Starting phenix.real_space_refine on Thu Jun 4 12:16:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x5z_66602/06_2026/9x5z_66602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x5z_66602/06_2026/9x5z_66602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x5z_66602/06_2026/9x5z_66602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x5z_66602/06_2026/9x5z_66602.map" model { file = "/net/cci-nas-00/data/ceres_data/9x5z_66602/06_2026/9x5z_66602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x5z_66602/06_2026/9x5z_66602.cif" } resolution = 2.59 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= 0.001 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 7876 2.51 5 N 2180 2.21 5 O 2499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12625 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 312} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 312} Chain: "M" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 312} Chain: "N" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "H" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 988 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.97, per 1000 atoms: 0.24 Number of scatterers: 12625 At special positions: 0 Unit cell: (85.49, 117.86, 172.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2499 8.00 N 2180 7.00 C 7876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 274 " distance=2.04 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS K 490 " - pdb=" SG CYS K 494 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 57 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS M 490 " - pdb=" SG CYS M 494 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 274 " distance=2.04 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS N 490 " - pdb=" SG CYS N 494 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 401 " - " ASN A 25 " " NAG A 402 " - " ASN A 167 " " NAG A 403 " - " ASN A 303 " " NAG A 404 " - " ASN A 332 " " NAG B 401 " - " ASN B 25 " " NAG B 402 " - " ASN B 167 " " NAG B 403 " - " ASN B 303 " " NAG B 404 " - " ASN B 332 " " NAG C 401 " - " ASN C 25 " " NAG C 402 " - " ASN C 167 " " NAG C 403 " - " ASN C 303 " " NAG C 404 " - " ASN C 332 " " NAG D 1 " - " ASN A 145 " " NAG E 1 " - " ASN A 196 " " NAG F 1 " - " ASN B 145 " " NAG G 1 " - " ASN B 196 " " NAG I 1 " - " ASN C 145 " " NAG J 1 " - " ASN C 196 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 604.3 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 37 sheets defined 21.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.805A pdb=" N GLY A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.573A pdb=" N ALA A 130 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.507A pdb=" N LYS A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 402 removed outlier: 3.870A pdb=" N GLU K 389 " --> pdb=" O LYS K 385 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA K 390 " --> pdb=" O SER K 386 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE K 391 " --> pdb=" O THR K 387 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE K 394 " --> pdb=" O ALA K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 455 Processing helix chain 'K' and resid 457 through 469 removed outlier: 3.877A pdb=" N LEU K 464 " --> pdb=" O HIS K 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.643A pdb=" N THR B 102 " --> pdb=" O HIS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.723A pdb=" N GLY B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.715A pdb=" N ALA B 130 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 205 Processing helix chain 'M' and resid 385 through 403 removed outlier: 3.549A pdb=" N ALA M 390 " --> pdb=" O SER M 386 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE M 394 " --> pdb=" O ALA M 390 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 455 removed outlier: 3.667A pdb=" N SER M 440 " --> pdb=" O ASP M 436 " (cutoff:3.500A) Processing helix chain 'M' and resid 458 through 473 removed outlier: 3.725A pdb=" N LEU M 462 " --> pdb=" O ASP M 458 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS M 467 " --> pdb=" O ALA M 463 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS M 470 " --> pdb=" O ARG M 466 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET M 471 " --> pdb=" O LYS M 467 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU M 472 " --> pdb=" O LEU M 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 106 through 113 removed outlier: 3.836A pdb=" N GLY C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.543A pdb=" N LYS C 129 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 130' Processing helix chain 'C' and resid 196 through 205 Processing helix chain 'N' and resid 387 through 403 removed outlier: 3.539A pdb=" N LYS N 393 " --> pdb=" O GLU N 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 420 through 455 Processing helix chain 'N' and resid 456 through 473 removed outlier: 3.741A pdb=" N LYS N 467 " --> pdb=" O ALA N 463 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU N 468 " --> pdb=" O LEU N 464 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS N 470 " --> pdb=" O ARG N 466 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET N 471 " --> pdb=" O LYS N 467 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY N 473 " --> pdb=" O LYS N 469 " (cutoff:3.500A) Processing helix chain 'N' and resid 491 through 495 Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.760A pdb=" N TYR H 37 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 removed outlier: 3.943A pdb=" N PHE L 99 " --> pdb=" O SER L 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 removed outlier: 3.509A pdb=" N THR A 34 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.175A pdb=" N ASN A 43 " --> pdb=" O ALA A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.768A pdb=" N ARG A 50 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 removed outlier: 7.401A pdb=" N VAL A 189 " --> pdb=" O PRO A 269 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 266 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP A 158 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AA8, first strand: chain 'A' and resid 172 through 176 Processing sheet with id=AA9, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AB1, first strand: chain 'K' and resid 369 through 371 Processing sheet with id=AB2, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.768A pdb=" N GLY B 6 " --> pdb=" O GLY M 369 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AB5, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.341A pdb=" N ASN B 43 " --> pdb=" O ALA B 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AB8, first strand: chain 'B' and resid 116 through 119 removed outlier: 7.267A pdb=" N VAL B 189 " --> pdb=" O PRO B 269 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL B 266 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP B 158 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 116 through 119 Processing sheet with id=AC1, first strand: chain 'B' and resid 172 through 176 Processing sheet with id=AC2, first strand: chain 'B' and resid 300 through 302 Processing sheet with id=AC3, first strand: chain 'C' and resid 6 through 7 removed outlier: 4.277A pdb=" N GLY C 6 " --> pdb=" O GLY N 369 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY N 369 " --> pdb=" O GLY C 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AC5, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AC6, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.255A pdb=" N ASN C 43 " --> pdb=" O ALA C 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AC8, first strand: chain 'C' and resid 116 through 119 removed outlier: 7.255A pdb=" N VAL C 189 " --> pdb=" O PRO C 269 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL C 266 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TRP C 158 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AD1, first strand: chain 'C' and resid 172 through 176 Processing sheet with id=AD2, first strand: chain 'C' and resid 300 through 302 Processing sheet with id=AD3, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 12 through 13 removed outlier: 6.831A pdb=" N MET H 39 " --> pdb=" O THR H 55 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 12 through 13 removed outlier: 3.731A pdb=" N HIS H 117 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AD8, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.886A pdb=" N ASP L 86 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER L 83 " --> pdb=" O ASP L 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 66 through 67 removed outlier: 6.629A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU L 39 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR L 117 " --> pdb=" O GLN L 106 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 66 through 67 removed outlier: 6.629A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU L 39 " --> pdb=" O SER L 55 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2094 1.31 - 1.45: 3359 1.45 - 1.58: 7318 1.58 - 1.72: 0 1.72 - 1.86: 97 Bond restraints: 12868 Sorted by residual: bond pdb=" C GLN A 172 " pdb=" O GLN A 172 " ideal model delta sigma weight residual 1.235 1.173 0.062 1.23e-02 6.61e+03 2.58e+01 bond pdb=" C GLN C 172 " pdb=" O GLN C 172 " ideal model delta sigma weight residual 1.235 1.181 0.055 1.23e-02 6.61e+03 1.98e+01 bond pdb=" C GLN B 172 " pdb=" O GLN B 172 " ideal model delta sigma weight residual 1.235 1.181 0.055 1.23e-02 6.61e+03 1.98e+01 bond pdb=" C ARG A 69 " pdb=" N PRO A 70 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.08e-02 8.57e+03 6.61e+00 bond pdb=" N HIS N 368 " pdb=" CA HIS N 368 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.23e-02 6.61e+03 6.57e+00 ... (remaining 12863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 17116 2.75 - 5.49: 281 5.49 - 8.24: 35 8.24 - 10.98: 9 10.98 - 13.73: 3 Bond angle restraints: 17444 Sorted by residual: angle pdb=" C GLY A 93 " pdb=" N CYS A 94 " pdb=" CA CYS A 94 " ideal model delta sigma weight residual 121.54 135.27 -13.73 1.91e+00 2.74e-01 5.17e+01 angle pdb=" N GLY C 238 " pdb=" CA GLY C 238 " pdb=" C GLY C 238 " ideal model delta sigma weight residual 111.67 117.96 -6.29 9.20e-01 1.18e+00 4.67e+01 angle pdb=" C GLY C 93 " pdb=" N CYS C 94 " pdb=" CA CYS C 94 " ideal model delta sigma weight residual 121.54 134.20 -12.66 1.91e+00 2.74e-01 4.39e+01 angle pdb=" C GLY B 93 " pdb=" N CYS B 94 " pdb=" CA CYS B 94 " ideal model delta sigma weight residual 121.54 133.64 -12.10 1.91e+00 2.74e-01 4.01e+01 angle pdb=" N GLN N 492 " pdb=" CA GLN N 492 " pdb=" C GLN N 492 " ideal model delta sigma weight residual 111.11 117.46 -6.35 1.20e+00 6.94e-01 2.80e+01 ... (remaining 17439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 7284 17.67 - 35.34: 674 35.34 - 53.00: 141 53.00 - 70.67: 28 70.67 - 88.34: 22 Dihedral angle restraints: 8149 sinusoidal: 3576 harmonic: 4573 Sorted by residual: dihedral pdb=" CB CYS K 490 " pdb=" SG CYS K 490 " pdb=" SG CYS K 494 " pdb=" CB CYS K 494 " ideal model delta sinusoidal sigma weight residual -86.00 -174.34 88.34 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS N 490 " pdb=" SG CYS N 490 " pdb=" SG CYS N 494 " pdb=" CB CYS N 494 " ideal model delta sinusoidal sigma weight residual -86.00 -162.48 76.48 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CA ASP A 236 " pdb=" C ASP A 236 " pdb=" N GLY A 237 " pdb=" CA GLY A 237 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 8146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1957 0.127 - 0.254: 76 0.254 - 0.380: 2 0.380 - 0.507: 2 0.507 - 0.634: 3 Chirality restraints: 2040 Sorted by residual: chirality pdb=" C1 NAG C 402 " pdb=" ND2 ASN C 167 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 167 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 145 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.55e+00 ... (remaining 2037 not shown) Planarity restraints: 2237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 94 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.05e+01 pdb=" C CYS A 94 " -0.078 2.00e-02 2.50e+03 pdb=" O CYS A 94 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE A 95 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 94 " 0.022 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C CYS B 94 " -0.074 2.00e-02 2.50e+03 pdb=" O CYS B 94 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE B 95 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 94 " -0.021 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C CYS C 94 " 0.071 2.00e-02 2.50e+03 pdb=" O CYS C 94 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE C 95 " -0.025 2.00e-02 2.50e+03 ... (remaining 2234 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 59 2.49 - 3.09: 7561 3.09 - 3.70: 18622 3.70 - 4.30: 29184 4.30 - 4.90: 48337 Nonbonded interactions: 103763 Sorted by model distance: nonbonded pdb=" O THR A 8 " pdb=" CE3 TRP K 367 " model vdw 1.888 3.340 nonbonded pdb=" O THR A 8 " pdb=" CZ3 TRP K 367 " model vdw 2.185 3.340 nonbonded pdb=" OD2 ASP A 64 " pdb=" OG SER A 92 " model vdw 2.277 3.040 nonbonded pdb=" OD2 ASP C 64 " pdb=" OG SER C 92 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR C 178 " pdb=" O GLU C 184 " model vdw 2.285 3.040 ... (remaining 103758 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.970 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.006 0.074 12912 Z= 0.283 Angle : 0.980 17.176 17556 Z= 0.505 Chirality : 0.062 0.634 2040 Planarity : 0.007 0.077 2219 Dihedral : 14.635 86.215 5165 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.22 % Allowed : 4.69 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.99 % 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: -2.65 (0.18), residues: 1584 helix: -3.31 (0.20), residues: 288 sheet: -0.39 (0.27), residues: 347 loop : -1.83 (0.17), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 48 TYR 0.016 0.002 TYR L 107 PHE 0.020 0.003 PHE A 192 TRP 0.020 0.002 TRP H 57 HIS 0.009 0.002 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.28 (12868) covalent geometry : angle 0.91987 / 0.49 (17444) SS BOND : bond 0.00592 / 0.43 ( 20) SS BOND : angle 2.49398 / 1.48 ( 40) hydrogen bonds : bond 0.22973 / 15.66 ( 445) hydrogen bonds : angle 9.05319 / 6.21 ( 1272) link_BETA1-4 : bond 0.01128 / 0.71 ( 6) link_BETA1-4 : angle 4.05991 / 2.15 ( 18) link_NAG-ASN : bond 0.01026 / 0.46 ( 18) link_NAG-ASN : angle 5.36080 / 3.80 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 224 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 471 MET cc_start: 0.5661 (mmm) cc_final: 0.5409 (mmm) REVERT: M 393 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8420 (tttm) REVERT: M 422 GLU cc_start: 0.8373 (mp0) cc_final: 0.8126 (mp0) REVERT: H 116 ASP cc_start: 0.7147 (m-30) cc_final: 0.6914 (m-30) outliers start: 3 outliers final: 1 residues processed: 226 average time/residue: 0.6544 time to fit residues: 159.5398 Evaluate side-chains 167 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 99 HIS A 109 ASN A 217 ASN A 233 GLN K 399 ASN K 455 ASN K 491 ASN B 85 HIS B 109 ASN B 172 GLN B 233 GLN M 388 GLN M 408 ASN M 421 ASN M 441 GLN M 455 ASN M 492 GLN C 99 HIS C 109 ASN C 172 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN N 408 ASN N 492 GLN H 38 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115134 restraints weight = 13230.738| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.31 r_work: 0.3054 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12912 Z= 0.184 Angle : 0.770 10.157 17556 Z= 0.374 Chirality : 0.050 0.412 2040 Planarity : 0.006 0.067 2219 Dihedral : 9.311 100.243 2220 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.71 % Allowed : 10.41 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.99 % 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: -1.47 (0.20), residues: 1584 helix: -0.78 (0.29), residues: 300 sheet: -0.15 (0.27), residues: 366 loop : -1.41 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 48 TYR 0.012 0.001 TYR L 107 PHE 0.015 0.002 PHE B 95 TRP 0.012 0.002 TRP M 367 HIS 0.005 0.001 HIS B 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (12868) covalent geometry : angle 0.73357 / 0.37 (17444) SS BOND : bond 0.00398 / 0.26 ( 20) SS BOND : angle 1.66416 / 0.98 ( 40) hydrogen bonds : bond 0.05065 / 3.42 ( 445) hydrogen bonds : angle 5.86149 / 4.04 ( 1272) link_BETA1-4 : bond 0.00314 / 0.20 ( 6) link_BETA1-4 : angle 2.65021 / 1.39 ( 18) link_NAG-ASN : bond 0.00522 / 0.23 ( 18) link_NAG-ASN : angle 3.78333 / 2.60 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8784 (tt0) REVERT: A 167 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7856 (t0) REVERT: K 447 LEU cc_start: 0.8404 (mt) cc_final: 0.8065 (tt) REVERT: K 471 MET cc_start: 0.5744 (mmm) cc_final: 0.5382 (mmm) REVERT: B 312 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8728 (tttp) REVERT: B 335 LYS cc_start: 0.8506 (tttm) cc_final: 0.8181 (tptp) REVERT: C 8 THR cc_start: 0.8324 (m) cc_final: 0.8025 (p) REVERT: C 115 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: N 418 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7209 (mt-10) REVERT: H 116 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: L 22 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7890 (m) REVERT: L 38 LYS cc_start: 0.8323 (mttm) cc_final: 0.8109 (mttt) outliers start: 37 outliers final: 11 residues processed: 186 average time/residue: 0.5848 time to fit residues: 118.1879 Evaluate side-chains 181 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain N residue 418 GLU Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 22 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 103 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 399 ASN B 99 HIS M 441 GLN C 199 GLN N 460 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115725 restraints weight = 13391.516| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.36 r_work: 0.3057 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12912 Z= 0.145 Angle : 0.697 13.417 17556 Z= 0.334 Chirality : 0.047 0.398 2040 Planarity : 0.005 0.060 2219 Dihedral : 8.300 95.304 2219 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.35 % Allowed : 13.86 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1584 helix: 0.34 (0.31), residues: 303 sheet: 0.04 (0.27), residues: 366 loop : -1.13 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 497 TYR 0.014 0.001 TYR H 112C PHE 0.013 0.002 PHE B 95 TRP 0.008 0.001 TRP H 118 HIS 0.005 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (12868) covalent geometry : angle 0.65944 / 0.33 (17444) SS BOND : bond 0.00301 / 0.19 ( 20) SS BOND : angle 1.25857 / 0.71 ( 40) hydrogen bonds : bond 0.04050 / 2.73 ( 445) hydrogen bonds : angle 5.39432 / 3.72 ( 1272) link_BETA1-4 : bond 0.00361 / 0.21 ( 6) link_BETA1-4 : angle 2.67265 / 1.40 ( 18) link_NAG-ASN : bond 0.00474 / 0.23 ( 18) link_NAG-ASN : angle 3.75972 / 2.71 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8797 (tt0) REVERT: A 167 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7844 (t0) REVERT: K 447 LEU cc_start: 0.8426 (mt) cc_final: 0.8082 (tt) REVERT: K 459 GLU cc_start: 0.7572 (pm20) cc_final: 0.7283 (pm20) REVERT: K 471 MET cc_start: 0.5704 (mmm) cc_final: 0.5361 (mmm) REVERT: B 298 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8034 (tp30) REVERT: B 312 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8651 (tttp) REVERT: B 335 LYS cc_start: 0.8519 (tttm) cc_final: 0.8099 (tptp) REVERT: C 8 THR cc_start: 0.8181 (m) cc_final: 0.7981 (p) REVERT: C 115 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8672 (tt0) REVERT: N 416 MET cc_start: 0.4461 (OUTLIER) cc_final: 0.4076 (mpp) REVERT: N 418 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7145 (mt-10) REVERT: H 116 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7212 (m-30) REVERT: L 38 LYS cc_start: 0.8320 (mttm) cc_final: 0.8104 (mttt) outliers start: 32 outliers final: 11 residues processed: 196 average time/residue: 0.5670 time to fit residues: 121.0991 Evaluate side-chains 182 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain K residue 454 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain M residue 407 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain N residue 410 GLN Chi-restraints excluded: chain N residue 416 MET Chi-restraints excluded: chain N residue 418 GLU Chi-restraints excluded: chain H residue 116 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 399 ASN M 441 GLN N 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111271 restraints weight = 13393.241| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.42 r_work: 0.2994 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 12912 Z= 0.278 Angle : 0.815 10.011 17556 Z= 0.389 Chirality : 0.053 0.429 2040 Planarity : 0.006 0.062 2219 Dihedral : 8.506 90.120 2219 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.23 % Allowed : 15.32 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1584 helix: 0.57 (0.31), residues: 300 sheet: 0.16 (0.27), residues: 363 loop : -1.15 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 105 TYR 0.015 0.002 TYR L 107 PHE 0.015 0.003 PHE A 95 TRP 0.011 0.002 TRP H 52 HIS 0.007 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.28 (12868) covalent geometry : angle 0.77520 / 0.38 (17444) SS BOND : bond 0.00499 / 0.32 ( 20) SS BOND : angle 1.67128 / 0.98 ( 40) hydrogen bonds : bond 0.04604 / 3.13 ( 445) hydrogen bonds : angle 5.51673 / 3.81 ( 1272) link_BETA1-4 : bond 0.00280 / 0.15 ( 6) link_BETA1-4 : angle 2.71312 / 1.45 ( 18) link_NAG-ASN : bond 0.00441 / 0.29 ( 18) link_NAG-ASN : angle 4.14285 / 2.83 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8795 (tt0) REVERT: A 175 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: A 251 MET cc_start: 0.8950 (tpp) cc_final: 0.8707 (tpp) REVERT: K 447 LEU cc_start: 0.8499 (mt) cc_final: 0.8167 (tt) REVERT: K 459 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: K 471 MET cc_start: 0.5856 (mmm) cc_final: 0.5502 (mmm) REVERT: B 17 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7909 (ttmt) REVERT: B 312 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8797 (tttp) REVERT: C 8 THR cc_start: 0.8313 (m) cc_final: 0.8099 (p) REVERT: C 115 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: N 416 MET cc_start: 0.4653 (OUTLIER) cc_final: 0.4426 (mpp) REVERT: N 418 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: N 434 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7800 (tmm-80) REVERT: H 116 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7286 (m-30) outliers start: 44 outliers final: 21 residues processed: 194 average time/residue: 0.5450 time to fit residues: 115.7483 Evaluate side-chains 191 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain K residue 454 ILE Chi-restraints excluded: chain K residue 459 GLU Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain N residue 406 VAL Chi-restraints excluded: chain N residue 410 GLN Chi-restraints excluded: chain N residue 416 MET Chi-restraints excluded: chain N residue 418 GLU Chi-restraints excluded: chain N residue 434 ARG Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 116 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 128 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 113 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 399 ASN K 441 GLN N 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113963 restraints weight = 13341.436| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.51 r_work: 0.3038 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12912 Z= 0.149 Angle : 0.702 10.007 17556 Z= 0.335 Chirality : 0.048 0.399 2040 Planarity : 0.005 0.055 2219 Dihedral : 8.104 92.854 2219 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.08 % Allowed : 16.72 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1584 helix: 1.09 (0.31), residues: 300 sheet: 0.18 (0.28), residues: 356 loop : -0.97 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.011 0.001 TYR L 107 PHE 0.012 0.002 PHE A 192 TRP 0.008 0.001 TRP H 52 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (12868) covalent geometry : angle 0.66597 / 0.33 (17444) SS BOND : bond 0.00283 / 0.18 ( 20) SS BOND : angle 1.11248 / 0.63 ( 40) hydrogen bonds : bond 0.03777 / 2.54 ( 445) hydrogen bonds : angle 5.28631 / 3.64 ( 1272) link_BETA1-4 : bond 0.00382 / 0.22 ( 6) link_BETA1-4 : angle 2.60037 / 1.37 ( 18) link_NAG-ASN : bond 0.00473 / 0.22 ( 18) link_NAG-ASN : angle 3.70589 / 2.65 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8816 (tt0) REVERT: A 175 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: A 251 MET cc_start: 0.8902 (tpp) cc_final: 0.8695 (tpp) REVERT: K 447 LEU cc_start: 0.8430 (mt) cc_final: 0.8096 (tt) REVERT: K 459 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: K 471 MET cc_start: 0.5747 (mmm) cc_final: 0.5407 (mmm) REVERT: B 17 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7944 (ttmt) REVERT: N 418 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: N 434 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7832 (tmm-80) REVERT: H 59 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6538 (m-30) REVERT: H 116 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7258 (m-30) outliers start: 42 outliers final: 20 residues processed: 193 average time/residue: 0.5317 time to fit residues: 112.2623 Evaluate side-chains 193 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 454 ILE Chi-restraints excluded: chain K residue 459 GLU Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain N residue 406 VAL Chi-restraints excluded: chain N residue 410 GLN Chi-restraints excluded: chain N residue 418 GLU Chi-restraints excluded: chain N residue 434 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 22 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 30 optimal weight: 0.0670 chunk 124 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 399 ASN N 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114404 restraints weight = 13320.755| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.37 r_work: 0.3038 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12912 Z= 0.153 Angle : 0.693 10.507 17556 Z= 0.330 Chirality : 0.048 0.391 2040 Planarity : 0.005 0.054 2219 Dihedral : 8.069 97.346 2219 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.86 % Allowed : 17.82 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.21), residues: 1584 helix: 1.39 (0.31), residues: 300 sheet: 0.21 (0.27), residues: 356 loop : -0.93 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.012 0.001 TYR L 107 PHE 0.012 0.002 PHE B 95 TRP 0.008 0.001 TRP H 118 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (12868) covalent geometry : angle 0.65853 / 0.32 (17444) SS BOND : bond 0.00294 / 0.19 ( 20) SS BOND : angle 1.05790 / 0.60 ( 40) hydrogen bonds : bond 0.03686 / 2.48 ( 445) hydrogen bonds : angle 5.20978 / 3.59 ( 1272) link_BETA1-4 : bond 0.00395 / 0.23 ( 6) link_BETA1-4 : angle 2.60641 / 1.38 ( 18) link_NAG-ASN : bond 0.00414 / 0.20 ( 18) link_NAG-ASN : angle 3.58869 / 2.39 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8820 (tt0) REVERT: A 251 MET cc_start: 0.8895 (tpp) cc_final: 0.8692 (tpp) REVERT: K 441 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: K 447 LEU cc_start: 0.8456 (mt) cc_final: 0.8113 (tt) REVERT: K 459 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: K 471 MET cc_start: 0.5721 (mmm) cc_final: 0.5392 (mmm) REVERT: B 17 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7939 (ttmt) REVERT: B 335 LYS cc_start: 0.8562 (tttm) cc_final: 0.8083 (tptp) REVERT: C 23 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.8014 (tp30) REVERT: C 115 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: N 418 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: N 434 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7780 (tmm-80) REVERT: H 116 ASP cc_start: 0.7493 (m-30) cc_final: 0.7271 (m-30) outliers start: 39 outliers final: 24 residues processed: 191 average time/residue: 0.5300 time to fit residues: 110.8898 Evaluate side-chains 195 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain K residue 454 ILE Chi-restraints excluded: chain K residue 459 GLU Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain N residue 406 VAL Chi-restraints excluded: chain N residue 410 GLN Chi-restraints excluded: chain N residue 418 GLU Chi-restraints excluded: chain N residue 434 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 13 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 126 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 399 ASN N 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113455 restraints weight = 13274.753| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.31 r_work: 0.3028 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12912 Z= 0.180 Angle : 0.703 9.822 17556 Z= 0.335 Chirality : 0.048 0.384 2040 Planarity : 0.005 0.053 2219 Dihedral : 7.860 96.226 2219 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.23 % Allowed : 17.89 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1584 helix: 1.43 (0.31), residues: 300 sheet: 0.22 (0.27), residues: 356 loop : -0.91 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 105 TYR 0.013 0.001 TYR L 107 PHE 0.013 0.002 PHE C 95 TRP 0.008 0.001 TRP H 118 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (12868) covalent geometry : angle 0.66855 / 0.33 (17444) SS BOND : bond 0.00330 / 0.21 ( 20) SS BOND : angle 1.11665 / 0.64 ( 40) hydrogen bonds : bond 0.03807 / 2.57 ( 445) hydrogen bonds : angle 5.21550 / 3.60 ( 1272) link_BETA1-4 : bond 0.00397 / 0.23 ( 6) link_BETA1-4 : angle 2.61307 / 1.39 ( 18) link_NAG-ASN : bond 0.00353 / 0.20 ( 18) link_NAG-ASN : angle 3.64772 / 2.54 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8819 (tt0) REVERT: A 251 MET cc_start: 0.8903 (tpp) cc_final: 0.8697 (tpp) REVERT: K 441 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: K 447 LEU cc_start: 0.8465 (mt) cc_final: 0.8122 (tt) REVERT: K 459 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7237 (pm20) REVERT: K 471 MET cc_start: 0.5747 (mmm) cc_final: 0.5413 (mmm) REVERT: B 17 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7955 (ttmt) REVERT: B 335 LYS cc_start: 0.8581 (tttm) cc_final: 0.8113 (tptp) REVERT: C 23 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8058 (tp30) REVERT: C 115 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8639 (tt0) REVERT: N 418 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: N 434 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7768 (tmm-80) REVERT: H 116 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7274 (m-30) REVERT: L 77 SER cc_start: 0.8134 (m) cc_final: 0.7790 (p) outliers start: 44 outliers final: 24 residues processed: 196 average time/residue: 0.5007 time to fit residues: 107.9700 Evaluate side-chains 199 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain K residue 454 ILE Chi-restraints excluded: chain K residue 459 GLU Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain N residue 406 VAL Chi-restraints excluded: chain N residue 410 GLN Chi-restraints excluded: chain N residue 418 GLU Chi-restraints excluded: chain N residue 434 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 22 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 15 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 77 optimal weight: 0.0040 chunk 31 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 126 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 399 ASN N 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115227 restraints weight = 13255.503| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.40 r_work: 0.3047 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12912 Z= 0.136 Angle : 0.658 9.847 17556 Z= 0.314 Chirality : 0.046 0.360 2040 Planarity : 0.004 0.051 2219 Dihedral : 7.718 101.818 2219 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.01 % Allowed : 18.40 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.21), residues: 1584 helix: 1.72 (0.31), residues: 300 sheet: 0.27 (0.27), residues: 356 loop : -0.85 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.010 0.001 TYR L 107 PHE 0.012 0.002 PHE C 95 TRP 0.007 0.001 TRP H 118 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (12868) covalent geometry : angle 0.62657 / 0.31 (17444) SS BOND : bond 0.00263 / 0.17 ( 20) SS BOND : angle 0.96490 / 0.54 ( 40) hydrogen bonds : bond 0.03484 / 2.34 ( 445) hydrogen bonds : angle 5.10418 / 3.52 ( 1272) link_BETA1-4 : bond 0.00424 / 0.25 ( 6) link_BETA1-4 : angle 2.59008 / 1.36 ( 18) link_NAG-ASN : bond 0.00380 / 0.20 ( 18) link_NAG-ASN : angle 3.29309 / 2.28 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8823 (tt0) REVERT: A 200 MET cc_start: 0.8810 (mmm) cc_final: 0.8577 (mmm) REVERT: K 441 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: K 447 LEU cc_start: 0.8436 (mt) cc_final: 0.8102 (tt) REVERT: K 459 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: K 471 MET cc_start: 0.5871 (mmm) cc_final: 0.5566 (mmm) REVERT: B 17 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7972 (ttmt) REVERT: B 335 LYS cc_start: 0.8557 (tttm) cc_final: 0.8082 (tptp) REVERT: C 23 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: C 115 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: N 418 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7208 (mt-10) REVERT: N 434 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7836 (tmm-80) REVERT: H 59 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: H 116 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: L 77 SER cc_start: 0.8167 (m) cc_final: 0.7866 (p) outliers start: 41 outliers final: 21 residues processed: 200 average time/residue: 0.5493 time to fit residues: 120.1768 Evaluate side-chains 199 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain K residue 454 ILE Chi-restraints excluded: chain K residue 459 GLU Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain N residue 400 SER Chi-restraints excluded: chain N residue 406 VAL Chi-restraints excluded: chain N residue 410 GLN Chi-restraints excluded: chain N residue 418 GLU Chi-restraints excluded: chain N residue 434 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 22 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 152 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 399 ASN M 441 GLN N 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114748 restraints weight = 13296.109| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.54 r_work: 0.3034 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12912 Z= 0.152 Angle : 0.675 9.816 17556 Z= 0.322 Chirality : 0.047 0.366 2040 Planarity : 0.004 0.052 2219 Dihedral : 7.708 102.639 2219 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.79 % Allowed : 18.70 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1584 helix: 2.16 (0.32), residues: 282 sheet: 0.29 (0.27), residues: 356 loop : -0.78 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.012 0.001 TYR L 107 PHE 0.013 0.002 PHE B 95 TRP 0.008 0.001 TRP H 118 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (12868) covalent geometry : angle 0.64361 / 0.31 (17444) SS BOND : bond 0.00279 / 0.19 ( 20) SS BOND : angle 1.30031 / 0.74 ( 40) hydrogen bonds : bond 0.03546 / 2.39 ( 445) hydrogen bonds : angle 5.10780 / 3.53 ( 1272) link_BETA1-4 : bond 0.00409 / 0.24 ( 6) link_BETA1-4 : angle 2.58073 / 1.36 ( 18) link_NAG-ASN : bond 0.00379 / 0.20 ( 18) link_NAG-ASN : angle 3.30699 / 2.29 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8837 (tt0) REVERT: K 441 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: K 447 LEU cc_start: 0.8449 (mt) cc_final: 0.8114 (tt) REVERT: K 459 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: K 471 MET cc_start: 0.5969 (mmm) cc_final: 0.5671 (mmm) REVERT: B 17 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7969 (ttmt) REVERT: B 335 LYS cc_start: 0.8582 (tttm) cc_final: 0.8115 (tptp) REVERT: C 115 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: N 418 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: N 434 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7792 (tmm-80) REVERT: H 116 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7254 (m-30) REVERT: L 77 SER cc_start: 0.8227 (m) cc_final: 0.7941 (p) outliers start: 38 outliers final: 24 residues processed: 192 average time/residue: 0.5178 time to fit residues: 108.8779 Evaluate side-chains 200 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain K residue 454 ILE Chi-restraints excluded: chain K residue 459 GLU Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain N residue 400 SER Chi-restraints excluded: chain N residue 406 VAL Chi-restraints excluded: chain N residue 410 GLN Chi-restraints excluded: chain N residue 418 GLU Chi-restraints excluded: chain N residue 434 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 25 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 399 ASN M 441 GLN N 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114334 restraints weight = 13354.648| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.48 r_work: 0.3028 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12912 Z= 0.163 Angle : 0.682 9.834 17556 Z= 0.325 Chirality : 0.047 0.371 2040 Planarity : 0.004 0.053 2219 Dihedral : 7.736 105.193 2219 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.86 % Allowed : 18.70 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1584 helix: 2.17 (0.32), residues: 282 sheet: 0.31 (0.28), residues: 356 loop : -0.80 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.012 0.001 TYR L 107 PHE 0.012 0.002 PHE B 95 TRP 0.008 0.001 TRP H 118 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (12868) covalent geometry : angle 0.65132 / 0.32 (17444) SS BOND : bond 0.00296 / 0.20 ( 20) SS BOND : angle 1.15753 / 0.67 ( 40) hydrogen bonds : bond 0.03621 / 2.44 ( 445) hydrogen bonds : angle 5.12940 / 3.54 ( 1272) link_BETA1-4 : bond 0.00402 / 0.23 ( 6) link_BETA1-4 : angle 2.59386 / 1.37 ( 18) link_NAG-ASN : bond 0.00339 / 0.19 ( 18) link_NAG-ASN : angle 3.31790 / 2.28 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8819 (tt0) REVERT: K 441 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8398 (tt0) REVERT: K 447 LEU cc_start: 0.8470 (mt) cc_final: 0.8122 (tt) REVERT: K 459 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: K 471 MET cc_start: 0.6021 (mmm) cc_final: 0.5750 (mmm) REVERT: B 17 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7972 (ttmt) REVERT: B 335 LYS cc_start: 0.8572 (tttm) cc_final: 0.8103 (tptp) REVERT: C 115 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: N 418 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: N 434 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7814 (tmm-80) REVERT: H 116 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: L 77 SER cc_start: 0.8356 (m) cc_final: 0.8030 (p) outliers start: 39 outliers final: 28 residues processed: 196 average time/residue: 0.5219 time to fit residues: 112.3154 Evaluate side-chains 201 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain K residue 454 ILE Chi-restraints excluded: chain K residue 459 GLU Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain N residue 400 SER Chi-restraints excluded: chain N residue 406 VAL Chi-restraints excluded: chain N residue 410 GLN Chi-restraints excluded: chain N residue 418 GLU Chi-restraints excluded: chain N residue 434 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 144 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 399 ASN M 441 GLN N 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115586 restraints weight = 13362.598| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.49 r_work: 0.3052 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12912 Z= 0.126 Angle : 0.648 9.795 17556 Z= 0.309 Chirality : 0.046 0.348 2040 Planarity : 0.004 0.051 2219 Dihedral : 7.554 104.891 2219 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.49 % Allowed : 19.28 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.21), residues: 1584 helix: 2.36 (0.32), residues: 282 sheet: 0.32 (0.28), residues: 356 loop : -0.73 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.010 0.001 TYR L 107 PHE 0.011 0.001 PHE B 95 TRP 0.007 0.001 TRP H 52 HIS 0.003 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (12868) covalent geometry : angle 0.61878 / 0.30 (17444) SS BOND : bond 0.00230 / 0.15 ( 20) SS BOND : angle 0.94438 / 0.54 ( 40) hydrogen bonds : bond 0.03327 / 2.23 ( 445) hydrogen bonds : angle 5.01770 / 3.47 ( 1272) link_BETA1-4 : bond 0.00413 / 0.23 ( 6) link_BETA1-4 : angle 2.57705 / 1.34 ( 18) link_NAG-ASN : bond 0.00408 / 0.23 ( 18) link_NAG-ASN : angle 3.15219 / 2.14 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5370.28 seconds wall clock time: 92 minutes 12.52 seconds (5532.52 seconds total)