Starting phenix.real_space_refine on Sat Feb 7 12:28:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ri6_19181/02_2026/8ri6_19181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ri6_19181/02_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_19181/02_2026/8ri6_19181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ri6_19181/02_2026/8ri6_19181.map" model { file = "/net/cci-nas-00/data/ceres_data/8ri6_19181/02_2026/8ri6_19181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ri6_19181/02_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 4 Unusual residues: {' MG': 2, ' NA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' NA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' NA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' NA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 8.05, per 1000 atoms: 0.24 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: 2.97 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: 1.58 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: 9.61 Time building geometry restraints manager: 3.96 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.640 Find NCS groups from input model: 0.800 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:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 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 covalent geometry : bond 0.00343 (33591) covalent geometry : angle 0.62175 (45830) hydrogen bonds : bond 0.17876 ( 1189) hydrogen bonds : angle 7.26177 ( 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 : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 520 average time/residue: 0.9324 time to fit residues: 556.1908 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 : 1.188 ------------------------------------------------------------------------------- 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: 4.9990 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: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3414 r_free = 0.3414 target = 0.123497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.103547 restraints weight = 26114.754| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 0.72 r_work: 0.2939 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work: 0.2643 rms_B_bonded: 3.91 restraints_weight: 0.1250 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.0521 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= 0.192 Angle : 0.679 12.054 45830 Z= 0.368 Chirality : 0.049 0.239 4801 Planarity : 0.005 0.045 6047 Dihedral : 6.216 56.441 4481 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.67 % Allowed : 11.55 % Favored : 86.78 % 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: 0.27 (0.13), residues: 4048 helix: -0.17 (0.21), residues: 556 sheet: 1.05 (0.14), residues: 1347 loop : -0.24 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 631 TYR 0.021 0.002 TYR C 101 PHE 0.013 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 covalent geometry : bond 0.00410 (33591) covalent geometry : angle 0.67895 (45830) hydrogen bonds : bond 0.05876 ( 1189) hydrogen bonds : angle 5.80690 ( 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 542 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 484 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7435 (p0) cc_final: 0.7207 (p0) REVERT: A 846 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7375 (mt0) REVERT: B 3 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6977 (tmt) REVERT: B 234 ASP cc_start: 0.7509 (p0) cc_final: 0.7274 (p0) REVERT: B 846 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: C 234 ASP cc_start: 0.7451 (p0) cc_final: 0.7187 (p0) REVERT: C 846 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: D 234 ASP cc_start: 0.7462 (p0) cc_final: 0.7234 (p0) REVERT: D 370 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8465 (tt0) outliers start: 58 outliers final: 26 residues processed: 516 average time/residue: 0.8725 time to fit residues: 517.3501 Evaluate side-chains 506 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 475 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 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 B residue 1022 CYS 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 743 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: 4.9990 chunk 59 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 289 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.123657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.103807 restraints weight = 26035.396| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 0.72 r_work: 0.2944 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work: 0.2641 rms_B_bonded: 3.96 restraints_weight: 0.1250 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.0620 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= 0.184 Angle : 0.665 11.965 45830 Z= 0.360 Chirality : 0.049 0.242 4801 Planarity : 0.005 0.044 6047 Dihedral : 6.048 56.295 4466 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.33 % Allowed : 11.41 % 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: -0.17 (0.21), residues: 556 sheet: 1.02 (0.13), residues: 1339 loop : -0.28 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 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 0.007 0.001 HIS B 978 Details of bonding type rmsd covalent geometry : bond 0.00394 (33591) covalent geometry : angle 0.66467 (45830) hydrogen bonds : bond 0.05601 ( 1189) hydrogen bonds : angle 5.68018 ( 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 565 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 484 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7499 (p0) cc_final: 0.7251 (p0) REVERT: A 846 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: B 3 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.7006 (tmt) REVERT: B 234 ASP cc_start: 0.7493 (p0) cc_final: 0.7243 (p0) REVERT: B 846 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7728 (mt0) REVERT: C 234 ASP cc_start: 0.7526 (p0) cc_final: 0.7271 (p0) REVERT: C 846 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: C 980 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8445 (mt-10) REVERT: D 370 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: D 891 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: D 1007 GLU cc_start: 0.8092 (pm20) cc_final: 0.7876 (pm20) outliers start: 81 outliers final: 30 residues processed: 532 average time/residue: 0.8371 time to fit residues: 511.8260 Evaluate side-chains 516 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 480 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR 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 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 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 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 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 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: 0.8980 chunk 217 optimal weight: 0.7980 chunk 274 optimal weight: 4.9990 chunk 319 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 336 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 259 optimal weight: 0.7980 chunk 298 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.125596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.105517 restraints weight = 26094.623| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 0.74 r_work: 0.2975 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work: 0.2683 rms_B_bonded: 4.02 restraints_weight: 0.1250 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.0778 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= 0.125 Angle : 0.583 10.292 45830 Z= 0.314 Chirality : 0.046 0.206 4801 Planarity : 0.004 0.043 6047 Dihedral : 5.753 59.542 4465 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.90 % Allowed : 11.75 % Favored : 86.35 % 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: 0.18 (0.22), residues: 556 sheet: 0.99 (0.13), residues: 1387 loop : -0.16 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 293 TYR 0.019 0.002 TYR A 101 PHE 0.013 0.001 PHE B 602 TRP 0.036 0.002 TRP A 554 HIS 0.004 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00262 (33591) covalent geometry : angle 0.58291 (45830) hydrogen bonds : bond 0.04543 ( 1189) hydrogen bonds : angle 5.37797 ( 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 567 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 501 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7465 (p0) cc_final: 0.7246 (p0) REVERT: A 756 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7531 (ttm170) REVERT: A 846 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7320 (mt0) REVERT: B 3 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7017 (tmt) REVERT: B 234 ASP cc_start: 0.7524 (p0) cc_final: 0.7265 (p0) REVERT: B 293 ARG cc_start: 0.8318 (mtt90) cc_final: 0.8092 (mtt90) REVERT: B 595 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6380 (p0) REVERT: C 234 ASP cc_start: 0.7553 (p0) cc_final: 0.7284 (p0) REVERT: D 234 ASP cc_start: 0.7426 (p0) cc_final: 0.7153 (p0) REVERT: D 370 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: D 595 ASP cc_start: 0.6432 (OUTLIER) cc_final: 0.6069 (p0) REVERT: D 756 ARG cc_start: 0.7802 (mtp180) cc_final: 0.7506 (ttm170) outliers start: 66 outliers final: 31 residues processed: 539 average time/residue: 0.9213 time to fit residues: 572.7764 Evaluate side-chains 527 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 491 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR 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 266 THR Chi-restraints excluded: chain B residue 439 GLU 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 827 THR Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain C residue 266 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 827 THR Chi-restraints excluded: chain C residue 891 GLN 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 439 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 595 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: 0.2980 chunk 282 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 347 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 377 optimal weight: 10.0000 chunk 143 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 891 GLN B 966 GLN 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 = 0.3438 r_free = 0.3438 target = 0.125271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.105499 restraints weight = 26242.830| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 0.70 r_work: 0.2977 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work: 0.2663 rms_B_bonded: 4.24 restraints_weight: 0.1250 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 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 : 0.003 0.036 33591 Z= 0.129 Angle : 0.588 10.427 45830 Z= 0.316 Chirality : 0.046 0.212 4801 Planarity : 0.004 0.041 6047 Dihedral : 5.714 59.896 4465 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.84 % Allowed : 12.10 % Favored : 86.06 % 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: 0.23 (0.22), residues: 556 sheet: 1.12 (0.14), residues: 1345 loop : -0.24 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 47 TYR 0.020 0.002 TYR A 101 PHE 0.011 0.001 PHE C 602 TRP 0.035 0.002 TRP C 554 HIS 0.003 0.001 HIS C 841 Details of bonding type rmsd covalent geometry : bond 0.00274 (33591) covalent geometry : angle 0.58799 (45830) hydrogen bonds : bond 0.04550 ( 1189) hydrogen bonds : angle 5.33464 ( 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 555 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 491 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7528 (p0) cc_final: 0.7301 (p0) REVERT: A 353 ARG cc_start: 0.9341 (OUTLIER) cc_final: 0.8603 (mtt90) REVERT: A 756 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7586 (ttm170) REVERT: A 846 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7304 (mt0) REVERT: A 891 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: B 3 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7038 (tmt) REVERT: B 135 LEU cc_start: 0.8302 (mt) cc_final: 0.8046 (mt) REVERT: B 234 ASP cc_start: 0.7603 (p0) cc_final: 0.7348 (p0) REVERT: B 353 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.8608 (mtt90) REVERT: B 595 ASP cc_start: 0.6711 (OUTLIER) cc_final: 0.6358 (p0) REVERT: B 980 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8421 (mt-10) REVERT: C 3 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7370 (tpp) REVERT: C 250 GLU cc_start: 0.7145 (pt0) cc_final: 0.6925 (pt0) REVERT: C 353 ARG cc_start: 0.9340 (OUTLIER) cc_final: 0.8603 (mtt90) REVERT: D 234 ASP cc_start: 0.7507 (p0) cc_final: 0.7225 (p0) REVERT: D 353 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8607 (mtt90) REVERT: D 370 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: D 595 ASP cc_start: 0.6414 (OUTLIER) cc_final: 0.6031 (p0) REVERT: D 756 ARG cc_start: 0.7837 (mtp180) cc_final: 0.7558 (ttm170) outliers start: 64 outliers final: 28 residues processed: 523 average time/residue: 0.9710 time to fit residues: 582.8096 Evaluate side-chains 525 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 486 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 353 ARG 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 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 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 802 ILE 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 266 THR Chi-restraints excluded: chain C residue 353 ARG 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 660 ASP 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 439 GLU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 827 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 368 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 202 optimal weight: 0.4980 chunk 356 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 262 optimal weight: 0.7980 chunk 234 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 94 HIS B 891 GLN B 966 GLN C 754 ASN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3441 r_free = 0.3441 target = 0.125498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105027 restraints weight = 26087.731| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 0.71 r_work: 0.2976 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work: 0.2671 rms_B_bonded: 4.18 restraints_weight: 0.1250 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.0905 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= 0.128 Angle : 0.586 10.317 45830 Z= 0.315 Chirality : 0.046 0.210 4801 Planarity : 0.004 0.043 6047 Dihedral : 5.648 59.143 4460 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.01 % Allowed : 12.07 % Favored : 85.92 % 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: 0.43 (0.13), residues: 4048 helix: 0.25 (0.22), residues: 556 sheet: 1.07 (0.13), residues: 1378 loop : -0.17 (0.13), residues: 2114 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 0.010 0.001 PHE C 602 TRP 0.034 0.002 TRP D 554 HIS 0.003 0.001 HIS C 841 Details of bonding type rmsd covalent geometry : bond 0.00272 (33591) covalent geometry : angle 0.58555 (45830) hydrogen bonds : bond 0.04490 ( 1189) hydrogen bonds : angle 5.28848 ( 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 559 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 489 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7516 (p0) cc_final: 0.7292 (p0) REVERT: A 353 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8603 (mtt90) REVERT: A 756 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7599 (ttm170) REVERT: A 846 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: A 891 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7455 (pm20) REVERT: B 3 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7004 (tmt) REVERT: B 135 LEU cc_start: 0.8331 (mt) cc_final: 0.8089 (mt) REVERT: B 234 ASP cc_start: 0.7539 (p0) cc_final: 0.7312 (p0) REVERT: B 353 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.8608 (mtt90) REVERT: B 595 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6256 (p0) REVERT: B 980 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8430 (mt-10) REVERT: C 3 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7348 (tpp) REVERT: C 234 ASP cc_start: 0.7522 (p0) cc_final: 0.7241 (p0) REVERT: C 353 ARG cc_start: 0.9338 (OUTLIER) cc_final: 0.8603 (mtt90) REVERT: C 891 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: D 234 ASP cc_start: 0.7518 (p0) cc_final: 0.7240 (p0) REVERT: D 353 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.8607 (mtt90) REVERT: D 370 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8445 (tt0) REVERT: D 595 ASP cc_start: 0.6379 (OUTLIER) cc_final: 0.6007 (p0) REVERT: D 756 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7571 (ttm170) outliers start: 70 outliers final: 26 residues processed: 529 average time/residue: 0.8652 time to fit residues: 527.2310 Evaluate side-chains 523 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 485 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 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 345 LEU 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 595 ASP 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 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 547 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 891 GLN 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 595 ASP 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: 0.4980 chunk 354 optimal weight: 0.1980 chunk 115 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 327 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 263 optimal weight: 0.9990 chunk 364 optimal weight: 4.9990 chunk 350 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 891 GLN B 966 GLN C 754 ASN C 825 GLN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3446 r_free = 0.3446 target = 0.125838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.105776 restraints weight = 26189.305| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 0.71 r_work: 0.2983 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work: 0.2682 rms_B_bonded: 4.09 restraints_weight: 0.1250 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.0965 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= 0.123 Angle : 0.579 10.126 45830 Z= 0.311 Chirality : 0.046 0.207 4801 Planarity : 0.004 0.041 6047 Dihedral : 5.602 59.952 4460 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.75 % Allowed : 12.61 % Favored : 85.63 % 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: 0.44 (0.13), residues: 4048 helix: 0.28 (0.22), residues: 556 sheet: 1.18 (0.14), residues: 1345 loop : -0.23 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 47 TYR 0.020 0.002 TYR A 101 PHE 0.010 0.001 PHE B 602 TRP 0.034 0.002 TRP D 554 HIS 0.003 0.001 HIS C 841 Details of bonding type rmsd covalent geometry : bond 0.00262 (33591) covalent geometry : angle 0.57876 (45830) hydrogen bonds : bond 0.04375 ( 1189) hydrogen bonds : angle 5.23513 ( 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 550 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 489 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7503 (p0) cc_final: 0.7266 (p0) REVERT: A 353 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.8598 (mtt90) REVERT: A 756 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7577 (ttm170) REVERT: A 846 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7302 (mt0) REVERT: A 891 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: B 3 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.7008 (tmt) REVERT: B 135 LEU cc_start: 0.8313 (mt) cc_final: 0.8083 (mt) REVERT: B 234 ASP cc_start: 0.7531 (p0) cc_final: 0.7308 (p0) REVERT: B 353 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.8599 (mtt90) REVERT: B 595 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.6151 (p0) REVERT: B 848 LYS cc_start: 0.8345 (tmtm) cc_final: 0.8055 (tptt) REVERT: C 3 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7344 (tpp) REVERT: C 234 ASP cc_start: 0.7470 (p0) cc_final: 0.7200 (p0) REVERT: C 353 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8593 (mtt90) REVERT: C 846 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: C 848 LYS cc_start: 0.8346 (tmtm) cc_final: 0.8055 (tptt) REVERT: C 891 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: D 234 ASP cc_start: 0.7523 (p0) cc_final: 0.7235 (p0) REVERT: D 353 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.8599 (mtt90) REVERT: D 370 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: D 595 ASP cc_start: 0.6298 (OUTLIER) cc_final: 0.5889 (p0) REVERT: D 756 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7565 (ttm170) REVERT: D 891 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7495 (pm20) outliers start: 61 outliers final: 23 residues processed: 523 average time/residue: 0.8788 time to fit residues: 527.5934 Evaluate side-chains 521 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 484 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 547 LEU 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 345 LEU 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 595 ASP 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 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 547 LEU Chi-restraints excluded: chain C residue 636 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 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 595 ASP 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: 4.9990 chunk 134 optimal weight: 0.0970 chunk 367 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 342 optimal weight: 0.6980 chunk 229 optimal weight: 0.0770 chunk 248 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 383 optimal weight: 0.7980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 GLN ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 90 ASN B 94 HIS B 298 ASN B 825 GLN B 891 GLN C 754 ASN C 825 GLN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN D 825 GLN ** D 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.129550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108196 restraints weight = 26470.464| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 0.80 r_work: 0.3047 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work: 0.2732 rms_B_bonded: 4.53 restraints_weight: 0.1250 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33591 Z= 0.095 Angle : 0.526 8.531 45830 Z= 0.281 Chirality : 0.044 0.170 4801 Planarity : 0.004 0.039 6047 Dihedral : 5.108 57.188 4456 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.44 % Allowed : 12.93 % Favored : 85.63 % 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: 0.58 (0.13), residues: 4048 helix: 0.62 (0.23), residues: 560 sheet: 1.22 (0.14), residues: 1374 loop : -0.20 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 47 TYR 0.016 0.001 TYR B 101 PHE 0.013 0.001 PHE B 602 TRP 0.036 0.001 TRP A 554 HIS 0.002 0.001 HIS A1016 Details of bonding type rmsd covalent geometry : bond 0.00203 (33591) covalent geometry : angle 0.52577 (45830) hydrogen bonds : bond 0.03477 ( 1189) hydrogen bonds : angle 4.92642 ( 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 571 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 521 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7604 (p0) cc_final: 0.7387 (p0) REVERT: A 353 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8535 (mtt90) REVERT: A 756 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7565 (ttm170) REVERT: A 846 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7204 (mt0) REVERT: B 3 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6962 (tmt) REVERT: B 135 LEU cc_start: 0.8294 (mt) cc_final: 0.8053 (mt) REVERT: B 234 ASP cc_start: 0.7578 (p0) cc_final: 0.7348 (p0) REVERT: B 353 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8525 (mtt90) REVERT: B 740 HIS cc_start: 0.7824 (t70) cc_final: 0.7603 (t-90) REVERT: B 756 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7606 (ttm170) REVERT: C 3 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7349 (tpp) REVERT: C 234 ASP cc_start: 0.7541 (p0) cc_final: 0.7265 (p0) REVERT: C 353 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8522 (mtt90) REVERT: C 740 HIS cc_start: 0.7755 (t70) cc_final: 0.7555 (t-90) REVERT: D 234 ASP cc_start: 0.7622 (p0) cc_final: 0.7379 (p0) REVERT: D 353 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8533 (mtt90) outliers start: 50 outliers final: 14 residues processed: 553 average time/residue: 0.8887 time to fit residues: 566.7735 Evaluate side-chains 515 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 494 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 547 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 779 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 D residue 266 THR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 660 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 393 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 317 optimal weight: 5.9990 chunk 173 optimal weight: 0.0170 chunk 227 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 overall best weight: 2.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 HIS A 825 GLN ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 94 HIS B 825 GLN B 891 GLN C 754 ASN C 825 GLN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN D 825 GLN ** D 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 966 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.102787 restraints weight = 25851.290| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 0.74 r_work: 0.2935 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work: 0.2633 rms_B_bonded: 4.03 restraints_weight: 0.1250 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33591 Z= 0.206 Angle : 0.692 11.819 45830 Z= 0.373 Chirality : 0.050 0.243 4801 Planarity : 0.005 0.064 6047 Dihedral : 5.800 59.431 4453 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.41 % Allowed : 13.07 % Favored : 85.52 % 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: 0.05 (0.21), residues: 556 sheet: 1.12 (0.14), residues: 1347 loop : -0.24 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 47 TYR 0.023 0.003 TYR A 101 PHE 0.014 0.002 PHE C 602 TRP 0.028 0.003 TRP D 554 HIS 0.005 0.001 HIS C 841 Details of bonding type rmsd covalent geometry : bond 0.00445 (33591) covalent geometry : angle 0.69249 (45830) hydrogen bonds : bond 0.05500 ( 1189) hydrogen bonds : angle 5.51910 ( 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 536 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 487 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7516 (p0) cc_final: 0.7286 (p0) REVERT: A 756 ARG cc_start: 0.7898 (mtp180) cc_final: 0.7628 (ttm170) REVERT: A 846 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7366 (mt0) REVERT: A 891 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: B 3 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7036 (tmt) REVERT: B 135 LEU cc_start: 0.8331 (mt) cc_final: 0.8109 (mt) REVERT: B 234 ASP cc_start: 0.7497 (p0) cc_final: 0.7266 (p0) REVERT: C 3 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7334 (tpp) REVERT: C 234 ASP cc_start: 0.7435 (p0) cc_final: 0.7152 (p0) REVERT: C 798 GLU cc_start: 0.4682 (OUTLIER) cc_final: 0.4395 (mm-30) REVERT: C 846 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: C 891 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7365 (pm20) REVERT: D 234 ASP cc_start: 0.7494 (p0) cc_final: 0.7226 (p0) REVERT: D 756 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7606 (ttm170) outliers start: 49 outliers final: 18 residues processed: 514 average time/residue: 0.9233 time to fit residues: 545.3281 Evaluate side-chains 508 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 483 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 743 THR Chi-restraints excluded: chain A residue 779 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 137 GLU 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 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 798 GLU 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 546 SER Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 779 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 143 optimal weight: 0.0980 chunk 353 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 740 HIS B 891 GLN C 754 ASN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN ** D 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 966 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.105277 restraints weight = 26269.388| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 0.74 r_work: 0.2999 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work: 0.2676 rms_B_bonded: 4.44 restraints_weight: 0.1250 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 33591 Z= 0.114 Angle : 0.584 9.563 45830 Z= 0.312 Chirality : 0.046 0.192 4801 Planarity : 0.004 0.053 6047 Dihedral : 5.462 59.570 4453 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.80 % Allowed : 13.74 % Favored : 85.46 % 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: 0.47 (0.13), residues: 4048 helix: 0.34 (0.22), residues: 556 sheet: 1.23 (0.14), residues: 1351 loop : -0.25 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 47 TYR 0.019 0.001 TYR B 101 PHE 0.012 0.001 PHE D 602 TRP 0.035 0.001 TRP D 554 HIS 0.003 0.001 HIS C 623 Details of bonding type rmsd covalent geometry : bond 0.00246 (33591) covalent geometry : angle 0.58443 (45830) hydrogen bonds : bond 0.04136 ( 1189) hydrogen bonds : angle 5.16563 ( 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 521 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 493 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7582 (p0) cc_final: 0.7347 (p0) REVERT: A 251 LEU cc_start: 0.7975 (mt) cc_final: 0.7682 (mt) REVERT: A 740 HIS cc_start: 0.7867 (t70) cc_final: 0.7649 (t-90) REVERT: A 756 ARG cc_start: 0.7881 (mtp180) cc_final: 0.7630 (ttm170) REVERT: A 846 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: B 3 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.7035 (tmt) REVERT: B 135 LEU cc_start: 0.8325 (mt) cc_final: 0.8095 (mt) REVERT: B 234 ASP cc_start: 0.7583 (p0) cc_final: 0.7332 (p0) REVERT: C 234 ASP cc_start: 0.7520 (p0) cc_final: 0.7233 (p0) REVERT: C 798 GLU cc_start: 0.4492 (OUTLIER) cc_final: 0.2921 (mp0) REVERT: C 846 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: D 234 ASP cc_start: 0.7581 (p0) cc_final: 0.7319 (p0) REVERT: D 756 ARG cc_start: 0.7863 (mtp180) cc_final: 0.7619 (ttm170) outliers start: 28 outliers final: 17 residues processed: 507 average time/residue: 0.9838 time to fit residues: 572.1529 Evaluate side-chains 507 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 486 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 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 547 LEU 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 547 LEU Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 798 GLU 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 547 LEU 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: 0.9980 chunk 360 optimal weight: 6.9990 chunk 300 optimal weight: 5.9990 chunk 343 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 HIS ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS C 740 HIS C 754 ASN ** C 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN D 966 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103665 restraints weight = 25972.142| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 0.74 r_work: 0.2950 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work: 0.2646 rms_B_bonded: 4.10 restraints_weight: 0.1250 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33591 Z= 0.169 Angle : 0.658 11.216 45830 Z= 0.353 Chirality : 0.049 0.233 4801 Planarity : 0.005 0.054 6047 Dihedral : 5.709 59.745 4453 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.92 % Allowed : 13.65 % Favored : 85.43 % 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: 0.13 (0.22), residues: 556 sheet: 1.14 (0.14), residues: 1341 loop : -0.27 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 47 TYR 0.022 0.002 TYR A 101 PHE 0.011 0.002 PHE C 602 TRP 0.029 0.002 TRP D 554 HIS 0.004 0.001 HIS C 841 Details of bonding type rmsd covalent geometry : bond 0.00364 (33591) covalent geometry : angle 0.65821 (45830) hydrogen bonds : bond 0.05047 ( 1189) hydrogen bonds : angle 5.40665 ( 3228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19057.98 seconds wall clock time: 323 minutes 36.77 seconds (19416.77 seconds total)