Starting phenix.real_space_refine on Sat Aug 8 09:59:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yle_73080/08_2026/9yle_73080.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yle_73080/08_2026/9yle_73080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yle_73080/08_2026/9yle_73080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yle_73080/08_2026/9yle_73080.map" model { file = "/net/cci-nas-00/data/ceres_data/9yle_73080/08_2026/9yle_73080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yle_73080/08_2026/9yle_73080.cif" } resolution = 3.63 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 119 5.16 5 C 15948 2.51 5 N 4792 2.21 5 O 5704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26853 Number of models: 1 Model: "" Number of chains: 28 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 5469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5469 Classifications: {'peptide': 687} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 655} Chain breaks: 2 Chain: "N" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2977 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 18, 'TRANS': 363} Chain breaks: 2 Chain: "T" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2397 Classifications: {'peptide': 297} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 273} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "P" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "Q" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 432 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.59, per 1000 atoms: 0.21 Number of scatterers: 26853 At special positions: 0 Unit cell: (144.48, 171.14, 208.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 P 290 15.00 O 5704 8.00 N 4792 7.00 C 15948 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4900 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 34 sheets defined 32.5% alpha, 13.9% beta 119 base pairs and 230 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'O' and resid 24 through 35 removed outlier: 3.629A pdb=" N ALA O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS O 29 " --> pdb=" O ASN O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 41 removed outlier: 3.877A pdb=" N GLN O 40 " --> pdb=" O PRO O 37 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN O 41 " --> pdb=" O PRO O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 41' Processing helix chain 'K' and resid 1388 through 1393 removed outlier: 3.572A pdb=" N HIS K1393 " --> pdb=" O ALA K1390 " (cutoff:3.500A) Processing helix chain 'K' and resid 1405 through 1410 removed outlier: 3.534A pdb=" N VAL K1409 " --> pdb=" O HIS K1405 " (cutoff:3.500A) Processing helix chain 'K' and resid 1415 through 1421 Processing helix chain 'K' and resid 1498 through 1506 removed outlier: 4.416A pdb=" N VAL K1505 " --> pdb=" O CYS K1501 " (cutoff:3.500A) Processing helix chain 'K' and resid 1531 through 1535 removed outlier: 3.915A pdb=" N CYS K1534 " --> pdb=" O HIS K1531 " (cutoff:3.500A) Processing helix chain 'K' and resid 1542 through 1550 removed outlier: 3.869A pdb=" N ALA K1546 " --> pdb=" O ASP K1542 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA K1547 " --> pdb=" O VAL K1543 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP K1548 " --> pdb=" O GLU K1544 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU K1549 " --> pdb=" O GLN K1545 " (cutoff:3.500A) Processing helix chain 'K' and resid 1553 through 1557 Processing helix chain 'K' and resid 5007 through 5017 removed outlier: 3.571A pdb=" N MET K5013 " --> pdb=" O VAL K5009 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU K5014 " --> pdb=" O ALA K5010 " (cutoff:3.500A) Processing helix chain 'K' and resid 5060 through 5065 Processing helix chain 'K' and resid 5079 through 5089 removed outlier: 3.513A pdb=" N LEU K5084 " --> pdb=" O VAL K5080 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS K5085 " --> pdb=" O GLU K5081 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG K5086 " --> pdb=" O VAL K5082 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU K5089 " --> pdb=" O HIS K5085 " (cutoff:3.500A) Processing helix chain 'K' and resid 5114 through 5121 removed outlier: 3.542A pdb=" N ILE K5119 " --> pdb=" O PHE K5115 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG K5120 " --> pdb=" O ALA K5116 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA K5121 " --> pdb=" O CYS K5117 " (cutoff:3.500A) Processing helix chain 'K' and resid 5133 through 5137 removed outlier: 4.184A pdb=" N LYS K5137 " --> pdb=" O PRO K5134 " (cutoff:3.500A) Processing helix chain 'K' and resid 5160 through 5170 removed outlier: 3.574A pdb=" N ILE K5165 " --> pdb=" O GLU K5161 " (cutoff:3.500A) Processing helix chain 'K' and resid 5259 through 5274 removed outlier: 3.719A pdb=" N TRP K5264 " --> pdb=" O PRO K5260 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE K5267 " --> pdb=" O VAL K5263 " (cutoff:3.500A) Proline residue: K5270 - end of helix Processing helix chain 'K' and resid 5284 through 5288 Processing helix chain 'K' and resid 5289 through 5294 removed outlier: 3.574A pdb=" N LEU K5293 " --> pdb=" O LYS K5289 " (cutoff:3.500A) Processing helix chain 'K' and resid 5298 through 5307 Processing helix chain 'K' and resid 5386 through 5390 removed outlier: 3.833A pdb=" N ARG K5390 " --> pdb=" O SER K5386 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 5386 through 5390' Processing helix chain 'K' and resid 5390 through 5398 removed outlier: 5.351A pdb=" N LYS K5396 " --> pdb=" O ARG K5392 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN K5397 " --> pdb=" O THR K5393 " (cutoff:3.500A) Processing helix chain 'K' and resid 5433 through 5446 removed outlier: 3.608A pdb=" N ASN K5437 " --> pdb=" O ASN K5433 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG K5438 " --> pdb=" O GLU K5434 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG K5439 " --> pdb=" O VAL K5435 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS K5441 " --> pdb=" O ASN K5437 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE K5442 " --> pdb=" O ARG K5438 " (cutoff:3.500A) Processing helix chain 'K' and resid 5469 through 5472 removed outlier: 3.533A pdb=" N TYR K5472 " --> pdb=" O PRO K5469 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 5469 through 5472' Processing helix chain 'N' and resid 228 through 234 Processing helix chain 'T' and resid 354 through 358 Processing helix chain 'T' and resid 369 through 371 No H-bonds generated for 'chain 'T' and resid 369 through 371' Processing helix chain 'T' and resid 462 through 464 No H-bonds generated for 'chain 'T' and resid 462 through 464' Processing helix chain 'T' and resid 496 through 501 removed outlier: 3.549A pdb=" N LYS T 500 " --> pdb=" O THR T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 525 through 533 removed outlier: 3.509A pdb=" N LYS T 531 " --> pdb=" O ASP T 527 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER T 532 " --> pdb=" O LYS T 528 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU T 533 " --> pdb=" O ALA T 529 " (cutoff:3.500A) Processing helix chain 'T' and resid 593 through 619 removed outlier: 4.283A pdb=" N MET T 597 " --> pdb=" O PRO T 593 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP T 599 " --> pdb=" O SER T 595 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL T 602 " --> pdb=" O GLY T 598 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL T 603 " --> pdb=" O TRP T 599 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU T 604 " --> pdb=" O GLY T 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.666A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.694A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.898A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 4.317A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.975A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.883A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.693A pdb=" N LEU C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.563A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.627A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.649A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 39 through 49 removed outlier: 3.531A pdb=" N VAL D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 81 removed outlier: 3.751A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.901A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.625A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.929A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.655A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN E 108 " --> pdb=" O PHE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.727A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.560A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.877A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.536A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.758A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.635A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.538A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 86 removed outlier: 3.941A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 39 through 49 removed outlier: 3.639A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 81 removed outlier: 3.739A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.611A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL H 118 " --> pdb=" O GLY H 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 58 removed outlier: 3.739A pdb=" N LEU P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 76 removed outlier: 3.665A pdb=" N LEU P 65 " --> pdb=" O VAL P 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN P 67 " --> pdb=" O PRO P 63 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA P 70 " --> pdb=" O LEU P 66 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL P 71 " --> pdb=" O GLN P 67 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU P 75 " --> pdb=" O VAL P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 91 Processing helix chain 'P' and resid 91 through 97 removed outlier: 4.385A pdb=" N PHE P 95 " --> pdb=" O ASN P 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP P 97 " --> pdb=" O ALA P 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 51 Processing helix chain 'Q' and resid 52 through 57 removed outlier: 3.535A pdb=" N TYR Q 56 " --> pdb=" O PRO Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 69 removed outlier: 3.704A pdb=" N LEU Q 65 " --> pdb=" O VAL Q 61 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN Q 67 " --> pdb=" O PRO Q 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU Q 69 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 76 removed outlier: 4.100A pdb=" N GLU Q 75 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 91 removed outlier: 3.745A pdb=" N ALA Q 85 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 3 through 6 removed outlier: 3.751A pdb=" N VAL O 5 " --> pdb=" O ILE O 13 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE O 13 " --> pdb=" O VAL O 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain 'K' and resid 1395 through 1396 removed outlier: 3.601A pdb=" N TYR K1404 " --> pdb=" O LEU K1395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 1443 through 1444 Processing sheet with id=AA5, first strand: chain 'K' and resid 5049 through 5053 removed outlier: 3.515A pdb=" N LEU K5050 " --> pdb=" O VAL K5058 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL K5058 " --> pdb=" O LEU K5050 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU K5052 " --> pdb=" O LEU K5056 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU K5056 " --> pdb=" O LEU K5052 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 5076 through 5077 Processing sheet with id=AA7, first strand: chain 'K' and resid 5179 through 5180 Processing sheet with id=AA8, first strand: chain 'K' and resid 5211 through 5217 removed outlier: 3.814A pdb=" N GLU K5240 " --> pdb=" O GLY K5233 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG K5238 " --> pdb=" O ASN K5235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 5399 through 5403 Processing sheet with id=AB1, first strand: chain 'K' and resid 5422 through 5426 removed outlier: 6.219A pdb=" N MET K5422 " --> pdb=" O SER K5498 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER K5498 " --> pdb=" O MET K5422 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE K5424 " --> pdb=" O ILE K5496 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE K5494 " --> pdb=" O TYR K5426 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE K5495 " --> pdb=" O GLU K5484 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU K5484 " --> pdb=" O ILE K5495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 5428 through 5432 removed outlier: 3.547A pdb=" N PHE K5453 " --> pdb=" O ILE K5461 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 20 through 21 removed outlier: 4.363A pdb=" N VAL N 318 " --> pdb=" O LEU N 21 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP N 300 " --> pdb=" O ILE N 313 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 30 through 32 removed outlier: 4.088A pdb=" N LYS N 60 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASP N 52 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE N 58 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 69 through 73 removed outlier: 6.707A pdb=" N ALA N 84 " --> pdb=" O CYS N 70 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU N 72 " --> pdb=" O VAL N 82 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL N 82 " --> pdb=" O LEU N 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 110 through 115 removed outlier: 3.810A pdb=" N LYS N 112 " --> pdb=" O CYS N 126 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL N 143 " --> pdb=" O MET N 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 155 through 159 removed outlier: 3.712A pdb=" N VAL N 156 " --> pdb=" O GLY N 169 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS N 174 " --> pdb=" O ASN N 170 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 201 through 206 removed outlier: 7.183A pdb=" N ASN N 216 " --> pdb=" O LYS N 202 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE N 204 " --> pdb=" O LEU N 214 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU N 214 " --> pdb=" O ILE N 204 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE N 206 " --> pdb=" O CYS N 212 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N CYS N 212 " --> pdb=" O PHE N 206 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG N 223 " --> pdb=" O ILE N 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 254 through 259 removed outlier: 4.270A pdb=" N LYS N 256 " --> pdb=" O GLY N 269 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA N 275 " --> pdb=" O SER N 270 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU N 276 " --> pdb=" O ILE N 289 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE N 289 " --> pdb=" O LEU N 276 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE N 278 " --> pdb=" O VAL N 287 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 373 through 375 removed outlier: 3.842A pdb=" N ILE T 344 " --> pdb=" O PHE T 520 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU T 518 " --> pdb=" O ALA T 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 383 through 388 removed outlier: 5.412A pdb=" N ASP T 387 " --> pdb=" O ARG T 411 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE T 566 " --> pdb=" O VAL T 410 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY T 439 " --> pdb=" O ALA T 565 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU T 438 " --> pdb=" O TRP T 460 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 393 through 394 removed outlier: 3.548A pdb=" N LYS T 393 " --> pdb=" O VAL T 402 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL T 401 " --> pdb=" O VAL T 574 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL T 574 " --> pdb=" O VAL T 401 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS T 572 " --> pdb=" O GLY T 403 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU T 424 " --> pdb=" O ASN T 577 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY T 419 " --> pdb=" O LEU T 492 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE T 423 " --> pdb=" O PHE T 488 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE T 425 " --> pdb=" O LEU T 486 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR T 544 " --> pdb=" O GLY T 487 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN T 491 " --> pdb=" O GLU T 540 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU T 540 " --> pdb=" O ASN T 491 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE T 541 " --> pdb=" O ALA T 553 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE T 543 " --> pdb=" O GLY T 551 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY T 551 " --> pdb=" O PHE T 543 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LYS T 545 " --> pdb=" O ASN T 549 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASN T 549 " --> pdb=" O LYS T 545 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.685A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AC6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.007A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.849A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AC9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AD1, first strand: chain 'R' and resid 36 through 41 removed outlier: 5.750A pdb=" N LEU R 37 " --> pdb=" O LYS R 331 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS R 331 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE R 39 " --> pdb=" O LEU R 329 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA R 308 " --> pdb=" O ALA R 317 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 48 through 53 removed outlier: 3.963A pdb=" N SER R 50 " --> pdb=" O SER R 63 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS R 52 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA R 61 " --> pdb=" O LYS R 52 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER R 64 " --> pdb=" O LEU R 68 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU R 68 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS R 81 " --> pdb=" O ILE R 71 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 90 through 95 removed outlier: 3.967A pdb=" N ASP R 92 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS R 112 " --> pdb=" O SER R 104 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER R 106 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR R 110 " --> pdb=" O SER R 106 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS R 123 " --> pdb=" O ILE R 113 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP R 115 " --> pdb=" O CYS R 121 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N CYS R 121 " --> pdb=" O ASP R 115 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 136 through 137 removed outlier: 3.706A pdb=" N SER R 146 " --> pdb=" O ARG R 154 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG R 154 " --> pdb=" O SER R 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 185 through 189 removed outlier: 6.826A pdb=" N ILE R 197 " --> pdb=" O LEU R 206 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 217 through 222 removed outlier: 3.611A pdb=" N PHE R 219 " --> pdb=" O ALA R 232 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS R 221 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR R 233 " --> pdb=" O THR R 237 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR R 237 " --> pdb=" O THR R 233 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 264 through 267 removed outlier: 3.637A pdb=" N ILE R 274 " --> pdb=" O TRP R 286 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU R 297 " --> pdb=" O VAL R 283 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE R 285 " --> pdb=" O GLN R 295 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN R 295 " --> pdb=" O ILE R 285 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 610 hydrogen bond angles 0 basepair planarities 119 basepair parallelities 230 stacking parallelities Total time for adding SS restraints: 8.34 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7203 1.33 - 1.45: 6015 1.45 - 1.57: 13887 1.57 - 1.69: 579 1.69 - 1.81: 159 Bond restraints: 27843 Sorted by residual: bond pdb=" C1' DC J 46 " pdb=" N1 DC J 46 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" C3' DG J 94 " pdb=" C2' DG J 94 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C1' DC J 16 " pdb=" N1 DC J 16 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.70e+00 bond pdb=" C1' DC I 26 " pdb=" N1 DC I 26 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.22e+00 bond pdb=" C1' DC I 36 " pdb=" N1 DC I 36 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 8.92e+00 ... (remaining 27838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 37810 1.87 - 3.74: 1066 3.74 - 5.61: 30 5.61 - 7.48: 2 7.48 - 9.35: 3 Bond angle restraints: 38911 Sorted by residual: angle pdb=" O4' DT I 89 " pdb=" C1' DT I 89 " pdb=" N1 DT I 89 " ideal model delta sigma weight residual 108.00 111.55 -3.55 7.00e-01 2.04e+00 2.57e+01 angle pdb=" O4' DT J 99 " pdb=" C1' DT J 99 " pdb=" N1 DT J 99 " ideal model delta sigma weight residual 108.00 111.38 -3.38 7.00e-01 2.04e+00 2.34e+01 angle pdb=" O4' DA I 90 " pdb=" C1' DA I 90 " pdb=" N9 DA I 90 " ideal model delta sigma weight residual 108.00 111.31 -3.31 7.00e-01 2.04e+00 2.23e+01 angle pdb=" O4' DA J 14 " pdb=" C4' DA J 14 " pdb=" C3' DA J 14 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" O4' DC J 26 " pdb=" C1' DC J 26 " pdb=" N1 DC J 26 " ideal model delta sigma weight residual 108.00 111.12 -3.12 7.00e-01 2.04e+00 1.98e+01 ... (remaining 38906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 14245 33.70 - 67.40: 1702 67.40 - 101.10: 52 101.10 - 134.80: 0 134.80 - 168.50: 4 Dihedral angle restraints: 16003 sinusoidal: 8404 harmonic: 7599 Sorted by residual: dihedral pdb=" CA PRO N 334 " pdb=" C PRO N 334 " pdb=" N ASP N 335 " pdb=" CA ASP N 335 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 28.50 -168.50 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 65.33 154.67 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 16000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3038 0.036 - 0.072: 731 0.072 - 0.109: 204 0.109 - 0.145: 281 0.145 - 0.181: 83 Chirality restraints: 4337 Sorted by residual: chirality pdb=" C3' DT J 105 " pdb=" C4' DT J 105 " pdb=" O3' DT J 105 " pdb=" C2' DT J 105 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" C3' DA J 19 " pdb=" C4' DA J 19 " pdb=" O3' DA J 19 " pdb=" C2' DA J 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" C3' DA I 20 " pdb=" C4' DA I 20 " pdb=" O3' DA I 20 " pdb=" C2' DA I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 4334 not shown) Planarity restraints: 3964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 41 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" CD GLU C 41 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU C 41 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 41 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 70 " 0.023 2.00e-02 2.50e+03 1.01e-02 3.07e+00 pdb=" N9 DG J 70 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG J 70 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 70 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG J 70 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG J 70 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG J 70 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG J 70 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG J 70 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG J 70 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG J 70 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG J 70 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 3 " -0.021 2.00e-02 2.50e+03 9.76e-03 2.86e+00 pdb=" N9 DG I 3 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG I 3 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 3 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 3 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG I 3 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 3 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 3 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 3 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG I 3 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 3 " 0.001 2.00e-02 2.50e+03 ... (remaining 3961 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 9831 2.89 - 3.39: 26477 3.39 - 3.89: 46045 3.89 - 4.40: 52847 4.40 - 4.90: 79531 Nonbonded interactions: 214731 Sorted by model distance: nonbonded pdb=" O GLY G 37 " pdb=" OD1 ASN G 38 " model vdw 2.387 3.040 nonbonded pdb=" O HIS T 613 " pdb=" OG1 THR T 616 " model vdw 2.396 3.040 nonbonded pdb=" O ALA N 17 " pdb=" O ILE N 320 " model vdw 2.421 3.040 nonbonded pdb=" O PRO O 37 " pdb=" OE1 GLN O 41 " model vdw 2.426 3.040 nonbonded pdb=" OD2 ASP R 108 " pdb=" OG1 THR R 110 " model vdw 2.439 3.040 ... (remaining 214726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 19 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } ncs_group { reference = chain 'P' selection = (chain 'Q' and (resid 46 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2)))) } 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 group one per residue 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: 11.380 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: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.240 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 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 : 0.004 0.104 27843 Z= 0.351 Angle : 0.645 9.352 38911 Z= 0.502 Chirality : 0.051 0.181 4337 Planarity : 0.003 0.043 3964 Dihedral : 22.979 168.504 11103 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.62 % Favored : 94.26 % Rotamer: Outliers : 1.60 % Allowed : 20.53 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.16), residues: 2580 helix: -1.19 (0.19), residues: 703 sheet: -1.82 (0.25), residues: 414 loop : -1.59 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 228 TYR 0.017 0.001 TYR D 40 PHE 0.007 0.001 PHE K5453 TRP 0.006 0.001 TRP R 286 HIS 0.004 0.001 HIS N 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.35 (27843) covalent geometry : angle 0.64489 / 0.50 (38911) hydrogen bonds : bond 0.23326 / 15.35 ( 928) hydrogen bonds : angle 8.33288 / 5.69 ( 2344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.7759 (tpp) cc_final: 0.7354 (tpp) REVERT: K 5053 ASP cc_start: 0.4763 (OUTLIER) cc_final: 0.4141 (m-30) REVERT: K 5196 MET cc_start: 0.4171 (tpt) cc_final: 0.1210 (mtt) REVERT: N 225 TYR cc_start: 0.8444 (m-80) cc_final: 0.8243 (m-80) REVERT: T 351 HIS cc_start: 0.2394 (OUTLIER) cc_final: 0.1587 (t70) REVERT: A 41 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6736 (t80) REVERT: E 59 GLU cc_start: 0.8485 (pp20) cc_final: 0.8245 (pp20) REVERT: F 20 LYS cc_start: 0.6068 (tptt) cc_final: 0.5776 (mmtt) REVERT: F 63 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7163 (mp0) REVERT: H 93 GLU cc_start: 0.8801 (mp0) cc_final: 0.8489 (mp0) outliers start: 36 outliers final: 25 residues processed: 193 average time/residue: 0.1869 time to fit residues: 58.0572 Evaluate side-chains 163 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1538 PHE Chi-restraints excluded: chain K residue 5020 LEU Chi-restraints excluded: chain K residue 5053 ASP Chi-restraints excluded: chain K residue 5070 TYR Chi-restraints excluded: chain K residue 5132 LEU Chi-restraints excluded: chain K residue 5226 CYS Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain T residue 351 HIS Chi-restraints excluded: chain T residue 594 MET Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 122 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 2 GLN K1377 GLN K5474 ASN T 334 HIS T 414 HIS T 448 GLN B 75 HIS C 38 ASN R 136 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.107535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.071099 restraints weight = 122576.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.071999 restraints weight = 60419.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.071710 restraints weight = 38081.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.072003 restraints weight = 35144.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.071759 restraints weight = 33258.660| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27843 Z= 0.188 Angle : 0.663 11.526 38911 Z= 0.367 Chirality : 0.046 0.265 4337 Planarity : 0.004 0.050 3964 Dihedral : 25.033 172.663 6085 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.81 % Favored : 94.15 % Rotamer: Outliers : 4.04 % Allowed : 19.56 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.16), residues: 2580 helix: -0.55 (0.19), residues: 745 sheet: -1.54 (0.25), residues: 410 loop : -1.57 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.019 0.002 TYR F 88 PHE 0.011 0.001 PHE K5241 TRP 0.010 0.001 TRP R 95 HIS 0.005 0.001 HIS T 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (27843) covalent geometry : angle 0.66301 / 0.37 (38911) hydrogen bonds : bond 0.06693 / 4.40 ( 928) hydrogen bonds : angle 5.78429 / 3.95 ( 2344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 147 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.8663 (tpp) cc_final: 0.8201 (tpp) REVERT: K 5011 GLU cc_start: -0.0035 (OUTLIER) cc_final: -0.0400 (pt0) REVERT: K 5024 LYS cc_start: 0.4744 (tppt) cc_final: 0.4300 (tptm) REVERT: K 5053 ASP cc_start: 0.5511 (m-30) cc_final: 0.5010 (m-30) REVERT: K 5196 MET cc_start: 0.4909 (tpt) cc_final: 0.1949 (mtt) REVERT: K 5294 PHE cc_start: 0.3356 (OUTLIER) cc_final: 0.2957 (m-80) REVERT: N 47 ARG cc_start: 0.2924 (OUTLIER) cc_final: 0.2685 (ttp-170) REVERT: A 41 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6823 (t80) REVERT: A 94 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: H 63 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8637 (t0) REVERT: H 109 HIS cc_start: 0.8462 (OUTLIER) cc_final: 0.8098 (m170) REVERT: Q 48 LEU cc_start: 0.7107 (tp) cc_final: 0.6596 (tp) outliers start: 91 outliers final: 53 residues processed: 219 average time/residue: 0.1808 time to fit residues: 64.3042 Evaluate side-chains 190 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 130 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain K residue 1530 MET Chi-restraints excluded: chain K residue 1538 PHE Chi-restraints excluded: chain K residue 5011 GLU Chi-restraints excluded: chain K residue 5020 LEU Chi-restraints excluded: chain K residue 5070 TYR Chi-restraints excluded: chain K residue 5135 MET Chi-restraints excluded: chain K residue 5167 SER Chi-restraints excluded: chain K residue 5294 PHE Chi-restraints excluded: chain K residue 5326 LEU Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain T residue 475 HIS Chi-restraints excluded: chain T residue 557 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 121 PRO Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain P residue 87 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 273 optimal weight: 20.0000 chunk 152 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 281 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 92 GLN ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.108336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073348 restraints weight = 121991.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.073516 restraints weight = 73074.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.073400 restraints weight = 44451.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.074952 restraints weight = 37605.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.073932 restraints weight = 38411.717| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27843 Z= 0.134 Angle : 0.582 9.718 38911 Z= 0.328 Chirality : 0.043 0.237 4337 Planarity : 0.003 0.060 3964 Dihedral : 25.132 172.643 6068 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 3.19 % Allowed : 21.11 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.16), residues: 2580 helix: -0.20 (0.19), residues: 740 sheet: -1.40 (0.25), residues: 422 loop : -1.50 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.024 0.001 TYR D 40 PHE 0.011 0.001 PHE Q 95 TRP 0.027 0.001 TRP T 440 HIS 0.005 0.001 HIS R 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (27843) covalent geometry : angle 0.58221 / 0.33 (38911) hydrogen bonds : bond 0.05444 / 3.58 ( 928) hydrogen bonds : angle 5.15522 / 3.52 ( 2344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 147 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.8754 (tpp) cc_final: 0.8188 (tpp) REVERT: O 45 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6397 (m-10) REVERT: K 5011 GLU cc_start: 0.0073 (OUTLIER) cc_final: -0.0231 (pt0) REVERT: K 5053 ASP cc_start: 0.5420 (m-30) cc_final: 0.4872 (m-30) REVERT: K 5196 MET cc_start: 0.4245 (tpt) cc_final: 0.1378 (mtt) REVERT: N 309 ILE cc_start: 0.9322 (mm) cc_final: 0.9110 (mt) REVERT: A 94 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: C 92 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7517 (tm-30) REVERT: F 84 MET cc_start: 0.8341 (tpp) cc_final: 0.7640 (tpp) REVERT: H 109 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8130 (m170) REVERT: R 304 VAL cc_start: -0.0018 (OUTLIER) cc_final: -0.0228 (p) outliers start: 72 outliers final: 47 residues processed: 206 average time/residue: 0.1704 time to fit residues: 58.3817 Evaluate side-chains 185 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 45 PHE Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain K residue 1538 PHE Chi-restraints excluded: chain K residue 5011 GLU Chi-restraints excluded: chain K residue 5020 LEU Chi-restraints excluded: chain K residue 5070 TYR Chi-restraints excluded: chain K residue 5090 THR Chi-restraints excluded: chain K residue 5135 MET Chi-restraints excluded: chain K residue 5326 LEU Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain T residue 475 HIS Chi-restraints excluded: chain T residue 557 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 248 CYS Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain P residue 87 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 171 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 239 optimal weight: 0.9980 chunk 273 optimal weight: 7.9990 chunk 161 optimal weight: 0.0970 chunk 111 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1410 ASN F 27 GLN ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.107321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.071034 restraints weight = 122671.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.071961 restraints weight = 60541.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.072318 restraints weight = 35193.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.071841 restraints weight = 37683.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.071900 restraints weight = 32488.788| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27843 Z= 0.176 Angle : 0.606 9.768 38911 Z= 0.332 Chirality : 0.044 0.253 4337 Planarity : 0.004 0.061 3964 Dihedral : 25.325 173.679 6066 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.85 % Favored : 94.11 % Rotamer: Outliers : 4.17 % Allowed : 21.24 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.16), residues: 2580 helix: -0.17 (0.19), residues: 742 sheet: -1.31 (0.25), residues: 419 loop : -1.52 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.025 0.001 TYR D 40 PHE 0.011 0.001 PHE N 159 TRP 0.013 0.001 TRP T 440 HIS 0.004 0.001 HIS R 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (27843) covalent geometry : angle 0.60563 / 0.33 (38911) hydrogen bonds : bond 0.05442 / 3.59 ( 928) hydrogen bonds : angle 4.94730 / 3.38 ( 2344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 137 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.8631 (tpp) cc_final: 0.8160 (tpp) REVERT: O 45 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6572 (m-10) REVERT: K 1556 CYS cc_start: -0.2408 (OUTLIER) cc_final: -0.2732 (p) REVERT: K 5008 GLU cc_start: -0.0733 (OUTLIER) cc_final: -0.1120 (tm-30) REVERT: K 5011 GLU cc_start: -0.0044 (OUTLIER) cc_final: -0.0521 (pt0) REVERT: K 5053 ASP cc_start: 0.5615 (m-30) cc_final: 0.5093 (m-30) REVERT: K 5196 MET cc_start: 0.4404 (tpt) cc_final: 0.1802 (mtt) REVERT: K 5274 MET cc_start: 0.3117 (pmm) cc_final: 0.2744 (pmm) REVERT: K 5327 MET cc_start: 0.1628 (ptt) cc_final: 0.1421 (ptt) REVERT: N 309 ILE cc_start: 0.9359 (mm) cc_final: 0.9144 (mt) REVERT: A 41 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.6672 (t80) REVERT: A 94 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: C 92 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7600 (tm-30) REVERT: H 109 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8178 (m-70) outliers start: 94 outliers final: 67 residues processed: 211 average time/residue: 0.1722 time to fit residues: 60.3123 Evaluate side-chains 201 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 PHE Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain K residue 1538 PHE Chi-restraints excluded: chain K residue 1556 CYS Chi-restraints excluded: chain K residue 5008 GLU Chi-restraints excluded: chain K residue 5011 GLU Chi-restraints excluded: chain K residue 5020 LEU Chi-restraints excluded: chain K residue 5070 TYR Chi-restraints excluded: chain K residue 5090 THR Chi-restraints excluded: chain K residue 5135 MET Chi-restraints excluded: chain K residue 5167 SER Chi-restraints excluded: chain K residue 5175 LEU Chi-restraints excluded: chain K residue 5474 ASN Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 235 ARG Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain T residue 468 PHE Chi-restraints excluded: chain T residue 475 HIS Chi-restraints excluded: chain T residue 557 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 248 CYS Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 81 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 27 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 230 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K5474 ASN ** N 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN H 49 HIS ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.105343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.068638 restraints weight = 122708.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.069473 restraints weight = 63082.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.069242 restraints weight = 38898.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.071129 restraints weight = 40048.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.069666 restraints weight = 34115.130| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 27843 Z= 0.281 Angle : 0.716 10.028 38911 Z= 0.382 Chirality : 0.048 0.233 4337 Planarity : 0.005 0.064 3964 Dihedral : 25.664 173.583 6065 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.79 % Rotamer: Outliers : 5.76 % Allowed : 21.24 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.16), residues: 2580 helix: -0.40 (0.19), residues: 743 sheet: -1.23 (0.25), residues: 395 loop : -1.68 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 154 TYR 0.034 0.002 TYR D 40 PHE 0.015 0.002 PHE N 159 TRP 0.011 0.002 TRP N 35 HIS 0.012 0.001 HIS R 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.28 (27843) covalent geometry : angle 0.71612 / 0.38 (38911) hydrogen bonds : bond 0.06513 / 4.32 ( 928) hydrogen bonds : angle 5.20339 / 3.56 ( 2344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 130 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.8739 (tpp) cc_final: 0.8240 (tpp) REVERT: O 45 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6484 (m-10) REVERT: K 5011 GLU cc_start: 0.0061 (OUTLIER) cc_final: -0.0299 (pt0) REVERT: K 5053 ASP cc_start: 0.5311 (m-30) cc_final: 0.4839 (m-30) REVERT: K 5196 MET cc_start: 0.4577 (tpt) cc_final: 0.1982 (mtt) REVERT: K 5274 MET cc_start: 0.3398 (pmm) cc_final: 0.2984 (pmm) REVERT: K 5294 PHE cc_start: 0.3543 (OUTLIER) cc_final: 0.2624 (m-80) REVERT: N 47 ARG cc_start: 0.3333 (OUTLIER) cc_final: 0.3080 (ttp-170) REVERT: N 309 ILE cc_start: 0.9375 (mm) cc_final: 0.8936 (tt) REVERT: T 454 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7869 (p0) REVERT: A 41 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7038 (t80) REVERT: A 94 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: C 18 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.8010 (p) REVERT: C 92 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7806 (tm-30) REVERT: E 59 GLU cc_start: 0.8340 (pp20) cc_final: 0.8124 (pp20) REVERT: G 99 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6630 (ptt90) REVERT: H 49 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.6941 (m90) REVERT: H 63 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8627 (t0) REVERT: H 109 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.8126 (m-70) outliers start: 130 outliers final: 77 residues processed: 241 average time/residue: 0.1697 time to fit residues: 68.2049 Evaluate side-chains 214 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 125 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 PHE Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain K residue 5011 GLU Chi-restraints excluded: chain K residue 5020 LEU Chi-restraints excluded: chain K residue 5070 TYR Chi-restraints excluded: chain K residue 5090 THR Chi-restraints excluded: chain K residue 5135 MET Chi-restraints excluded: chain K residue 5167 SER Chi-restraints excluded: chain K residue 5175 LEU Chi-restraints excluded: chain K residue 5186 HIS Chi-restraints excluded: chain K residue 5294 PHE Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain K residue 5474 ASN Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 235 ARG Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 328 ASN Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 468 PHE Chi-restraints excluded: chain T residue 475 HIS Chi-restraints excluded: chain T residue 552 VAL Chi-restraints excluded: chain T residue 557 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 121 PRO Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 49 HIS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 150 ASP Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 310 HIS Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain P residue 87 TYR Chi-restraints excluded: chain Q residue 81 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 134 optimal weight: 7.9990 chunk 224 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 92 optimal weight: 8.9990 chunk 281 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 249 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K5170 GLN ** K5407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.104844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.068340 restraints weight = 122804.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.069273 restraints weight = 67970.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068959 restraints weight = 40910.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.068982 restraints weight = 40203.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.069136 restraints weight = 38861.082| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 27843 Z= 0.306 Angle : 0.733 10.019 38911 Z= 0.389 Chirality : 0.049 0.240 4337 Planarity : 0.005 0.064 3964 Dihedral : 25.795 172.547 6061 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.40 % Favored : 92.52 % Rotamer: Outliers : 5.01 % Allowed : 22.13 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.16), residues: 2580 helix: -0.53 (0.19), residues: 745 sheet: -1.32 (0.25), residues: 404 loop : -1.71 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 86 TYR 0.029 0.002 TYR D 40 PHE 0.014 0.002 PHE N 32 TRP 0.011 0.002 TRP N 35 HIS 0.013 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.31 (27843) covalent geometry : angle 0.73339 / 0.39 (38911) hydrogen bonds : bond 0.06444 / 4.30 ( 928) hydrogen bonds : angle 5.21502 / 3.57 ( 2344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 126 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.8651 (tpp) cc_final: 0.8228 (tpp) REVERT: O 45 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6809 (m-10) REVERT: K 5011 GLU cc_start: 0.0263 (OUTLIER) cc_final: -0.0059 (pt0) REVERT: K 5053 ASP cc_start: 0.5039 (m-30) cc_final: 0.4488 (m-30) REVERT: K 5196 MET cc_start: 0.4699 (tpt) cc_final: 0.1994 (mtt) REVERT: K 5274 MET cc_start: 0.3150 (pmm) cc_final: 0.2849 (pmm) REVERT: K 5294 PHE cc_start: 0.3572 (OUTLIER) cc_final: 0.2628 (m-80) REVERT: N 47 ARG cc_start: 0.2882 (OUTLIER) cc_final: 0.2642 (ttp-170) REVERT: N 228 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6474 (ptm-80) REVERT: N 309 ILE cc_start: 0.9381 (mm) cc_final: 0.8952 (tt) REVERT: N 330 SER cc_start: 0.6130 (OUTLIER) cc_final: 0.5783 (p) REVERT: N 456 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7557 (t0) REVERT: T 454 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7873 (p0) REVERT: A 41 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.6948 (t80) REVERT: A 94 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: C 18 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8063 (p) REVERT: C 92 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7835 (tm-30) REVERT: G 99 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6632 (ptt90) REVERT: G 110 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8635 (p0) REVERT: H 109 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.8108 (m-70) REVERT: R 331 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8109 (tmmt) outliers start: 113 outliers final: 78 residues processed: 220 average time/residue: 0.1695 time to fit residues: 61.1102 Evaluate side-chains 214 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 121 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 PHE Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain K residue 1538 PHE Chi-restraints excluded: chain K residue 5011 GLU Chi-restraints excluded: chain K residue 5020 LEU Chi-restraints excluded: chain K residue 5070 TYR Chi-restraints excluded: chain K residue 5090 THR Chi-restraints excluded: chain K residue 5135 MET Chi-restraints excluded: chain K residue 5167 SER Chi-restraints excluded: chain K residue 5175 LEU Chi-restraints excluded: chain K residue 5186 HIS Chi-restraints excluded: chain K residue 5226 CYS Chi-restraints excluded: chain K residue 5294 PHE Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain K residue 5474 ASN Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 228 ARG Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 235 ARG Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 330 SER Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 386 PHE Chi-restraints excluded: chain N residue 456 ASN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 468 PHE Chi-restraints excluded: chain T residue 475 HIS Chi-restraints excluded: chain T residue 557 ILE Chi-restraints excluded: chain T residue 594 MET Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 121 PRO Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 310 HIS Chi-restraints excluded: chain R residue 331 LYS Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 81 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 275 optimal weight: 9.9990 chunk 83 optimal weight: 0.0570 chunk 277 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 268 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 217 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1410 ASN K5036 HIS K5480 ASN ** N 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS H 49 HIS ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.105361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.068944 restraints weight = 121229.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.070259 restraints weight = 64538.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.069595 restraints weight = 40811.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.069331 restraints weight = 41612.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.069422 restraints weight = 38148.649| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27843 Z= 0.230 Angle : 0.676 13.930 38911 Z= 0.361 Chirality : 0.047 0.272 4337 Planarity : 0.004 0.064 3964 Dihedral : 25.776 171.759 6060 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 4.83 % Allowed : 22.93 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.16), residues: 2580 helix: -0.39 (0.19), residues: 736 sheet: -1.27 (0.25), residues: 397 loop : -1.71 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 86 TYR 0.026 0.002 TYR H 83 PHE 0.013 0.001 PHE H 65 TRP 0.009 0.001 TRP K5395 HIS 0.006 0.001 HIS R 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 (27843) covalent geometry : angle 0.67554 / 0.36 (38911) hydrogen bonds : bond 0.05554 / 3.72 ( 928) hydrogen bonds : angle 4.93967 / 3.38 ( 2344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 132 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.8625 (tpp) cc_final: 0.8216 (tpp) REVERT: O 45 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6915 (m-10) REVERT: K 5011 GLU cc_start: 0.0088 (OUTLIER) cc_final: -0.0301 (pt0) REVERT: K 5053 ASP cc_start: 0.5029 (OUTLIER) cc_final: 0.4449 (m-30) REVERT: K 5196 MET cc_start: 0.4771 (tpt) cc_final: 0.2173 (mtt) REVERT: N 47 ARG cc_start: 0.2960 (OUTLIER) cc_final: 0.2745 (ttp-170) REVERT: N 228 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6521 (ptm-80) REVERT: N 309 ILE cc_start: 0.9371 (mm) cc_final: 0.8968 (tt) REVERT: N 456 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7591 (t0) REVERT: A 94 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: C 18 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.8070 (p) REVERT: C 92 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7735 (tm-30) REVERT: G 64 GLU cc_start: 0.7780 (tp30) cc_final: 0.7191 (tp30) REVERT: G 99 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6608 (ptt90) REVERT: G 110 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8614 (p0) REVERT: H 49 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.7044 (m90) REVERT: H 109 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.8039 (m-70) REVERT: R 331 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8142 (tmmt) outliers start: 109 outliers final: 73 residues processed: 221 average time/residue: 0.1492 time to fit residues: 54.5993 Evaluate side-chains 212 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 126 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 PHE Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain K residue 1538 PHE Chi-restraints excluded: chain K residue 5011 GLU Chi-restraints excluded: chain K residue 5020 LEU Chi-restraints excluded: chain K residue 5053 ASP Chi-restraints excluded: chain K residue 5070 TYR Chi-restraints excluded: chain K residue 5090 THR Chi-restraints excluded: chain K residue 5132 LEU Chi-restraints excluded: chain K residue 5135 MET Chi-restraints excluded: chain K residue 5155 VAL Chi-restraints excluded: chain K residue 5167 SER Chi-restraints excluded: chain K residue 5175 LEU Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 228 ARG Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 456 ASN Chi-restraints excluded: chain T residue 468 PHE Chi-restraints excluded: chain T residue 475 HIS Chi-restraints excluded: chain T residue 557 ILE Chi-restraints excluded: chain T residue 594 MET Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 121 PRO Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 49 HIS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 310 HIS Chi-restraints excluded: chain R residue 331 LYS Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 81 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 270 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 28 optimal weight: 0.0470 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 212 optimal weight: 0.9980 chunk 264 optimal weight: 20.0000 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.106698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.070641 restraints weight = 122542.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.071423 restraints weight = 60992.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.071220 restraints weight = 38921.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.071254 restraints weight = 35624.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.071190 restraints weight = 35704.597| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27843 Z= 0.132 Angle : 0.615 11.411 38911 Z= 0.333 Chirality : 0.044 0.259 4337 Planarity : 0.004 0.066 3964 Dihedral : 25.627 171.685 6060 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 3.90 % Allowed : 23.99 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.16), residues: 2580 helix: -0.09 (0.20), residues: 732 sheet: -1.35 (0.24), residues: 426 loop : -1.58 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.035 0.001 TYR T 506 PHE 0.012 0.001 PHE R 137 TRP 0.010 0.001 TRP R 286 HIS 0.040 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (27843) covalent geometry : angle 0.61478 / 0.33 (38911) hydrogen bonds : bond 0.04693 / 3.14 ( 928) hydrogen bonds : angle 4.62171 / 3.15 ( 2344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 138 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.8648 (tpp) cc_final: 0.8234 (tpp) REVERT: O 45 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.6972 (m-10) REVERT: K 5011 GLU cc_start: 0.0012 (OUTLIER) cc_final: -0.0381 (pt0) REVERT: K 5053 ASP cc_start: 0.5243 (OUTLIER) cc_final: 0.4680 (m-30) REVERT: K 5196 MET cc_start: 0.4699 (tpt) cc_final: 0.2158 (mtt) REVERT: N 228 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6451 (ptm-80) REVERT: N 242 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7975 (mmm) REVERT: N 309 ILE cc_start: 0.9338 (mm) cc_final: 0.8948 (tt) REVERT: N 456 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7565 (t0) REVERT: A 94 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: C 92 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7662 (tm-30) REVERT: G 99 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6591 (ptt90) REVERT: G 110 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8642 (p0) REVERT: H 109 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.8058 (m-70) REVERT: R 156 TRP cc_start: 0.7438 (OUTLIER) cc_final: 0.7179 (m100) outliers start: 88 outliers final: 67 residues processed: 211 average time/residue: 0.1460 time to fit residues: 50.9967 Evaluate side-chains 202 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 124 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 PHE Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain K residue 1538 PHE Chi-restraints excluded: chain K residue 1553 CYS Chi-restraints excluded: chain K residue 5011 GLU Chi-restraints excluded: chain K residue 5020 LEU Chi-restraints excluded: chain K residue 5053 ASP Chi-restraints excluded: chain K residue 5070 TYR Chi-restraints excluded: chain K residue 5090 THR Chi-restraints excluded: chain K residue 5135 MET Chi-restraints excluded: chain K residue 5167 SER Chi-restraints excluded: chain K residue 5175 LEU Chi-restraints excluded: chain K residue 5226 CYS Chi-restraints excluded: chain K residue 5393 THR Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 228 ARG Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 456 ASN Chi-restraints excluded: chain T residue 468 PHE Chi-restraints excluded: chain T residue 475 HIS Chi-restraints excluded: chain T residue 557 ILE Chi-restraints excluded: chain T residue 594 MET Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 156 TRP Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 310 HIS Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 81 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 171 optimal weight: 0.0870 chunk 137 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 246 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 225 optimal weight: 10.0000 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 40 GLN ** N 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.106297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.070375 restraints weight = 122202.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.070938 restraints weight = 61127.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.071545 restraints weight = 38253.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.070907 restraints weight = 37378.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.070895 restraints weight = 35748.602| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27843 Z= 0.161 Angle : 0.628 11.706 38911 Z= 0.335 Chirality : 0.045 0.274 4337 Planarity : 0.004 0.067 3964 Dihedral : 25.634 172.008 6060 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.57 % Rotamer: Outliers : 3.86 % Allowed : 24.43 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.16), residues: 2580 helix: -0.13 (0.19), residues: 748 sheet: -1.31 (0.24), residues: 438 loop : -1.57 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.031 0.002 TYR R 284 PHE 0.012 0.001 PHE R 137 TRP 0.015 0.001 TRP R 286 HIS 0.005 0.001 HIS R 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (27843) covalent geometry : angle 0.62770 / 0.34 (38911) hydrogen bonds : bond 0.04813 / 3.22 ( 928) hydrogen bonds : angle 4.60629 / 3.14 ( 2344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 130 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.8725 (tpp) cc_final: 0.8287 (tpp) REVERT: O 45 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.6934 (m-10) REVERT: K 5011 GLU cc_start: 0.0067 (OUTLIER) cc_final: -0.0355 (pt0) REVERT: K 5053 ASP cc_start: 0.5110 (OUTLIER) cc_final: 0.4540 (m-30) REVERT: K 5196 MET cc_start: 0.4595 (tpt) cc_final: 0.1966 (mtt) REVERT: K 5274 MET cc_start: 0.3394 (ptp) cc_final: 0.3062 (pmm) REVERT: N 228 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6394 (ptm-80) REVERT: N 309 ILE cc_start: 0.9339 (mm) cc_final: 0.8904 (tt) REVERT: N 330 SER cc_start: 0.6192 (OUTLIER) cc_final: 0.5870 (p) REVERT: N 456 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7512 (t0) REVERT: T 594 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6267 (pmm) REVERT: A 41 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6683 (t80) REVERT: A 94 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7415 (mt-10) REVERT: C 92 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7734 (tm-30) REVERT: G 99 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6623 (ptt90) REVERT: G 110 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8645 (p0) REVERT: H 109 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.8072 (m-70) REVERT: R 191 TYR cc_start: 0.7968 (m-80) cc_final: 0.7745 (m-80) REVERT: R 331 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8123 (tmmt) outliers start: 87 outliers final: 72 residues processed: 201 average time/residue: 0.1582 time to fit residues: 52.4594 Evaluate side-chains 212 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 127 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 PHE Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain K residue 1538 PHE Chi-restraints excluded: chain K residue 1553 CYS Chi-restraints excluded: chain K residue 5011 GLU Chi-restraints excluded: chain K residue 5020 LEU Chi-restraints excluded: chain K residue 5053 ASP Chi-restraints excluded: chain K residue 5070 TYR Chi-restraints excluded: chain K residue 5090 THR Chi-restraints excluded: chain K residue 5135 MET Chi-restraints excluded: chain K residue 5155 VAL Chi-restraints excluded: chain K residue 5167 SER Chi-restraints excluded: chain K residue 5175 LEU Chi-restraints excluded: chain K residue 5226 CYS Chi-restraints excluded: chain K residue 5393 THR Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 228 ARG Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 328 ASN Chi-restraints excluded: chain N residue 330 SER Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 456 ASN Chi-restraints excluded: chain T residue 468 PHE Chi-restraints excluded: chain T residue 557 ILE Chi-restraints excluded: chain T residue 594 MET Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 310 HIS Chi-restraints excluded: chain R residue 331 LYS Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 81 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 229 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 241 optimal weight: 0.0970 chunk 164 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 chunk 219 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 242 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 109 optimal weight: 0.3980 chunk 210 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.107244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.071747 restraints weight = 121880.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.072205 restraints weight = 61298.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.072321 restraints weight = 39230.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.072244 restraints weight = 35359.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.072379 restraints weight = 32632.872| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27843 Z= 0.120 Angle : 0.600 11.783 38911 Z= 0.323 Chirality : 0.043 0.271 4337 Planarity : 0.003 0.067 3964 Dihedral : 25.524 171.592 6057 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.50 % Rotamer: Outliers : 3.46 % Allowed : 24.75 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.16), residues: 2580 helix: 0.05 (0.20), residues: 741 sheet: -1.26 (0.25), residues: 427 loop : -1.50 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.028 0.001 TYR R 284 PHE 0.012 0.001 PHE R 137 TRP 0.019 0.001 TRP R 286 HIS 0.014 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (27843) covalent geometry : angle 0.59976 / 0.32 (38911) hydrogen bonds : bond 0.04246 / 2.83 ( 928) hydrogen bonds : angle 4.38808 / 2.99 ( 2344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 137 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.8720 (tpp) cc_final: 0.8256 (tpp) REVERT: O 45 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: K 5011 GLU cc_start: 0.0091 (OUTLIER) cc_final: -0.0313 (pt0) REVERT: K 5053 ASP cc_start: 0.5226 (OUTLIER) cc_final: 0.4667 (m-30) REVERT: K 5196 MET cc_start: 0.4419 (tpt) cc_final: 0.1813 (mtt) REVERT: K 5274 MET cc_start: 0.3334 (ptp) cc_final: 0.2970 (pmm) REVERT: N 228 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6508 (ptm-80) REVERT: N 309 ILE cc_start: 0.9306 (mm) cc_final: 0.8885 (tt) REVERT: N 456 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7431 (t0) REVERT: T 594 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6286 (pmm) REVERT: A 41 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6634 (t80) REVERT: A 94 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: C 92 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7654 (tm-30) REVERT: E 59 GLU cc_start: 0.8313 (pp20) cc_final: 0.8080 (pp20) REVERT: G 99 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6589 (ptt90) REVERT: G 110 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8633 (p0) REVERT: H 109 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.8032 (m-70) REVERT: R 156 TRP cc_start: 0.7486 (OUTLIER) cc_final: 0.7228 (m100) outliers start: 78 outliers final: 63 residues processed: 199 average time/residue: 0.1645 time to fit residues: 54.6355 Evaluate side-chains 205 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 130 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 PHE Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain K residue 1538 PHE Chi-restraints excluded: chain K residue 1553 CYS Chi-restraints excluded: chain K residue 5011 GLU Chi-restraints excluded: chain K residue 5020 LEU Chi-restraints excluded: chain K residue 5053 ASP Chi-restraints excluded: chain K residue 5070 TYR Chi-restraints excluded: chain K residue 5090 THR Chi-restraints excluded: chain K residue 5135 MET Chi-restraints excluded: chain K residue 5155 VAL Chi-restraints excluded: chain K residue 5167 SER Chi-restraints excluded: chain K residue 5175 LEU Chi-restraints excluded: chain K residue 5226 CYS Chi-restraints excluded: chain K residue 5393 THR Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 228 ARG Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 456 ASN Chi-restraints excluded: chain T residue 468 PHE Chi-restraints excluded: chain T residue 557 ILE Chi-restraints excluded: chain T residue 594 MET Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 156 TRP Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain P residue 87 TYR Chi-restraints excluded: chain Q residue 81 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 130 optimal weight: 0.0670 chunk 246 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 196 optimal weight: 0.0270 chunk 79 optimal weight: 7.9990 chunk 202 optimal weight: 0.1980 chunk 129 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 50.0000 chunk 184 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K5114 HIS ** N 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.107650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.072745 restraints weight = 121233.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.073387 restraints weight = 65797.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.072809 restraints weight = 45382.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.073015 restraints weight = 39673.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.073070 restraints weight = 38141.523| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 27843 Z= 0.119 Angle : 0.590 12.322 38911 Z= 0.318 Chirality : 0.043 0.254 4337 Planarity : 0.003 0.067 3964 Dihedral : 25.476 172.395 6057 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 3.46 % Allowed : 25.10 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.16), residues: 2580 helix: 0.13 (0.20), residues: 764 sheet: -1.17 (0.24), residues: 424 loop : -1.47 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 228 TYR 0.026 0.001 TYR F 88 PHE 0.014 0.001 PHE R 137 TRP 0.021 0.001 TRP R 286 HIS 0.013 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (27843) covalent geometry : angle 0.58998 / 0.32 (38911) hydrogen bonds : bond 0.04077 / 2.72 ( 928) hydrogen bonds : angle 4.23233 / 2.88 ( 2344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6119.07 seconds wall clock time: 105 minutes 49.82 seconds (6349.82 seconds total)