LEU B 901 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU B 901 " --> pdb=" O THR B 942 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 944 " --> pdb=" O LEU B 899 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 24 through 25 removed outlier: 6.764A pdb=" N LEU C 153 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR C 162 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE C 151 " --> pdb=" O TYR C 162 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 150 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY C 181 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR C 127 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N GLU C 58 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.501A pdb=" N ILE C 100 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR C 102 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET C 203 " --> pdb=" O THR C 102 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 222 through 232 removed outlier: 5.419A pdb=" N ILE C 223 " --> pdb=" O CYS C 248 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N CYS C 248 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 266 through 274 removed outlier: 5.855A pdb=" N GLN C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN C 263 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 269 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR C 318 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C 323 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 336 through 339 Processing sheet with id=AD7, first strand: chain 'C' and resid 485 through 486 removed outlier: 8.152A pdb=" N GLN C 486 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TRP C 457 " --> pdb=" O GLN C 486 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 410 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N SER C 458 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP C 412 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU C 413 " --> pdb=" O CYS C 390 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG C 353 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ARG C 389 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 355 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU C 534 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N PHE C 567 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU C 536 " --> pdb=" O PHE C 567 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 576 through 579 Processing sheet with id=AD9, first strand: chain 'C' and resid 628 through 633 Processing sheet with id=AE1, first strand: chain 'C' and resid 662 through 670 removed outlier: 5.800A pdb=" N LEU C 659 " --> pdb=" O PRO C 663 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY C 693 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU C 725 " --> pdb=" O GLY C 693 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU C 695 " --> pdb=" O LEU C 723 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 717 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN C 703 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE C 715 " --> pdb=" O GLN C 703 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 740 through 743 removed outlier: 6.376A pdb=" N ASN C 760 " --> pdb=" O LEU C 766 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU C 766 " --> pdb=" O ASN C 760 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 777 through 784 removed outlier: 6.438A pdb=" N GLN C 888 " --> pdb=" O LEU C 778 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN C 886 " --> pdb=" O PRO C 780 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG C 782 " --> pdb=" O GLY C 884 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY C 884 " --> pdb=" O ARG C 782 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN C 784 " --> pdb=" O ARG C 882 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG C 882 " --> pdb=" O GLN C 784 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 883 " --> pdb=" O GLY C 989 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE C 990 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ASP C 955 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP C 955 " --> pdb=" O GLN C1018 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN C1018 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N GLN C 957 " --> pdb=" O HIS C1016 " (cutoff:3.500A) removed outlier: 13.524A pdb=" N HIS C1016 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 20.610A pdb=" N ASN C 959 " --> pdb=" O ARG C1014 " (cutoff:3.500A) removed outlier: 23.687A pdb=" N ARG C1014 " --> pdb=" O ASN C 959 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N HIS C 845 " --> pdb=" O THR C 849 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 851 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA C 842 " --> pdb=" O LEU C 823 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 823 " --> pdb=" O ALA C 842 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLN C 844 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ALA C 821 " --> pdb=" O GLN C 844 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 777 through 784 removed outlier: 6.438A pdb=" N GLN C 888 " --> pdb=" O LEU C 778 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN C 886 " --> pdb=" O PRO C 780 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG C 782 " --> pdb=" O GLY C 884 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY C 884 " --> pdb=" O ARG C 782 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN C 784 " --> pdb=" O ARG C 882 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG C 882 " --> pdb=" O GLN C 784 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 883 " --> pdb=" O GLY C 989 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE C 990 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ASP C 955 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG C 943 " --> pdb=" O GLY C 954 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE C 956 " --> pdb=" O GLY C 941 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 941 " --> pdb=" O PHE C 956 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR C 942 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU C 901 " --> pdb=" O THR C 942 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 24 through 25 removed outlier: 6.764A pdb=" N LEU D 153 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR D 162 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE D 151 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 150 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 181 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR D 127 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N GLU D 58 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AE7, first strand: chain 'D' and resid 100 through 102 removed outlier: 4.193A pdb=" N THR D 102 " --> pdb=" O MET D 203 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET D 203 " --> pdb=" O THR D 102 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 222 through 232 removed outlier: 5.430A pdb=" N ILE D 223 " --> pdb=" O CYS D 248 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N CYS D 248 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 266 through 274 removed outlier: 5.826A pdb=" N GLN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN D 263 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 269 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR D 318 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU D 323 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 336 through 339 Processing sheet with id=AF2, first strand: chain 'D' and resid 485 through 486 removed outlier: 8.181A pdb=" N GLN D 486 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TRP D 457 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 410 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N SER D 458 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP D 412 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU D 413 " --> pdb=" O CYS D 390 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG D 353 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ARG D 389 " --> pdb=" O ARG D 353 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL D 355 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU D 534 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N PHE D 567 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 536 " --> pdb=" O PHE D 567 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 576 through 579 Processing sheet with id=AF4, first strand: chain 'D' and resid 628 through 632 Processing sheet with id=AF5, first strand: chain 'D' and resid 662 through 670 removed outlier: 5.829A pdb=" N LEU D 659 " --> pdb=" O PRO D 663 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY D 693 " --> pdb=" O GLU D 725 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU D 725 " --> pdb=" O GLY D 693 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU D 695 " --> pdb=" O LEU D 723 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA D 717 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN D 703 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE D 715 " --> pdb=" O GLN D 703 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 740 through 743 removed outlier: 6.374A pdb=" N ASN D 760 " --> pdb=" O LEU D 766 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU D 766 " --> pdb=" O ASN D 760 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 777 through 784 removed outlier: 6.469A pdb=" N GLN D 888 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASN D 886 " --> pdb=" O PRO D 780 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG D 782 " --> pdb=" O GLY D 884 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY D 884 " --> pdb=" O ARG D 782 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN D 784 " --> pdb=" O ARG D 882 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG D 882 " --> pdb=" O GLN D 784 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE D 883 " --> pdb=" O GLY D 989 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE D 990 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 11.820A pdb=" N ASP D 955 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP D 955 " --> pdb=" O GLN D1018 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN D1018 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N GLN D 957 " --> pdb=" O HIS D1016 " (cutoff:3.500A) removed outlier: 13.534A pdb=" N HIS D1016 " --> pdb=" O GLN D 957 " (cutoff:3.500A) removed outlier: 20.612A pdb=" N ASN D 959 " --> pdb=" O ARG D1014 " (cutoff:3.500A) removed outlier: 23.690A pdb=" N ARG D1014 " --> pdb=" O ASN D 959 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP D 843 " --> pdb=" O LEU D 850 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE D 852 " --> pdb=" O HIS D 841 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS D 841 " --> pdb=" O ILE D 852 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG D 854 " --> pdb=" O THR D 839 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 839 " --> pdb=" O ARG D 854 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR D 856 " --> pdb=" O ILE D 837 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 837 " --> pdb=" O THR D 856 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG D 858 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL D 835 " --> pdb=" O ARG D 858 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA D 842 " --> pdb=" O LEU D 823 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU D 823 " --> pdb=" O ALA D 842 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN D 844 " --> pdb=" O ALA D 821 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ALA D 821 " --> pdb=" O GLN D 844 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 777 through 784 removed outlier: 6.469A pdb=" N GLN D 888 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASN D 886 " --> pdb=" O PRO D 780 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG D 782 " --> pdb=" O GLY D 884 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY D 884 " --> pdb=" O ARG D 782 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN D 784 " --> pdb=" O ARG D 882 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG D 882 " --> pdb=" O GLN D 784 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE D 883 " --> pdb=" O GLY D 989 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE D 990 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 11.820A pdb=" N ASP D 955 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG D 943 " --> pdb=" O GLY D 954 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE D 956 " --> pdb=" O GLY D 941 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY D 941 " --> pdb=" O PHE D 956 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3228 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: 9.27 Time building geometry restraints manager: 3.15 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: 10775 1.34 - 1.46: 5883 1.46 - 1.58: 16685 1.58 - 1.70: 0 1.70 - 1.82: 248 Bond restraints: 33591 Sorted by residual: bond pdb=" N SER C 526 " pdb=" CA SER C 526 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.22e-02 6.72e+03 8.87e+00 bond pdb=" N SER A 526 " pdb=" CA SER A 526 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.22e-02 6.72e+03 8.72e+00 bond pdb=" N VAL C 110 " pdb=" CA VAL C 110 " ideal model delta sigma weight residual 1.460 1.493 -0.032 1.10e-02 8.26e+03 8.69e+00 bond pdb=" N VAL B 110 " pdb=" CA VAL B 110 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.10e-02 8.26e+03 8.23e+00 bond pdb=" N GLU C 297 " pdb=" CA GLU C 297 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.33e-02 5.65e+03 6.64e+00 ... (remaining 33586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 44896 1.91 - 3.81: 827 3.81 - 5.72: 89 5.72 - 7.62: 10 7.62 - 9.53: 8 Bond angle restraints: 45830 Sorted by residual: angle pdb=" C GLY A 661 " pdb=" N LYS A 662 " pdb=" CA LYS A 662 " ideal model delta sigma weight residual 121.70 129.48 -7.78 1.80e+00 3.09e-01 1.87e+01 angle pdb=" CA TRP B 554 " pdb=" CB TRP B 554 " pdb=" CG TRP B 554 " ideal model delta sigma weight residual 113.60 105.84 7.76 1.90e+00 2.77e-01 1.67e+01 angle pdb=" CA TRP A 554 " pdb=" CB TRP A 554 " pdb=" CG TRP A 554 " ideal model delta sigma weight residual 113.60 105.86 7.74 1.90e+00 2.77e-01 1.66e+01 angle pdb=" CA TRP C 554 " pdb=" CB TRP C 554 " pdb=" CG TRP C 554 " ideal model delta sigma weight residual 113.60 105.86 7.74 1.90e+00 2.77e-01 1.66e+01 angle pdb=" N PRO B 88 " pdb=" CA PRO B 88 " pdb=" C PRO B 88 " ideal model delta sigma weight residual 112.10 121.63 -9.53 2.60e+00 1.48e-01 1.34e+01 ... (remaining 45825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17466 17.95 - 35.90: 1598 35.90 - 53.86: 389 53.86 - 71.81: 166 71.81 - 89.76: 63 Dihedral angle restraints: 19682 sinusoidal: 7942 harmonic: 11740 Sorted by residual: dihedral pdb=" CA ILE B 771 " pdb=" C ILE B 771 " pdb=" N GLY B 772 " pdb=" CA GLY B 772 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA TRP B 770 " pdb=" C TRP B 770 " pdb=" N ILE B 771 " pdb=" CA ILE B 771 " ideal model delta harmonic sigma weight residual 180.00 152.98 27.02 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA THR C 596 " pdb=" C THR C 596 " pdb=" N PRO C 597 " pdb=" CA PRO C 597 " ideal model delta harmonic sigma weight residual -180.00 -156.10 -23.90 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 19679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3285 0.043 - 0.086: 1074 0.086 - 0.129: 405 0.129 - 0.172: 36 0.172 - 0.215: 1 Chirality restraints: 4801 Sorted by residual: chirality pdb=" CA PRO B 88 " pdb=" N PRO B 88 " pdb=" C PRO B 88 " pdb=" CB PRO B 88 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA TRP B 554 " pdb=" N TRP B 554 " pdb=" C TRP B 554 " pdb=" CB TRP B 554 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA TRP C 554 " pdb=" N TRP C 554 " pdb=" C TRP C 554 " pdb=" CB TRP C 554 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 4798 not shown) Planarity restraints: 6047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 109 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" C THR C 109 " -0.048 2.00e-02 2.50e+03 pdb=" O THR C 109 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 110 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 109 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.12e+00 pdb=" C THR B 109 " -0.046 2.00e-02 2.50e+03 pdb=" O THR B 109 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL B 110 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 554 " 0.028 2.00e-02 2.50e+03 1.52e-02 5.74e+00 pdb=" CG TRP A 554 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 554 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 554 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 554 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 554 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 554 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 554 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 554 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 554 " 0.004 2.00e-02 2.50e+03 ... (remaining 6044 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 726 2.64 - 3.20: 29461 3.20 - 3.77: 57473 3.77 - 4.33: 83320 4.33 - 4.90: 132970 Nonbonded interactions: 303950 Sorted by model distance: nonbonded pdb=" OE1 GLU C 462 " pdb="MG MG C2001 " model vdw 2.071 2.170 nonbonded pdb=" OE1 GLU A 462 " pdb="MG MG A2001 " model vdw 2.071 2.170 nonbonded pdb=" OE1 GLU B 462 " pdb="MG MG B2001 " model vdw 2.071 2.170 nonbonded pdb=" OE1 GLU D 462 " pdb="MG MG D1101 " model vdw 2.073 2.170 nonbonded pdb=" OE2 GLU D 417 " pdb="MG MG D1101 " model vdw 2.096 2.170 ... (remaining 303945 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 731 or resid 737 through 2004)) selection = (chain 'B' and (resid 3 through 731 or resid 737 through 2004)) selection = (chain 'C' and resid 3 through 2004) selection = (chain 'D' and (resid 3 through 731 or resid 737 through 1104)) } 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.890 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 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 0.041 33591 Z= 0.167 Angle : 0.622 9.529 45830 Z= 0.335 Chirality : 0.047 0.215 4801 Planarity : 0.005 0.060 6047 Dihedral : 16.751 89.761 12122 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.88 % Favored : 96.10 % Rotamer: Outliers : 1.03 % Allowed : 12.13 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.26 % 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: 0.30 (0.13), residues: 4048 helix: -0.19 (0.21), residues: 556 sheet: 0.93 (0.14), residues: 1398 loop : -0.12 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 293 TYR 0.019 0.002 TYR A 101 PHE 0.010 0.002 PHE B 748 TRP 0.038 0.002 TRP C 554 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (33591) covalent geometry : angle 0.62175 / 0.33 (45830) hydrogen bonds : bond 0.17876 / 11.68 ( 1189) hydrogen bonds : angle 7.26177 / 5.16 ( 3228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 490 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 520 average time/residue: 0.7869 time to fit residues: 473.4057 Evaluate side-chains 510 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 485 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 779 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0470 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 HIS B 784 GLN B 891 GLN B 966 GLN B 978 HIS D 754 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.103654 restraints weight = 26141.351| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 0.74 r_work: 0.2943 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work: 0.2653 rms_B_bonded: 3.87 restraints_weight: 0.1250 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33591 Z= 0.181 Angle : 0.665 11.815 45830 Z= 0.360 Chirality : 0.049 0.235 4801 Planarity : 0.005 0.045 6047 Dihedral : 6.185 56.725 4481 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.75 % Allowed : 11.44 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.26 % 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: 4048 helix: -0.13 (0.21), residues: 556 sheet: 1.06 (0.14), residues: 1347 loop : -0.23 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 631 TYR 0.020 0.002 TYR C 101 PHE 0.014 0.002 PHE D 602 TRP 0.039 0.002 TRP A 554 HIS 0.008 0.001 HIS B 978 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (33591) covalent geometry : angle 0.66542 / 0.36 (45830) hydrogen bonds : bond 0.05752 / 3.73 ( 1189) hydrogen bonds : angle 5.76213 / 4.08 ( 3228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 485 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7419 (p0) cc_final: 0.7192 (p0) REVERT: A 846 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7373 (mt0) REVERT: A 848 LYS cc_start: 0.8290 (tmtm) cc_final: 0.8083 (tptt) REVERT: B 3 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6978 (tmt) REVERT: B 234 ASP cc_start: 0.7490 (p0) cc_final: 0.7260 (p0) REVERT: B 846 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7710 (mt0) REVERT: C 234 ASP cc_start: 0.7436 (p0) cc_final: 0.7178 (p0) REVERT: C 846 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: D 234 ASP cc_start: 0.7462 (p0) cc_final: 0.7231 (p0) REVERT: D 370 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8449 (tt0) outliers start: 61 outliers final: 25 residues processed: 522 average time/residue: 0.8241 time to fit residues: 497.2721 Evaluate side-chains 511 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 481 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 846 GLN Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 846 GLN Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain D residue 827 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 176 optimal weight: 8.9990 chunk 397 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 282 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 891 GLN B 966 GLN B 978 HIS C 754 ASN C 891 GLN D 754 ASN ** D 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103790 restraints weight = 26042.328| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 0.72 r_work: 0.2946 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work: 0.2645 rms_B_bonded: 3.96 restraints_weight: 0.1250 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9180 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33591 Z= 0.187 Angle : 0.669 12.011 45830 Z= 0.362 Chirality : 0.049 0.243 4801 Planarity : 0.005 0.044 6047 Dihedral : 6.054 56.110 4466 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.24 % Allowed : 11.49 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.26 % 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: 0.22 (0.13), residues: 4048 helix: -0.18 (0.21), residues: 556 sheet: 1.01 (0.13), residues: 1339 loop : -0.28 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 293 TYR 0.021 0.002 TYR B 101 PHE 0.013 0.002 PHE D 602 TRP 0.039 0.002 TRP C 554 HIS 0.008 0.001 HIS B 978 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (33591) covalent geometry : angle 0.66909 / 0.36 (45830) hydrogen bonds : bond 0.05670 / 3.66 ( 1189) hydrogen bonds : angle 5.68891 / 4.03 ( 3228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 482 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7496 (p0) cc_final: 0.7251 (p0) REVERT: A 846 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7364 (mt0) REVERT: B 3 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7025 (tmt) REVERT: B 234 ASP cc_start: 0.7489 (p0) cc_final: 0.7236 (p0) REVERT: B 846 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7727 (mt0) REVERT: C 846 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: D 234 ASP cc_start: 0.7518 (p0) cc_final: 0.7260 (p0) REVERT: D 370 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8445 (tt0) REVERT: D 891 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: D 1007 GLU cc_start: 0.8096 (pm20) cc_final: 0.7886 (pm20) outliers start: 78 outliers final: 27 residues processed: 527 average time/residue: 0.7844 time to fit residues: 478.2340 Evaluate side-chains 514 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 481 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 846 GLN Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 846 GLN Chi-restraints excluded: chain C residue 891 GLN Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 891 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 253 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 274 optimal weight: 4.9990 chunk 319 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 336 optimal weight: 0.9990 chunk 246 optimal weight: 4.9990 chunk 371 optimal weight: 8.9990 chunk 259 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 966 GLN B 94 HIS B 776 GLN B 891 GLN B 966 GLN C 754 ASN C 891 GLN C 966 GLN D 754 ASN ** D 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104445 restraints weight = 26076.942| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 0.72 r_work: 0.2989 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work: 0.2687 rms_B_bonded: 4.00 restraints_weight: 0.1250 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 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 : 0.003 0.036 33591 Z= 0.119 Angle : 0.576 10.170 45830 Z= 0.310 Chirality : 0.046 0.204 4801 Planarity : 0.004 0.044 6047 Dihedral : 5.727 59.693 4465 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.98 % Allowed : 11.72 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.26 % 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: 0.39 (0.13), residues: 4048 helix: 0.20 (0.22), residues: 556 sheet: 1.00 (0.13), residues: 1389 loop : -0.16 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 293 TYR 0.019 0.001 TYR A 101 PHE 0.013 0.001 PHE B 602 TRP 0.036 0.002 TRP D 554 HIS 0.003 0.001 HIS C 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (33591) covalent geometry : angle 0.57598 / 0.31 (45830) hydrogen bonds : bond 0.04452 / 2.90 ( 1189) hydrogen bonds : angle 5.35268 / 3.78 ( 3228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 504 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7533 (p0) cc_final: 0.7295 (p0) REVERT: A 756 ARG cc_start: 0.7826 (mtp180) cc_final: 0.7535 (ttm170) REVERT: A 846 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7291 (mt0) REVERT: B 3 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7006 (tmt) REVERT: B 234 ASP cc_start: 0.7521 (p0) cc_final: 0.7284 (p0) REVERT: B 595 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6340 (p0) REVERT: B 980 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8400 (mt-10) REVERT: C 234 ASP cc_start: 0.7503 (p0) cc_final: 0.7218 (p0) REVERT: C 980 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8401 (mt-10) REVERT: D 370 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: D 595 ASP cc_start: 0.6408 (OUTLIER) cc_final: 0.6027 (p0) REVERT: D 756 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7509 (ttm170) outliers start: 69 outliers final: 26 residues processed: 546 average time/residue: 0.8013 time to fit residues: 507.7520 Evaluate side-chains 520 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 489 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain D residue 827 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 157 optimal weight: 5.9990 chunk 364 optimal weight: 1.9990 chunk 255 optimal weight: 0.0970 chunk 282 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 347 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 377 optimal weight: 8.9990 chunk 143 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 GLN ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 891 GLN C 754 ASN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 966 GLN D 754 ASN ** D 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103581 restraints weight = 26104.558| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 0.73 r_work: 0.2949 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work: 0.2649 rms_B_bonded: 4.08 restraints_weight: 0.1250 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33591 Z= 0.166 Angle : 0.637 11.416 45830 Z= 0.343 Chirality : 0.048 0.234 4801 Planarity : 0.005 0.045 6047 Dihedral : 5.889 58.376 4464 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.87 % Allowed : 12.01 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.26 % 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: 0.30 (0.13), residues: 4048 helix: 0.05 (0.21), residues: 556 sheet: 1.05 (0.13), residues: 1339 loop : -0.26 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 293 TYR 0.021 0.002 TYR A 101 PHE 0.013 0.002 PHE A 602 TRP 0.036 0.002 TRP D 554 HIS 0.004 0.001 HIS C 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (33591) covalent geometry : angle 0.63697 / 0.34 (45830) hydrogen bonds : bond 0.05157 / 3.33 ( 1189) hydrogen bonds : angle 5.50574 / 3.90 ( 3228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 489 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7521 (p0) cc_final: 0.7297 (p0) REVERT: A 756 ARG cc_start: 0.7862 (mtp180) cc_final: 0.7568 (ttm170) REVERT: A 846 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: A 891 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: B 3 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7067 (tmt) REVERT: B 135 LEU cc_start: 0.8342 (mt) cc_final: 0.8101 (mt) REVERT: B 234 ASP cc_start: 0.7511 (p0) cc_final: 0.7272 (p0) REVERT: B 250 GLU cc_start: 0.7153 (pt0) cc_final: 0.6914 (pt0) REVERT: B 846 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: C 3 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7367 (tpp) REVERT: C 234 ASP cc_start: 0.7518 (p0) cc_final: 0.7230 (p0) REVERT: C 891 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: C 980 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8411 (mt-10) REVERT: D 234 ASP cc_start: 0.7513 (p0) cc_final: 0.7238 (p0) REVERT: D 250 GLU cc_start: 0.7204 (pt0) cc_final: 0.6877 (pt0) REVERT: D 370 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: D 756 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7546 (ttm170) REVERT: D 891 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7475 (pm20) outliers start: 65 outliers final: 26 residues processed: 523 average time/residue: 0.7872 time to fit residues: 476.9391 Evaluate side-chains 523 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 489 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 846 GLN Chi-restraints excluded: chain B residue 891 GLN Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 891 GLN Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 891 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 368 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 356 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 chunk 234 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 94 HIS B 891 GLN C 754 ASN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 966 GLN D 754 ASN ** D 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104556 restraints weight = 25982.740| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 0.71 r_work: 0.2971 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work: 0.2667 rms_B_bonded: 4.08 restraints_weight: 0.1250 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33591 Z= 0.137 Angle : 0.602 10.617 45830 Z= 0.324 Chirality : 0.047 0.217 4801 Planarity : 0.004 0.045 6047 Dihedral : 5.762 59.555 4462 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.01 % Allowed : 11.78 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.26 % 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: 4048 helix: 0.14 (0.21), residues: 556 sheet: 1.10 (0.14), residues: 1343 loop : -0.25 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 47 TYR 0.020 0.002 TYR A 101 PHE 0.011 0.001 PHE C 602 TRP 0.036 0.002 TRP D 554 HIS 0.003 0.001 HIS C 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (33591) covalent geometry : angle 0.60160 / 0.32 (45830) hydrogen bonds : bond 0.04681 / 3.04 ( 1189) hydrogen bonds : angle 5.37631 / 3.80 ( 3228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 490 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7527 (p0) cc_final: 0.7306 (p0) REVERT: A 353 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8617 (mtt90) REVERT: A 756 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7554 (ttm170) REVERT: A 846 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7305 (mt0) REVERT: A 891 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: B 3 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7052 (tmt) REVERT: B 135 LEU cc_start: 0.8324 (mt) cc_final: 0.8079 (mt) REVERT: B 234 ASP cc_start: 0.7551 (p0) cc_final: 0.7319 (p0) REVERT: B 353 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.8619 (mtt90) REVERT: B 980 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8411 (mt-10) REVERT: C 3 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7359 (tpp) REVERT: C 234 ASP cc_start: 0.7470 (p0) cc_final: 0.7192 (p0) REVERT: C 353 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8617 (mtt90) REVERT: C 980 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8398 (mt-10) REVERT: D 234 ASP cc_start: 0.7500 (p0) cc_final: 0.7225 (p0) REVERT: D 353 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8624 (mtt90) REVERT: D 370 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: D 756 ARG cc_start: 0.7818 (mtp180) cc_final: 0.7541 (ttm170) outliers start: 70 outliers final: 23 residues processed: 532 average time/residue: 0.7830 time to fit residues: 482.7282 Evaluate side-chains 520 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 488 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain D residue 827 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 6 optimal weight: 6.9990 chunk 354 optimal weight: 0.0070 chunk 115 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 364 optimal weight: 0.7980 chunk 350 optimal weight: 0.8980 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 94 HIS C 754 ASN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 966 GLN D 754 ASN ** D 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.104789 restraints weight = 26058.156| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 0.71 r_work: 0.2966 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work: 0.2660 rms_B_bonded: 4.11 restraints_weight: 0.1250 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33591 Z= 0.145 Angle : 0.614 10.909 45830 Z= 0.330 Chirality : 0.047 0.224 4801 Planarity : 0.004 0.045 6047 Dihedral : 5.769 59.678 4460 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.87 % Allowed : 12.39 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.26 % 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: 0.34 (0.13), residues: 4048 helix: 0.12 (0.21), residues: 556 sheet: 1.09 (0.14), residues: 1341 loop : -0.26 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 293 TYR 0.020 0.002 TYR A 101 PHE 0.011 0.001 PHE D 602 TRP 0.036 0.002 TRP D 554 HIS 0.003 0.001 HIS C 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (33591) covalent geometry : angle 0.61377 / 0.33 (45830) hydrogen bonds : bond 0.04804 / 3.11 ( 1189) hydrogen bonds : angle 5.38944 / 3.81 ( 3228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 489 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7544 (p0) cc_final: 0.7319 (p0) REVERT: A 250 GLU cc_start: 0.6910 (tt0) cc_final: 0.6670 (pt0) REVERT: A 353 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.8635 (mtt90) REVERT: A 756 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7569 (ttm170) REVERT: A 846 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7324 (mt0) REVERT: A 891 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: B 3 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7041 (tmt) REVERT: B 135 LEU cc_start: 0.8320 (mt) cc_final: 0.8096 (mt) REVERT: B 234 ASP cc_start: 0.7574 (p0) cc_final: 0.7328 (p0) REVERT: B 353 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.8636 (mtt90) REVERT: B 980 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8420 (mt-10) REVERT: C 3 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7380 (tpp) REVERT: C 234 ASP cc_start: 0.7472 (p0) cc_final: 0.7175 (p0) REVERT: C 353 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.8609 (mtt90) REVERT: C 798 GLU cc_start: 0.5031 (OUTLIER) cc_final: 0.4802 (mm-30) REVERT: C 891 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: D 234 ASP cc_start: 0.7518 (p0) cc_final: 0.7244 (p0) REVERT: D 353 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.8643 (mtt90) REVERT: D 370 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: D 756 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7555 (ttm170) REVERT: D 891 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7466 (pm20) outliers start: 65 outliers final: 28 residues processed: 529 average time/residue: 0.8003 time to fit residues: 491.1727 Evaluate side-chains 527 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 487 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 891 GLN Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 891 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 307 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 367 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 342 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 383 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 94 HIS B 891 GLN C 754 ASN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 966 GLN D 754 ASN ** D 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104911 restraints weight = 26107.381| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 0.72 r_work: 0.2979 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work: 0.2668 rms_B_bonded: 4.17 restraints_weight: 0.1250 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33591 Z= 0.133 Angle : 0.597 10.397 45830 Z= 0.321 Chirality : 0.046 0.212 4801 Planarity : 0.004 0.042 6047 Dihedral : 5.703 59.573 4460 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.61 % Allowed : 12.59 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.26 % 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: 0.39 (0.13), residues: 4048 helix: 0.18 (0.22), residues: 556 sheet: 1.14 (0.14), residues: 1343 loop : -0.24 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 293 TYR 0.020 0.002 TYR A 101 PHE 0.010 0.001 PHE C 602 TRP 0.036 0.002 TRP D 554 HIS 0.003 0.001 HIS C 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (33591) covalent geometry : angle 0.59650 / 0.32 (45830) hydrogen bonds : bond 0.04556 / 2.96 ( 1189) hydrogen bonds : angle 5.31227 / 3.75 ( 3228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 492 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7544 (p0) cc_final: 0.7316 (p0) REVERT: A 353 ARG cc_start: 0.9340 (OUTLIER) cc_final: 0.8611 (mtt90) REVERT: A 756 ARG cc_start: 0.7842 (mtp180) cc_final: 0.7578 (ttm170) REVERT: A 846 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: A 891 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: B 3 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.7048 (tmt) REVERT: B 135 LEU cc_start: 0.8318 (mt) cc_final: 0.8091 (mt) REVERT: B 234 ASP cc_start: 0.7606 (p0) cc_final: 0.7363 (p0) REVERT: B 353 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.8616 (mtt90) REVERT: B 980 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8439 (mt-10) REVERT: C 3 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7361 (tpp) REVERT: C 234 ASP cc_start: 0.7517 (p0) cc_final: 0.7247 (p0) REVERT: C 353 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8613 (mtt90) REVERT: C 798 GLU cc_start: 0.5033 (OUTLIER) cc_final: 0.4775 (mm-30) REVERT: D 234 ASP cc_start: 0.7539 (p0) cc_final: 0.7259 (p0) REVERT: D 353 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.8618 (mtt90) REVERT: D 370 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: D 756 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7563 (ttm170) outliers start: 56 outliers final: 28 residues processed: 526 average time/residue: 0.7875 time to fit residues: 479.4087 Evaluate side-chains 529 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 491 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain D residue 827 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 393 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 271 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 891 GLN C 754 ASN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.101599 restraints weight = 25792.486| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 0.73 r_work: 0.2928 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work: 0.2613 rms_B_bonded: 4.12 restraints_weight: 0.1250 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 33591 Z= 0.259 Angle : 0.752 12.825 45830 Z= 0.408 Chirality : 0.053 0.271 4801 Planarity : 0.005 0.048 6047 Dihedral : 6.142 56.085 4460 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.58 % Allowed : 12.53 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4048 helix: -0.29 (0.21), residues: 556 sheet: 0.97 (0.13), residues: 1347 loop : -0.32 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1014 TYR 0.024 0.003 TYR D 101 PHE 0.019 0.003 PHE B 602 TRP 0.034 0.003 TRP D 554 HIS 0.005 0.002 HIS B 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.26 (33591) covalent geometry : angle 0.75186 / 0.41 (45830) hydrogen bonds : bond 0.06132 / 3.94 ( 1189) hydrogen bonds : angle 5.75006 / 4.07 ( 3228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 480 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7555 (p0) cc_final: 0.7315 (p0) REVERT: A 756 ARG cc_start: 0.7925 (mtp180) cc_final: 0.7635 (ttm170) REVERT: A 798 GLU cc_start: 0.5220 (OUTLIER) cc_final: 0.5000 (mm-30) REVERT: A 846 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7404 (mt0) REVERT: A 891 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: B 3 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7115 (tmt) REVERT: B 135 LEU cc_start: 0.8361 (mt) cc_final: 0.8124 (mt) REVERT: B 179 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7389 (ptt90) REVERT: B 234 ASP cc_start: 0.7584 (p0) cc_final: 0.7329 (p0) REVERT: B 293 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7977 (mtt-85) REVERT: C 3 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7377 (tpp) REVERT: C 234 ASP cc_start: 0.7505 (p0) cc_final: 0.7194 (p0) REVERT: C 798 GLU cc_start: 0.5077 (OUTLIER) cc_final: 0.3546 (mp0) REVERT: C 891 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: D 234 ASP cc_start: 0.7541 (p0) cc_final: 0.7238 (p0) REVERT: D 370 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8530 (tt0) REVERT: D 756 ARG cc_start: 0.7910 (mtp180) cc_final: 0.7615 (ttm170) outliers start: 55 outliers final: 23 residues processed: 517 average time/residue: 0.7953 time to fit residues: 475.4621 Evaluate side-chains 510 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 478 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 891 GLN Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain D residue 827 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 143 optimal weight: 0.5980 chunk 353 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 198 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 94 HIS B 891 GLN C 754 ASN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 966 GLN D 754 ASN ** D 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.105110 restraints weight = 26158.296| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 0.72 r_work: 0.2993 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work: 0.2667 rms_B_bonded: 4.36 restraints_weight: 0.1250 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9150 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33591 Z= 0.121 Angle : 0.589 9.909 45830 Z= 0.316 Chirality : 0.046 0.198 4801 Planarity : 0.004 0.044 6047 Dihedral : 5.703 59.821 4459 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.98 % Allowed : 13.30 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.26 % 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: 4048 helix: 0.20 (0.22), residues: 556 sheet: 1.00 (0.13), residues: 1387 loop : -0.21 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 293 TYR 0.019 0.002 TYR D 101 PHE 0.011 0.001 PHE C 602 TRP 0.039 0.002 TRP D 554 HIS 0.004 0.001 HIS C 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (33591) covalent geometry : angle 0.58902 / 0.32 (45830) hydrogen bonds : bond 0.04322 / 2.82 ( 1189) hydrogen bonds : angle 5.27952 / 3.73 ( 3228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 490 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7575 (p0) cc_final: 0.7336 (p0) REVERT: A 746 MET cc_start: 0.7476 (mpp) cc_final: 0.7233 (mpp) REVERT: A 756 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7617 (ttm170) REVERT: A 846 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7346 (mt0) REVERT: B 3 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7060 (tmt) REVERT: B 135 LEU cc_start: 0.8328 (mt) cc_final: 0.8110 (mt) REVERT: B 179 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7292 (ptt90) REVERT: B 234 ASP cc_start: 0.7633 (p0) cc_final: 0.7374 (p0) REVERT: B 980 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8466 (mt-10) REVERT: C 3 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7363 (tpp) REVERT: C 234 ASP cc_start: 0.7602 (p0) cc_final: 0.7344 (p0) REVERT: D 234 ASP cc_start: 0.7545 (p0) cc_final: 0.7241 (p0) REVERT: D 756 ARG cc_start: 0.7876 (mtp180) cc_final: 0.7602 (ttm170) outliers start: 34 outliers final: 20 residues processed: 512 average time/residue: 0.8094 time to fit residues: 478.7889 Evaluate side-chains 511 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 487 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain D residue 827 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 156 optimal weight: 1.9990 chunk 360 optimal weight: 6.9990 chunk 300 optimal weight: 8.9990 chunk 343 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 334 optimal weight: 0.7980 chunk 268 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 328 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 94 HIS B 891 GLN C 263 GLN C 740 HIS C 754 ASN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 966 GLN D 754 ASN D 891 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105392 restraints weight = 25854.780| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 0.72 r_work: 0.2977 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work: 0.2674 rms_B_bonded: 4.08 restraints_weight: 0.1250 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33591 Z= 0.136 Angle : 0.610 10.571 45830 Z= 0.328 Chirality : 0.047 0.212 4801 Planarity : 0.004 0.041 6047 Dihedral : 5.730 59.769 4459 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.86 % Allowed : 13.30 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.26 % 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: 0.38 (0.13), residues: 4048 helix: 0.19 (0.22), residues: 556 sheet: 1.04 (0.14), residues: 1366 loop : -0.19 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 293 TYR 0.019 0.002 TYR B 101 PHE 0.010 0.001 PHE D 602 TRP 0.036 0.002 TRP A 554 HIS 0.003 0.001 HIS C 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (33591) covalent geometry : angle 0.61000 / 0.33 (45830) hydrogen bonds : bond 0.04615 / 2.99 ( 1189) hydrogen bonds : angle 5.32521 / 3.76 ( 3228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16971.59 seconds wall clock time: 287 minutes 52.05 seconds (17272.05 seconds total)