Starting phenix.real_space_refine on Mon Oct 26 12:51:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yby_72759/10_2026/9yby_72759.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yby_72759/10_2026/9yby_72759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yby_72759/10_2026/9yby_72759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yby_72759/10_2026/9yby_72759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yby_72759/10_2026/9yby_72759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yby_72759/10_2026/9yby_72759.map" } resolution = 2.9 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= 0.002 sd= 0.033 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 102 5.16 5 C 13050 2.51 5 N 3507 2.21 5 O 4032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20691 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2689 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 13, 'TRANS': 342} Chain: "C" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "D" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2689 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 13, 'TRANS': 342} Chain: "E" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "F" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2689 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 13, 'TRANS': 342} Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 922 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "H" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 807 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 922 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "J" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 807 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 922 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 807 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "N" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "O" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "P" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "R" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.22, per 1000 atoms: 0.20 Number of scatterers: 20691 At special positions: 0 Unit cell: (137.164, 142.34, 131.988, 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 102 16.00 O 4032 8.00 N 3507 7.00 C 13050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 366 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 334 " - pdb=" SG CYS D 343 " distance=2.03 Simple disulfide: pdb=" SG CYS D 358 " - pdb=" SG CYS D 366 " distance=2.03 Simple disulfide: pdb=" SG CYS D 390 " - pdb=" SG CYS D 395 " distance=2.03 Simple disulfide: pdb=" SG CYS D 397 " - pdb=" SG CYS D 420 " distance=2.03 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS F 195 " distance=2.02 Simple disulfide: pdb=" SG CYS F 334 " - pdb=" SG CYS F 343 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 366 " distance=2.03 Simple disulfide: pdb=" SG CYS F 390 " - pdb=" SG CYS F 395 " distance=2.03 Simple disulfide: pdb=" SG CYS F 397 " - pdb=" SG CYS F 420 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 201 " - " ASN A 29 " " NAG C 201 " - " ASN C 29 " " NAG E 201 " - " ASN E 29 " " NAG S 1 " - " ASN A 61 " " NAG T 1 " - " ASN A 67 " " NAG U 1 " - " ASN C 61 " " NAG V 1 " - " ASN C 67 " " NAG W 1 " - " ASN E 61 " " NAG X 1 " - " ASN E 67 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 854.6 milliseconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4854 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 49 sheets defined 21.9% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.527A pdb=" N ILE A 33 " --> pdb=" O ASN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 68 Processing helix chain 'A' and resid 69 through 97 removed outlier: 3.976A pdb=" N THR A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Proline residue: A 86 - end of helix Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 128 through 141 Processing helix chain 'B' and resid 146 through 156 removed outlier: 3.645A pdb=" N THR B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 194 through 218 Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 255 through 262 removed outlier: 3.694A pdb=" N ILE B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 361 Processing helix chain 'B' and resid 442 through 446 Processing helix chain 'B' and resid 455 through 469 removed outlier: 3.789A pdb=" N GLY B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 466 " --> pdb=" O ASN B 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.699A pdb=" N LEU C 30 " --> pdb=" O HIS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 68 Processing helix chain 'C' and resid 69 through 97 removed outlier: 3.918A pdb=" N THR C 82 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 128 through 141 Processing helix chain 'D' and resid 146 through 156 removed outlier: 3.642A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 185 Processing helix chain 'D' and resid 194 through 218 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 255 through 262 removed outlier: 3.900A pdb=" N ILE D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 361 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 442 through 446 Processing helix chain 'D' and resid 455 through 470 removed outlier: 3.601A pdb=" N LEU D 463 " --> pdb=" O VAL D 459 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY D 464 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN D 465 " --> pdb=" O THR D 461 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA D 466 " --> pdb=" O ASN D 462 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU D 470 " --> pdb=" O ALA D 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 removed outlier: 3.624A pdb=" N LEU E 30 " --> pdb=" O HIS E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 68 Processing helix chain 'E' and resid 69 through 97 removed outlier: 3.890A pdb=" N THR E 82 " --> pdb=" O ARG E 78 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL E 83 " --> pdb=" O LEU E 79 " (cutoff:3.500A) Proline residue: E 86 - end of helix Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 128 through 141 Processing helix chain 'F' and resid 146 through 156 removed outlier: 3.704A pdb=" N THR F 156 " --> pdb=" O ALA F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 185 Processing helix chain 'F' and resid 194 through 218 removed outlier: 3.652A pdb=" N ILE F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 222 Processing helix chain 'F' and resid 242 through 250 Processing helix chain 'F' and resid 255 through 262 removed outlier: 3.509A pdb=" N ILE F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 361 Processing helix chain 'F' and resid 362 through 366 Processing helix chain 'F' and resid 442 through 446 Processing helix chain 'F' and resid 455 through 470 removed outlier: 3.845A pdb=" N GLY F 464 " --> pdb=" O GLY F 460 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN F 465 " --> pdb=" O THR F 461 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA F 466 " --> pdb=" O ASN F 462 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU F 470 " --> pdb=" O ALA F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.114A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.581A pdb=" N ILE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.084A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.687A pdb=" N ILE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.175A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.651A pdb=" N ASP M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing helix chain 'M' and resid 53 through 56 Processing helix chain 'M' and resid 62 through 65 removed outlier: 3.910A pdb=" N LYS M 65 " --> pdb=" O ASP M 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 62 through 65' Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.693A pdb=" N ASP M 90 " --> pdb=" O ARG M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.594A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.716A pdb=" N ASP O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 28 through 32' Processing helix chain 'O' and resid 53 through 56 Processing helix chain 'O' and resid 62 through 65 removed outlier: 3.607A pdb=" N LYS O 65 " --> pdb=" O ASP O 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 62 through 65' Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.672A pdb=" N ASP O 90 " --> pdb=" O ARG O 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.669A pdb=" N ASP Q 31 " --> pdb=" O THR Q 28 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE Q 32 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 28 through 32' Processing helix chain 'Q' and resid 53 through 56 Processing helix chain 'Q' and resid 62 through 65 removed outlier: 3.850A pdb=" N LYS Q 65 " --> pdb=" O ASP Q 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 65' Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.752A pdb=" N ASP Q 90 " --> pdb=" O ARG Q 87 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR Q 91 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 87 through 91' Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.610A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 161 through 164 removed outlier: 6.667A pdb=" N VAL A 36 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU B 299 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 38 " --> pdb=" O HIS B 297 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N HIS B 297 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N SER A 40 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE B 295 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N SER A 42 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 9.431A pdb=" N GLY B 293 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS A 44 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 291 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N MET A 46 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 289 " --> pdb=" O MET A 46 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG A 48 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR B 287 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER A 50 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 285 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 229 through 230 removed outlier: 5.718A pdb=" N ALA B 267 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA B 284 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE B 269 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N SER B 282 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 285 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER A 50 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR B 287 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG A 48 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 289 " --> pdb=" O MET A 46 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N MET A 46 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 291 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS A 44 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 9.431A pdb=" N GLY B 293 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N SER A 42 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE B 295 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N SER A 40 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N HIS B 297 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 38 " --> pdb=" O HIS B 297 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU B 299 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 36 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR B 341 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER A 42 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N CYS B 343 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS A 44 " --> pdb=" O CYS B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 6.844A pdb=" N VAL B 116 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLN D 431 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 118 " --> pdb=" O GLN D 431 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AA5, first strand: chain 'B' and resid 304 through 306 Processing sheet with id=AA6, first strand: chain 'B' and resid 413 through 415 Processing sheet with id=AA7, first strand: chain 'B' and resid 396 through 397 removed outlier: 4.546A pdb=" N THR B 429 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 325 through 327 removed outlier: 9.433A pdb=" N GLU D 290 " --> pdb=" O MET C 46 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N MET C 46 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.072A pdb=" N LYS D 292 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N LYS C 44 " --> pdb=" O LYS D 292 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL D 294 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER C 42 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL D 296 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER C 40 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG D 298 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR D 341 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER C 42 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N CYS D 343 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS C 44 " --> pdb=" O CYS D 343 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 161 through 164 removed outlier: 4.520A pdb=" N SER C 50 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR D 285 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER D 282 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE D 269 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA D 284 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA D 267 " --> pdb=" O ALA D 284 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.916A pdb=" N VAL D 116 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N GLN F 431 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU D 118 " --> pdb=" O GLN F 431 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AB3, first strand: chain 'D' and resid 304 through 306 Processing sheet with id=AB4, first strand: chain 'F' and resid 161 through 164 removed outlier: 6.791A pdb=" N VAL E 36 " --> pdb=" O LEU F 299 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU F 299 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE E 38 " --> pdb=" O HIS F 297 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N HIS F 297 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N SER E 40 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ILE F 295 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N SER E 42 " --> pdb=" O GLY F 293 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N GLY F 293 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS E 44 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE F 291 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N MET E 46 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER F 289 " --> pdb=" O MET E 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ARG E 48 " --> pdb=" O THR F 287 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR F 287 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER E 50 " --> pdb=" O TYR F 285 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR F 285 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 229 through 230 removed outlier: 5.767A pdb=" N ALA F 267 " --> pdb=" O ALA F 284 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA F 284 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE F 269 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER F 282 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS F 271 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR F 285 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER E 50 " --> pdb=" O TYR F 285 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR F 287 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ARG E 48 " --> pdb=" O THR F 287 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER F 289 " --> pdb=" O MET E 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N MET E 46 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE F 291 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS E 44 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N GLY F 293 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N SER E 42 " --> pdb=" O GLY F 293 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ILE F 295 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N SER E 40 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N HIS F 297 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE E 38 " --> pdb=" O HIS F 297 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU F 299 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL E 36 " --> pdb=" O LEU F 299 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR F 341 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER E 42 " --> pdb=" O THR F 341 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N CYS F 343 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS E 44 " --> pdb=" O CYS F 343 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 304 through 306 Processing sheet with id=AB7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.750A pdb=" N GLU G 10 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.750A pdb=" N GLU G 10 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR G 108 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'H' and resid 4 through 6 removed outlier: 4.288A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.566A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.517A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.756A pdb=" N TYR I 108 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.573A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.774A pdb=" N GLU K 10 " --> pdb=" O THR K 116 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA K 92 " --> pdb=" O VAL K 115 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.774A pdb=" N GLU K 10 " --> pdb=" O THR K 116 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA K 92 " --> pdb=" O VAL K 115 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR K 108 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.577A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'M' and resid 58 through 60 removed outlier: 6.664A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS M 96 " --> pdb=" O TRP M 113 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TRP M 113 " --> pdb=" O CYS M 96 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG M 98 " --> pdb=" O ASP M 111 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 58 through 60 removed outlier: 6.664A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AD9, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.613A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.613A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.677A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG O 98 " --> pdb=" O ASP O 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.677A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'P' and resid 53 through 54 removed outlier: 6.596A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 53 through 54 removed outlier: 6.596A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.651A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR Q 112 " --> pdb=" O ARG Q 98 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL Q 100 " --> pdb=" O PHE Q 110 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE Q 110 " --> pdb=" O VAL Q 100 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.651A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.593A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR R 97 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.593A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2319 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: 4.21 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6692 1.34 - 1.46: 5113 1.46 - 1.58: 9138 1.58 - 1.70: 0 1.70 - 1.83: 150 Bond restraints: 21093 Sorted by residual: bond pdb=" CB CYS E 68 " pdb=" SG CYS E 68 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.49e+00 bond pdb=" CB CYS F 195 " pdb=" SG CYS F 195 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.42e+00 bond pdb=" N THR D 313 " pdb=" CA THR D 313 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.35e+00 bond pdb=" C GLN J 38 " pdb=" N LYS J 39 " ideal model delta sigma weight residual 1.340 1.276 0.064 5.87e-02 2.90e+02 1.19e+00 bond pdb=" N THR B 313 " pdb=" CA THR B 313 " ideal model delta sigma weight residual 1.460 1.475 -0.015 1.42e-02 4.96e+03 1.13e+00 ... (remaining 21088 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 28054 1.78 - 3.57: 481 3.57 - 5.35: 84 5.35 - 7.13: 16 7.13 - 8.91: 3 Bond angle restraints: 28638 Sorted by residual: angle pdb=" C LEU D 221 " pdb=" N ARG D 222 " pdb=" CA ARG D 222 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C LEU F 221 " pdb=" N ARG F 222 " pdb=" CA ARG F 222 " ideal model delta sigma weight residual 121.54 127.74 -6.20 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C LEU B 221 " pdb=" N ARG B 222 " pdb=" CA ARG B 222 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.61e+00 angle pdb=" C SER F 194 " pdb=" N CYS F 195 " pdb=" CA CYS F 195 " ideal model delta sigma weight residual 122.38 117.14 5.24 1.81e+00 3.05e-01 8.39e+00 angle pdb=" N GLY F 264 " pdb=" CA GLY F 264 " pdb=" C GLY F 264 " ideal model delta sigma weight residual 113.18 119.81 -6.63 2.37e+00 1.78e-01 7.83e+00 ... (remaining 28633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10900 17.97 - 35.94: 1395 35.94 - 53.91: 379 53.91 - 71.87: 103 71.87 - 89.84: 27 Dihedral angle restraints: 12804 sinusoidal: 5160 harmonic: 7644 Sorted by residual: dihedral pdb=" CB CYS E 68 " pdb=" SG CYS E 68 " pdb=" SG CYS F 195 " pdb=" CB CYS F 195 " ideal model delta sinusoidal sigma weight residual -86.00 -160.55 74.55 1 1.00e+01 1.00e-02 7.04e+01 dihedral pdb=" CB CYS F 397 " pdb=" SG CYS F 397 " pdb=" SG CYS F 420 " pdb=" CB CYS F 420 " ideal model delta sinusoidal sigma weight residual -86.00 -124.96 38.96 1 1.00e+01 1.00e-02 2.13e+01 dihedral pdb=" CB CYS D 397 " pdb=" SG CYS D 397 " pdb=" SG CYS D 420 " pdb=" CB CYS D 420 " ideal model delta sinusoidal sigma weight residual -86.00 -123.75 37.75 1 1.00e+01 1.00e-02 2.01e+01 ... (remaining 12801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 3265 0.137 - 0.273: 26 0.273 - 0.410: 0 0.410 - 0.547: 1 0.547 - 0.683: 2 Chirality restraints: 3294 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN C 67 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.45e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN E 67 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.40e+00 ... (remaining 3291 not shown) Planarity restraints: 3645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 67 " -0.024 2.00e-02 2.50e+03 2.30e-02 6.60e+00 pdb=" CG ASN C 67 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 67 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 67 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 223 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO F 224 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 224 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 224 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 223 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO B 224 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 224 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 224 " -0.030 5.00e-02 4.00e+02 ... (remaining 3642 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1309 2.73 - 3.27: 19281 3.27 - 3.81: 33486 3.81 - 4.36: 40663 4.36 - 4.90: 71739 Nonbonded interactions: 166478 Sorted by model distance: nonbonded pdb=" OG SER B 382 " pdb=" OH TYR B 437 " model vdw 2.186 3.040 nonbonded pdb=" OE1 GLU D 300 " pdb=" N GLY D 301 " model vdw 2.191 3.120 nonbonded pdb=" OG1 THR B 363 " pdb=" O ASP B 447 " model vdw 2.193 3.040 nonbonded pdb=" NH2 ARG G 67 " pdb=" OD2 ASP G 90 " model vdw 2.198 3.120 nonbonded pdb=" OD1 ASP L 50 " pdb=" OH TYR L 91 " model vdw 2.204 3.040 ... (remaining 166473 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 6.730 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: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.240 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.005 0.064 21132 Z= 0.202 Angle : 0.625 10.344 28731 Z= 0.318 Chirality : 0.049 0.683 3294 Planarity : 0.004 0.055 3636 Dihedral : 17.611 89.843 7878 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.96 % Allowed : 29.55 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2616 helix: 1.12 (0.25), residues: 441 sheet: 0.75 (0.20), residues: 723 loop : -0.49 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 58 TYR 0.023 0.002 TYR M 50 PHE 0.017 0.002 PHE B 278 TRP 0.012 0.002 TRP I 105 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (21093) covalent geometry : angle 0.60159 / 0.31 (28638) SS BOND : bond 0.00465 / 0.33 ( 24) SS BOND : angle 1.19923 / 0.87 ( 48) hydrogen bonds : bond 0.13478 / 9.20 ( 813) hydrogen bonds : angle 6.78100 / 4.81 ( 2319) link_BETA1-4 : bond 0.01274 / 0.59 ( 6) link_BETA1-4 : angle 3.55668 / 2.29 ( 18) link_NAG-ASN : bond 0.00654 / 0.26 ( 9) link_NAG-ASN : angle 4.54662 / 3.36 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 439 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: B 158 ASN cc_start: 0.8083 (p0) cc_final: 0.7723 (p0) REVERT: B 176 GLN cc_start: 0.8495 (tp40) cc_final: 0.7959 (tm-30) REVERT: B 261 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6603 (tp30) REVERT: B 298 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.7016 (ttt-90) REVERT: B 305 ASN cc_start: 0.6437 (m110) cc_final: 0.6003 (m-40) REVERT: B 318 TYR cc_start: 0.8191 (m-80) cc_final: 0.7962 (m-80) REVERT: B 407 ASP cc_start: 0.3693 (OUTLIER) cc_final: 0.3049 (m-30) REVERT: B 410 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.6043 (mptt) REVERT: B 425 VAL cc_start: 0.7888 (OUTLIER) cc_final: 0.7559 (m) REVERT: B 428 VAL cc_start: 0.7650 (t) cc_final: 0.7222 (m) REVERT: D 176 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8097 (tm-30) REVERT: D 261 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: D 305 ASN cc_start: 0.6842 (m110) cc_final: 0.6297 (m-40) REVERT: D 377 ASN cc_start: 0.7012 (t0) cc_final: 0.6462 (t0) REVERT: D 398 TYR cc_start: 0.8255 (t80) cc_final: 0.7861 (t80) REVERT: D 428 VAL cc_start: 0.7983 (t) cc_final: 0.7624 (m) REVERT: F 158 ASN cc_start: 0.7937 (p0) cc_final: 0.7616 (p0) REVERT: F 222 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7129 (ptm-80) REVERT: F 261 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6180 (tp30) REVERT: F 305 ASN cc_start: 0.6552 (m110) cc_final: 0.6241 (m-40) REVERT: F 339 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: F 356 GLN cc_start: 0.7488 (mt0) cc_final: 0.7186 (mp10) REVERT: F 378 ARG cc_start: 0.7860 (mmt90) cc_final: 0.6998 (tpp80) REVERT: F 389 ASN cc_start: 0.7587 (t0) cc_final: 0.6854 (t0) REVERT: G 3 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: G 68 LEU cc_start: 0.8752 (tp) cc_final: 0.8519 (mt) REVERT: I 71 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8377 (p) REVERT: K 3 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: K 50 ARG cc_start: 0.8865 (ptt180) cc_final: 0.8638 (ptm160) REVERT: K 68 LEU cc_start: 0.8725 (tp) cc_final: 0.8516 (tp) REVERT: M 83 MET cc_start: 0.8450 (mtm) cc_final: 0.8032 (mtm) REVERT: N 22 THR cc_start: 0.8031 (m) cc_final: 0.7492 (t) REVERT: N 77 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7401 (p) REVERT: O 43 LYS cc_start: 0.8443 (mttt) cc_final: 0.8060 (mmtt) REVERT: P 93 ARG cc_start: 0.8466 (mmt-90) cc_final: 0.8244 (mpt180) REVERT: P 102 THR cc_start: 0.8919 (m) cc_final: 0.8693 (t) REVERT: R 106 ILE cc_start: 0.5694 (OUTLIER) cc_final: 0.5305 (mp) outliers start: 89 outliers final: 65 residues processed: 502 average time/residue: 0.4998 time to fit residues: 289.1217 Evaluate side-chains 515 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 436 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 339 GLU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 93 HIS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain R residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 71] chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN B 328 ASN D 191 ASN D 328 ASN D 385 ASN E 26 HIS F 130 GLN I 6 GLN O 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.130399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.108156 restraints weight = 31797.270| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.28 r_work: 0.3290 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 21132 Z= 0.234 Angle : 0.639 10.538 28731 Z= 0.322 Chirality : 0.050 0.602 3294 Planarity : 0.004 0.057 3636 Dihedral : 8.192 72.938 3379 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 6.14 % Allowed : 26.84 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2616 helix: 1.06 (0.25), residues: 447 sheet: 0.61 (0.19), residues: 738 loop : -0.60 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 58 TYR 0.022 0.002 TYR M 50 PHE 0.021 0.002 PHE B 278 TRP 0.013 0.002 TRP I 105 HIS 0.004 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (21093) covalent geometry : angle 0.61419 / 0.32 (28638) SS BOND : bond 0.00469 / 0.33 ( 24) SS BOND : angle 1.37861 / 1.04 ( 48) hydrogen bonds : bond 0.04405 / 3.02 ( 813) hydrogen bonds : angle 5.15302 / 3.63 ( 2319) link_BETA1-4 : bond 0.01287 / 0.58 ( 6) link_BETA1-4 : angle 3.74199 / 2.40 ( 18) link_NAG-ASN : bond 0.00487 / 0.22 ( 9) link_NAG-ASN : angle 4.59991 / 3.32 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 444 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8387 (p0) cc_final: 0.7959 (p0) REVERT: B 261 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6276 (tp30) REVERT: B 298 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7546 (ttt-90) REVERT: B 305 ASN cc_start: 0.7084 (m110) cc_final: 0.6645 (m-40) REVERT: B 407 ASP cc_start: 0.3824 (OUTLIER) cc_final: 0.3186 (m-30) REVERT: B 428 VAL cc_start: 0.7888 (t) cc_final: 0.7446 (m) REVERT: D 176 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7929 (tm-30) REVERT: D 205 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8290 (mptp) REVERT: D 261 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: D 305 ASN cc_start: 0.7422 (m110) cc_final: 0.6848 (m-40) REVERT: D 377 ASN cc_start: 0.7443 (t0) cc_final: 0.7088 (t0) REVERT: D 398 TYR cc_start: 0.8420 (t80) cc_final: 0.8067 (t80) REVERT: D 428 VAL cc_start: 0.8323 (t) cc_final: 0.8046 (m) REVERT: F 158 ASN cc_start: 0.8359 (p0) cc_final: 0.7992 (p0) REVERT: F 292 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8233 (mppt) REVERT: F 305 ASN cc_start: 0.7221 (m110) cc_final: 0.6902 (m-40) REVERT: F 356 GLN cc_start: 0.7709 (mt0) cc_final: 0.7210 (mp10) REVERT: F 378 ARG cc_start: 0.8056 (mmt90) cc_final: 0.7267 (tpp80) REVERT: F 389 ASN cc_start: 0.7839 (t0) cc_final: 0.6985 (t0) REVERT: G 38 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7768 (ttm170) REVERT: G 106 TYR cc_start: 0.8776 (m-80) cc_final: 0.8499 (m-80) REVERT: H 4 MET cc_start: 0.8114 (mtp) cc_final: 0.7894 (mmm) REVERT: K 3 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: M 5 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8198 (m) REVERT: N 22 THR cc_start: 0.8288 (m) cc_final: 0.7913 (t) REVERT: N 31 ASN cc_start: 0.6271 (OUTLIER) cc_final: 0.6020 (p0) REVERT: O 60 TYR cc_start: 0.8854 (m-80) cc_final: 0.8649 (m-80) REVERT: P 32 TYR cc_start: 0.8524 (m-80) cc_final: 0.8309 (m-80) REVERT: P 61 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7747 (ptt-90) REVERT: P 102 THR cc_start: 0.8868 (m) cc_final: 0.8625 (m) REVERT: Q 83 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7838 (mtm) outliers start: 138 outliers final: 74 residues processed: 536 average time/residue: 0.4838 time to fit residues: 299.9920 Evaluate side-chains 526 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 441 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 328 ASN Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 120 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 71 SER Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 100 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [20, 86, 63, 235, 159, 194, 179, 178, 141, 238, 126] chunk 20 optimal weight: 0.0070 chunk 86 optimal weight: 5.9990 chunk 63 optimal weight: 0.0980 chunk 235 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 97 ASN B 328 ASN C 92 ASN D 166 GLN D 191 ASN D 328 ASN D 385 ASN F 130 GLN G 111 GLN I 6 GLN N 27 GLN O 84 ASN P 96 GLN R 96 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109310 restraints weight = 31960.173| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.30 r_work: 0.3303 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21132 Z= 0.157 Angle : 0.579 10.307 28731 Z= 0.292 Chirality : 0.048 0.537 3294 Planarity : 0.004 0.056 3636 Dihedral : 7.070 59.948 3307 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.21 % Allowed : 28.35 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2616 helix: 1.22 (0.25), residues: 447 sheet: 0.64 (0.19), residues: 744 loop : -0.56 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 165 TYR 0.016 0.001 TYR O 50 PHE 0.017 0.001 PHE F 278 TRP 0.011 0.001 TRP I 105 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (21093) covalent geometry : angle 0.55601 / 0.29 (28638) SS BOND : bond 0.00364 / 0.25 ( 24) SS BOND : angle 1.04750 / 0.78 ( 48) hydrogen bonds : bond 0.03856 / 2.66 ( 813) hydrogen bonds : angle 4.79701 / 3.38 ( 2319) link_BETA1-4 : bond 0.01151 / 0.53 ( 6) link_BETA1-4 : angle 3.31264 / 2.12 ( 18) link_NAG-ASN : bond 0.00504 / 0.23 ( 9) link_NAG-ASN : angle 4.36932 / 3.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 444 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8358 (p0) cc_final: 0.7959 (p0) REVERT: B 171 MET cc_start: 0.7882 (tpt) cc_final: 0.7530 (tpp) REVERT: B 261 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6287 (tp30) REVERT: B 298 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7563 (ttt-90) REVERT: B 305 ASN cc_start: 0.7088 (m110) cc_final: 0.6635 (m-40) REVERT: B 407 ASP cc_start: 0.3820 (OUTLIER) cc_final: 0.3225 (m-30) REVERT: B 428 VAL cc_start: 0.7872 (t) cc_final: 0.7437 (m) REVERT: D 176 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7923 (tm-30) REVERT: D 205 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8267 (mptp) REVERT: D 212 GLU cc_start: 0.8158 (tp30) cc_final: 0.7930 (tp30) REVERT: D 221 LEU cc_start: 0.8534 (tp) cc_final: 0.8273 (mt) REVERT: D 232 GLN cc_start: 0.8568 (mp10) cc_final: 0.8141 (mt0) REVERT: D 261 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6201 (mp0) REVERT: D 268 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7721 (ptp90) REVERT: D 305 ASN cc_start: 0.7411 (m110) cc_final: 0.6827 (m-40) REVERT: D 377 ASN cc_start: 0.7471 (t0) cc_final: 0.7127 (t0) REVERT: D 398 TYR cc_start: 0.8422 (t80) cc_final: 0.8079 (t80) REVERT: D 428 VAL cc_start: 0.8282 (t) cc_final: 0.8000 (m) REVERT: F 158 ASN cc_start: 0.8332 (p0) cc_final: 0.7969 (p0) REVERT: F 261 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5979 (tp30) REVERT: F 305 ASN cc_start: 0.7225 (m110) cc_final: 0.6882 (m-40) REVERT: F 356 GLN cc_start: 0.7681 (mt0) cc_final: 0.7178 (mp10) REVERT: F 378 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7274 (tpp80) REVERT: F 389 ASN cc_start: 0.7828 (t0) cc_final: 0.6985 (t0) REVERT: G 106 TYR cc_start: 0.8803 (m-80) cc_final: 0.8516 (m-80) REVERT: K 3 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: N 9 SER cc_start: 0.7949 (t) cc_final: 0.7741 (t) REVERT: N 22 THR cc_start: 0.8306 (m) cc_final: 0.7913 (t) REVERT: N 31 ASN cc_start: 0.6204 (OUTLIER) cc_final: 0.5959 (p0) REVERT: O 17 SER cc_start: 0.8056 (p) cc_final: 0.7764 (t) REVERT: P 77 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7718 (p) REVERT: P 102 THR cc_start: 0.8870 (m) cc_final: 0.8401 (p) REVERT: Q 83 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7902 (mtm) outliers start: 117 outliers final: 71 residues processed: 518 average time/residue: 0.4865 time to fit residues: 291.9533 Evaluate side-chains 524 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 443 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 117 ILE Chi-restraints excluded: chain O residue 120 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 76 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [234, 129, 111, 241, 84, 147, 231, 160, 248, 100, 171] chunk 234 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 241 optimal weight: 0.8980 chunk 84 optimal weight: 0.0470 chunk 147 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 chunk 248 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN B 130 GLN B 328 ASN D 191 ASN D 328 ASN D 385 ASN F 130 GLN G 111 GLN I 6 GLN O 84 ASN R 96 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109728 restraints weight = 31835.070| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.29 r_work: 0.3317 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21132 Z= 0.121 Angle : 0.558 10.239 28731 Z= 0.282 Chirality : 0.047 0.516 3294 Planarity : 0.004 0.054 3636 Dihedral : 6.739 59.253 3292 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.03 % Allowed : 28.17 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.16), residues: 2616 helix: 1.27 (0.25), residues: 450 sheet: 0.58 (0.19), residues: 753 loop : -0.55 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 208 TYR 0.015 0.001 TYR O 50 PHE 0.016 0.001 PHE F 278 TRP 0.011 0.001 TRP I 105 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (21093) covalent geometry : angle 0.53726 / 0.28 (28638) SS BOND : bond 0.00298 / 0.20 ( 24) SS BOND : angle 0.88160 / 0.63 ( 48) hydrogen bonds : bond 0.03515 / 2.43 ( 813) hydrogen bonds : angle 4.60925 / 3.25 ( 2319) link_BETA1-4 : bond 0.01093 / 0.50 ( 6) link_BETA1-4 : angle 3.07577 / 1.98 ( 18) link_NAG-ASN : bond 0.00533 / 0.24 ( 9) link_NAG-ASN : angle 4.24589 / 3.09 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 438 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8362 (p0) cc_final: 0.7979 (p0) REVERT: B 171 MET cc_start: 0.7880 (tpt) cc_final: 0.7532 (tpp) REVERT: B 222 ARG cc_start: 0.8340 (ptt-90) cc_final: 0.8139 (ptm-80) REVERT: B 261 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6291 (tp30) REVERT: B 298 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7560 (ttt-90) REVERT: B 305 ASN cc_start: 0.7122 (m110) cc_final: 0.6680 (m-40) REVERT: B 407 ASP cc_start: 0.3818 (OUTLIER) cc_final: 0.3225 (m-30) REVERT: B 428 VAL cc_start: 0.7867 (t) cc_final: 0.7442 (m) REVERT: D 158 ASN cc_start: 0.8423 (p0) cc_final: 0.8026 (p0) REVERT: D 176 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7896 (tm-30) REVERT: D 212 GLU cc_start: 0.8157 (tp30) cc_final: 0.7910 (tp30) REVERT: D 221 LEU cc_start: 0.8513 (tp) cc_final: 0.8237 (mt) REVERT: D 232 GLN cc_start: 0.8562 (mp10) cc_final: 0.8151 (mt0) REVERT: D 261 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: D 268 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7738 (ptp90) REVERT: D 305 ASN cc_start: 0.7451 (m110) cc_final: 0.6875 (m-40) REVERT: D 377 ASN cc_start: 0.7476 (t0) cc_final: 0.7114 (t0) REVERT: D 398 TYR cc_start: 0.8422 (t80) cc_final: 0.8023 (t80) REVERT: D 428 VAL cc_start: 0.8248 (t) cc_final: 0.7963 (m) REVERT: F 158 ASN cc_start: 0.8312 (p0) cc_final: 0.7974 (p0) REVERT: F 222 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7466 (ptm-80) REVERT: F 261 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.5957 (tp30) REVERT: F 283 ILE cc_start: 0.8635 (mm) cc_final: 0.8394 (mp) REVERT: F 305 ASN cc_start: 0.7249 (m110) cc_final: 0.6893 (m-40) REVERT: F 356 GLN cc_start: 0.7645 (mt0) cc_final: 0.7189 (mp10) REVERT: F 378 ARG cc_start: 0.8031 (mmt90) cc_final: 0.7270 (tpp80) REVERT: F 389 ASN cc_start: 0.7833 (t0) cc_final: 0.7001 (t0) REVERT: F 398 TYR cc_start: 0.7823 (t80) cc_final: 0.7324 (t80) REVERT: G 106 TYR cc_start: 0.8809 (m-80) cc_final: 0.8557 (m-80) REVERT: H 4 MET cc_start: 0.8063 (mtp) cc_final: 0.7582 (mmm) REVERT: H 55 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: H 56 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.7985 (t) REVERT: K 3 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: M 5 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8213 (m) REVERT: M 83 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8357 (mtm) REVERT: N 22 THR cc_start: 0.8313 (m) cc_final: 0.7924 (t) REVERT: N 31 ASN cc_start: 0.6139 (OUTLIER) cc_final: 0.5899 (p0) REVERT: O 17 SER cc_start: 0.8022 (p) cc_final: 0.7743 (t) REVERT: P 77 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7474 (p) REVERT: P 79 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: P 102 THR cc_start: 0.8841 (m) cc_final: 0.8398 (p) REVERT: Q 83 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7896 (mtm) outliers start: 113 outliers final: 69 residues processed: 507 average time/residue: 0.4757 time to fit residues: 279.7461 Evaluate side-chains 519 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 435 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 117 ILE Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 76 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [251, 169, 231, 163, 114, 43, 11, 212, 92, 28, 117] chunk 251 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 114 optimal weight: 0.0030 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 117 optimal weight: 0.0470 overall best weight: 0.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN B 130 GLN B 328 ASN D 159 GLN D 166 GLN D 191 ASN D 328 ASN D 385 ASN F 130 GLN I 6 GLN L 53 ASN O 84 ASN Q 84 ASN R 96 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.132802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110679 restraints weight = 31900.373| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.30 r_work: 0.3335 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21132 Z= 0.101 Angle : 0.535 9.856 28731 Z= 0.270 Chirality : 0.046 0.498 3294 Planarity : 0.004 0.052 3636 Dihedral : 6.467 59.869 3285 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.85 % Allowed : 28.44 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.17), residues: 2616 helix: 1.38 (0.25), residues: 456 sheet: 0.69 (0.19), residues: 774 loop : -0.48 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 208 TYR 0.013 0.001 TYR O 50 PHE 0.015 0.001 PHE F 278 TRP 0.010 0.001 TRP I 105 HIS 0.002 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (21093) covalent geometry : angle 0.51541 / 0.27 (28638) SS BOND : bond 0.00269 / 0.18 ( 24) SS BOND : angle 0.72733 / 0.52 ( 48) hydrogen bonds : bond 0.03179 / 2.20 ( 813) hydrogen bonds : angle 4.40159 / 3.12 ( 2319) link_BETA1-4 : bond 0.00983 / 0.46 ( 6) link_BETA1-4 : angle 2.83078 / 1.82 ( 18) link_NAG-ASN : bond 0.00569 / 0.25 ( 9) link_NAG-ASN : angle 4.04887 / 2.95 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 431 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8350 (p0) cc_final: 0.8004 (p0) REVERT: B 171 MET cc_start: 0.7852 (tpt) cc_final: 0.7505 (tpp) REVERT: B 176 GLN cc_start: 0.8130 (tp40) cc_final: 0.7635 (tm-30) REVERT: B 261 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6252 (tp30) REVERT: B 305 ASN cc_start: 0.7142 (m110) cc_final: 0.6706 (m-40) REVERT: B 377 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.7100 (t0) REVERT: B 407 ASP cc_start: 0.3790 (OUTLIER) cc_final: 0.3239 (m-30) REVERT: B 428 VAL cc_start: 0.7850 (t) cc_final: 0.7463 (m) REVERT: D 158 ASN cc_start: 0.8428 (p0) cc_final: 0.8033 (p0) REVERT: D 176 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7831 (tm-30) REVERT: D 212 GLU cc_start: 0.8163 (tp30) cc_final: 0.7924 (tp30) REVERT: D 221 LEU cc_start: 0.8444 (tp) cc_final: 0.8152 (mt) REVERT: D 232 GLN cc_start: 0.8537 (mp10) cc_final: 0.8114 (mt0) REVERT: D 261 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: D 268 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7714 (ptp90) REVERT: D 305 ASN cc_start: 0.7469 (m110) cc_final: 0.6900 (m-40) REVERT: D 377 ASN cc_start: 0.7463 (t0) cc_final: 0.7088 (t0) REVERT: D 398 TYR cc_start: 0.8402 (t80) cc_final: 0.7995 (t80) REVERT: D 428 VAL cc_start: 0.8224 (t) cc_final: 0.7944 (m) REVERT: F 158 ASN cc_start: 0.8309 (p0) cc_final: 0.8037 (p0) REVERT: F 222 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7473 (ptm-80) REVERT: F 261 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5954 (tp30) REVERT: F 283 ILE cc_start: 0.8605 (mm) cc_final: 0.8363 (mp) REVERT: F 305 ASN cc_start: 0.7284 (m110) cc_final: 0.6913 (m-40) REVERT: F 356 GLN cc_start: 0.7629 (mt0) cc_final: 0.7237 (mp10) REVERT: F 378 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7268 (tpp80) REVERT: F 389 ASN cc_start: 0.7839 (t0) cc_final: 0.7035 (t0) REVERT: F 398 TYR cc_start: 0.7825 (t80) cc_final: 0.7316 (t80) REVERT: G 102 SER cc_start: 0.8859 (m) cc_final: 0.8657 (t) REVERT: G 106 TYR cc_start: 0.8826 (m-80) cc_final: 0.8539 (m-80) REVERT: H 4 MET cc_start: 0.8044 (mtp) cc_final: 0.7536 (mmm) REVERT: H 55 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: K 3 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: M 21 SER cc_start: 0.8248 (m) cc_final: 0.7797 (p) REVERT: N 22 THR cc_start: 0.8300 (m) cc_final: 0.7905 (t) REVERT: O 17 SER cc_start: 0.7981 (p) cc_final: 0.7705 (t) REVERT: P 61 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7711 (ptt-90) REVERT: P 79 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: P 93 ARG cc_start: 0.8640 (mmt-90) cc_final: 0.8425 (mpt180) REVERT: P 102 THR cc_start: 0.8817 (m) cc_final: 0.8426 (p) REVERT: Q 5 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8170 (m) outliers start: 109 outliers final: 68 residues processed: 505 average time/residue: 0.4867 time to fit residues: 287.2207 Evaluate side-chains 507 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 427 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 117 ILE Chi-restraints excluded: chain O residue 120 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 76 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [230, 97, 110, 215, 200, 223, 213, 80, 0, 221, 83] chunk 230 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 200 optimal weight: 0.6980 chunk 223 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 130 GLN B 328 ASN D 191 ASN D 328 ASN D 385 ASN F 130 GLN I 6 GLN O 84 ASN P 96 GLN Q 84 ASN R 96 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110079 restraints weight = 31609.939| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.29 r_work: 0.3320 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21132 Z= 0.138 Angle : 0.557 9.970 28731 Z= 0.279 Chirality : 0.047 0.515 3294 Planarity : 0.004 0.054 3636 Dihedral : 6.372 59.550 3280 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.03 % Allowed : 28.93 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2616 helix: 1.36 (0.25), residues: 456 sheet: 0.62 (0.19), residues: 753 loop : -0.49 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 208 TYR 0.018 0.001 TYR O 50 PHE 0.017 0.001 PHE F 278 TRP 0.009 0.001 TRP I 105 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (21093) covalent geometry : angle 0.53642 / 0.27 (28638) SS BOND : bond 0.00318 / 0.21 ( 24) SS BOND : angle 0.89493 / 0.66 ( 48) hydrogen bonds : bond 0.03421 / 2.36 ( 813) hydrogen bonds : angle 4.44059 / 3.13 ( 2319) link_BETA1-4 : bond 0.01098 / 0.51 ( 6) link_BETA1-4 : angle 3.09853 / 1.99 ( 18) link_NAG-ASN : bond 0.00484 / 0.22 ( 9) link_NAG-ASN : angle 4.12479 / 3.00 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 427 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8355 (p0) cc_final: 0.7999 (p0) REVERT: B 171 MET cc_start: 0.7851 (tpt) cc_final: 0.7508 (tpp) REVERT: B 176 GLN cc_start: 0.8141 (tp40) cc_final: 0.7614 (tm-30) REVERT: B 261 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6245 (tp30) REVERT: B 305 ASN cc_start: 0.7146 (m110) cc_final: 0.6684 (m-40) REVERT: B 377 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7134 (t0) REVERT: B 407 ASP cc_start: 0.3812 (OUTLIER) cc_final: 0.3239 (m-30) REVERT: B 428 VAL cc_start: 0.7862 (t) cc_final: 0.7476 (m) REVERT: D 158 ASN cc_start: 0.8466 (p0) cc_final: 0.8065 (p0) REVERT: D 165 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8237 (ptp90) REVERT: D 176 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7863 (tm-30) REVERT: D 205 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8273 (mptp) REVERT: D 212 GLU cc_start: 0.8159 (tp30) cc_final: 0.7921 (tp30) REVERT: D 232 GLN cc_start: 0.8577 (mp10) cc_final: 0.8152 (mt0) REVERT: D 261 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: D 268 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7706 (ptp90) REVERT: D 305 ASN cc_start: 0.7459 (m110) cc_final: 0.6889 (m-40) REVERT: D 377 ASN cc_start: 0.7473 (t0) cc_final: 0.7114 (t0) REVERT: D 398 TYR cc_start: 0.8418 (t80) cc_final: 0.8025 (t80) REVERT: D 428 VAL cc_start: 0.8252 (t) cc_final: 0.7965 (m) REVERT: F 158 ASN cc_start: 0.8332 (p0) cc_final: 0.8039 (p0) REVERT: F 222 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7488 (ptm-80) REVERT: F 261 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.5965 (tp30) REVERT: F 283 ILE cc_start: 0.8612 (mm) cc_final: 0.8383 (mp) REVERT: F 305 ASN cc_start: 0.7285 (m110) cc_final: 0.6881 (m-40) REVERT: F 356 GLN cc_start: 0.7655 (mt0) cc_final: 0.7184 (mp10) REVERT: F 378 ARG cc_start: 0.8029 (mmt90) cc_final: 0.7286 (tpp80) REVERT: F 389 ASN cc_start: 0.7833 (t0) cc_final: 0.6974 (t0) REVERT: F 398 TYR cc_start: 0.7822 (t80) cc_final: 0.7317 (t80) REVERT: G 63 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7981 (ttpt) REVERT: G 102 SER cc_start: 0.8872 (m) cc_final: 0.8662 (t) REVERT: G 106 TYR cc_start: 0.8822 (m-80) cc_final: 0.8578 (m-80) REVERT: H 4 MET cc_start: 0.8082 (mtp) cc_final: 0.7579 (mmm) REVERT: H 55 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: H 56 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.7850 (t) REVERT: K 3 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: K 50 ARG cc_start: 0.8618 (ptt180) cc_final: 0.8414 (ptm160) REVERT: M 21 SER cc_start: 0.8301 (m) cc_final: 0.7842 (p) REVERT: N 22 THR cc_start: 0.8302 (m) cc_final: 0.7928 (t) REVERT: N 31 ASN cc_start: 0.6030 (OUTLIER) cc_final: 0.5773 (p0) REVERT: O 17 SER cc_start: 0.7998 (p) cc_final: 0.7728 (t) REVERT: P 61 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7706 (ptt-90) REVERT: P 77 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7509 (p) REVERT: P 79 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: P 95 SER cc_start: 0.8754 (m) cc_final: 0.8521 (p) REVERT: P 102 THR cc_start: 0.8840 (m) cc_final: 0.8442 (p) REVERT: Q 5 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8185 (m) outliers start: 113 outliers final: 74 residues processed: 503 average time/residue: 0.4882 time to fit residues: 284.7577 Evaluate side-chains 516 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 425 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 117 ILE Chi-restraints excluded: chain O residue 120 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 76 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [59, 175, 149, 181, 57, 188, 64, 136, 142, 215, 192] chunk 59 optimal weight: 0.8980 chunk 175 optimal weight: 0.0050 chunk 149 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 130 GLN B 328 ASN D 191 ASN D 328 ASN D 385 ASN F 130 GLN I 6 GLN O 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109440 restraints weight = 31879.279| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.29 r_work: 0.3315 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21132 Z= 0.142 Angle : 0.561 10.097 28731 Z= 0.281 Chirality : 0.047 0.524 3294 Planarity : 0.004 0.053 3636 Dihedral : 6.313 59.553 3277 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.21 % Allowed : 28.48 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2616 helix: 1.33 (0.25), residues: 456 sheet: 0.58 (0.19), residues: 753 loop : -0.50 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 58 TYR 0.017 0.001 TYR M 50 PHE 0.017 0.001 PHE F 278 TRP 0.010 0.001 TRP I 105 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (21093) covalent geometry : angle 0.54008 / 0.28 (28638) SS BOND : bond 0.00331 / 0.22 ( 24) SS BOND : angle 0.99409 / 0.75 ( 48) hydrogen bonds : bond 0.03485 / 2.41 ( 813) hydrogen bonds : angle 4.45578 / 3.14 ( 2319) link_BETA1-4 : bond 0.01114 / 0.52 ( 6) link_BETA1-4 : angle 3.14826 / 2.02 ( 18) link_NAG-ASN : bond 0.00494 / 0.22 ( 9) link_NAG-ASN : angle 4.19326 / 3.04 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 425 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8368 (p0) cc_final: 0.7995 (p0) REVERT: B 171 MET cc_start: 0.7844 (tpt) cc_final: 0.7507 (tpp) REVERT: B 176 GLN cc_start: 0.8144 (tp40) cc_final: 0.7625 (tm-30) REVERT: B 261 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6241 (tp30) REVERT: B 305 ASN cc_start: 0.7141 (m110) cc_final: 0.6681 (m-40) REVERT: B 377 ASN cc_start: 0.7805 (m110) cc_final: 0.7111 (t0) REVERT: B 407 ASP cc_start: 0.3890 (OUTLIER) cc_final: 0.3280 (m-30) REVERT: B 425 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7734 (m) REVERT: B 428 VAL cc_start: 0.7867 (t) cc_final: 0.7466 (m) REVERT: D 158 ASN cc_start: 0.8445 (p0) cc_final: 0.8037 (p0) REVERT: D 176 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7866 (tm-30) REVERT: D 205 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8268 (mptp) REVERT: D 212 GLU cc_start: 0.8167 (tp30) cc_final: 0.7927 (tp30) REVERT: D 221 LEU cc_start: 0.8460 (tp) cc_final: 0.8210 (mt) REVERT: D 232 GLN cc_start: 0.8594 (mp10) cc_final: 0.8170 (mt0) REVERT: D 261 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6235 (mp0) REVERT: D 268 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7693 (ptp90) REVERT: D 300 GLU cc_start: 0.6098 (tp30) cc_final: 0.5790 (tp30) REVERT: D 305 ASN cc_start: 0.7447 (m110) cc_final: 0.6870 (m-40) REVERT: D 377 ASN cc_start: 0.7452 (t0) cc_final: 0.6902 (t0) REVERT: D 398 TYR cc_start: 0.8426 (t80) cc_final: 0.8037 (t80) REVERT: D 428 VAL cc_start: 0.8264 (t) cc_final: 0.7967 (m) REVERT: F 158 ASN cc_start: 0.8330 (p0) cc_final: 0.8032 (p0) REVERT: F 222 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7496 (ptm-80) REVERT: F 261 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.5957 (tp30) REVERT: F 283 ILE cc_start: 0.8624 (mm) cc_final: 0.8402 (mp) REVERT: F 305 ASN cc_start: 0.7271 (m110) cc_final: 0.6866 (m-40) REVERT: F 339 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: F 356 GLN cc_start: 0.7668 (mt0) cc_final: 0.7186 (mp10) REVERT: F 378 ARG cc_start: 0.8039 (mmt90) cc_final: 0.7282 (tpp80) REVERT: F 389 ASN cc_start: 0.7838 (t0) cc_final: 0.7019 (t0) REVERT: G 102 SER cc_start: 0.8870 (m) cc_final: 0.8661 (t) REVERT: G 106 TYR cc_start: 0.8829 (m-80) cc_final: 0.8558 (m-80) REVERT: H 4 MET cc_start: 0.8116 (mtp) cc_final: 0.7598 (mmm) REVERT: H 55 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: H 56 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.7844 (t) REVERT: K 3 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: K 50 ARG cc_start: 0.8633 (ptt180) cc_final: 0.8429 (ptm160) REVERT: M 5 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8173 (m) REVERT: M 21 SER cc_start: 0.8343 (m) cc_final: 0.7883 (p) REVERT: N 22 THR cc_start: 0.8311 (m) cc_final: 0.7915 (t) REVERT: N 31 ASN cc_start: 0.5999 (OUTLIER) cc_final: 0.5728 (p0) REVERT: O 17 SER cc_start: 0.7992 (p) cc_final: 0.7732 (t) REVERT: P 61 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7737 (ptt-90) REVERT: P 79 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: P 95 SER cc_start: 0.8746 (m) cc_final: 0.8502 (p) REVERT: P 102 THR cc_start: 0.8853 (m) cc_final: 0.8477 (p) REVERT: Q 5 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8203 (m) outliers start: 117 outliers final: 81 residues processed: 504 average time/residue: 0.4856 time to fit residues: 283.2152 Evaluate side-chains 521 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 423 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 339 GLU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 120 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 76 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [18, 1, 107, 195, 43, 68, 254, 35, 236, 179, 147] chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 ASN D 191 ASN D 328 ASN D 385 ASN F 130 GLN I 6 GLN O 84 ASN Q 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.107555 restraints weight = 31648.721| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.27 r_work: 0.3277 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 21132 Z= 0.271 Angle : 0.664 10.604 28731 Z= 0.330 Chirality : 0.051 0.575 3294 Planarity : 0.004 0.058 3636 Dihedral : 6.576 58.456 3275 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.30 % Allowed : 28.66 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 2616 helix: 1.05 (0.25), residues: 447 sheet: 0.42 (0.19), residues: 753 loop : -0.61 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 208 TYR 0.027 0.002 TYR M 50 PHE 0.022 0.002 PHE B 278 TRP 0.014 0.002 TRP M 113 HIS 0.004 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.27 (21093) covalent geometry : angle 0.63839 / 0.32 (28638) SS BOND : bond 0.00493 / 0.34 ( 24) SS BOND : angle 1.52753 / 1.17 ( 48) hydrogen bonds : bond 0.04334 / 3.00 ( 813) hydrogen bonds : angle 4.79933 / 3.37 ( 2319) link_BETA1-4 : bond 0.01456 / 0.67 ( 6) link_BETA1-4 : angle 4.07465 / 2.61 ( 18) link_NAG-ASN : bond 0.00389 / 0.17 ( 9) link_NAG-ASN : angle 4.62751 / 3.31 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 438 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8370 (p0) cc_final: 0.7946 (p0) REVERT: B 171 MET cc_start: 0.7906 (tpt) cc_final: 0.7582 (tpp) REVERT: B 176 GLN cc_start: 0.8231 (tp40) cc_final: 0.7623 (tm-30) REVERT: B 222 ARG cc_start: 0.8400 (ptt-90) cc_final: 0.8085 (ptt-90) REVERT: B 232 GLN cc_start: 0.8448 (mp10) cc_final: 0.8066 (mp10) REVERT: B 261 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6228 (tp30) REVERT: B 305 ASN cc_start: 0.7123 (m110) cc_final: 0.6620 (m-40) REVERT: B 407 ASP cc_start: 0.4028 (OUTLIER) cc_final: 0.3327 (m-30) REVERT: B 428 VAL cc_start: 0.7892 (t) cc_final: 0.7455 (m) REVERT: D 158 ASN cc_start: 0.8458 (p0) cc_final: 0.8063 (p0) REVERT: D 176 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7909 (tm-30) REVERT: D 212 GLU cc_start: 0.8161 (tp30) cc_final: 0.7899 (tp30) REVERT: D 232 GLN cc_start: 0.8592 (mp10) cc_final: 0.8156 (mt0) REVERT: D 261 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: D 268 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7629 (ptp90) REVERT: D 283 ILE cc_start: 0.8849 (mm) cc_final: 0.8619 (mp) REVERT: D 377 ASN cc_start: 0.7483 (t0) cc_final: 0.7089 (t0) REVERT: D 398 TYR cc_start: 0.8469 (t80) cc_final: 0.8091 (t80) REVERT: D 428 VAL cc_start: 0.8308 (t) cc_final: 0.7999 (m) REVERT: F 158 ASN cc_start: 0.8366 (p0) cc_final: 0.8007 (p0) REVERT: F 165 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8076 (mmm-85) REVERT: F 222 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7555 (ptm-80) REVERT: F 261 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5947 (tp30) REVERT: F 283 ILE cc_start: 0.8702 (mm) cc_final: 0.8493 (mp) REVERT: F 305 ASN cc_start: 0.7193 (m110) cc_final: 0.6762 (m-40) REVERT: F 339 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: F 356 GLN cc_start: 0.7721 (mt0) cc_final: 0.7224 (mp10) REVERT: F 378 ARG cc_start: 0.8067 (mmt90) cc_final: 0.7290 (tpp80) REVERT: F 389 ASN cc_start: 0.7856 (t0) cc_final: 0.6972 (t0) REVERT: G 102 SER cc_start: 0.8913 (m) cc_final: 0.8697 (t) REVERT: H 4 MET cc_start: 0.8170 (mtp) cc_final: 0.7837 (mmm) REVERT: H 55 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: H 56 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.7862 (t) REVERT: M 5 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8194 (m) REVERT: N 22 THR cc_start: 0.8303 (m) cc_final: 0.7914 (t) REVERT: N 31 ASN cc_start: 0.6328 (OUTLIER) cc_final: 0.6066 (p0) REVERT: O 17 SER cc_start: 0.8079 (p) cc_final: 0.7816 (t) REVERT: P 61 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7861 (ptt-90) REVERT: P 77 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7447 (p) REVERT: P 79 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: P 95 SER cc_start: 0.8783 (m) cc_final: 0.8548 (p) REVERT: P 102 THR cc_start: 0.8899 (m) cc_final: 0.8513 (p) outliers start: 119 outliers final: 74 residues processed: 517 average time/residue: 0.4816 time to fit residues: 288.5162 Evaluate side-chains 521 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 432 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 339 GLU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 120 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 76 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [135, 115, 155, 182, 83, 32, 9, 133, 201, 159, 223] chunk 135 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 182 optimal weight: 0.0770 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 ASN C 97 ASN D 191 ASN D 328 ASN D 385 ASN F 130 GLN G 111 GLN I 6 GLN O 59 ASN O 84 ASN R 96 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110185 restraints weight = 31756.680| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.29 r_work: 0.3324 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21132 Z= 0.110 Angle : 0.558 10.167 28731 Z= 0.280 Chirality : 0.047 0.511 3294 Planarity : 0.004 0.052 3636 Dihedral : 6.247 58.817 3270 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.83 % Allowed : 30.04 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2616 helix: 1.24 (0.25), residues: 450 sheet: 0.49 (0.19), residues: 753 loop : -0.55 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 208 TYR 0.016 0.001 TYR R 87 PHE 0.014 0.001 PHE D 278 TRP 0.011 0.001 TRP I 105 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (21093) covalent geometry : angle 0.53862 / 0.28 (28638) SS BOND : bond 0.00288 / 0.19 ( 24) SS BOND : angle 0.87181 / 0.66 ( 48) hydrogen bonds : bond 0.03378 / 2.33 ( 813) hydrogen bonds : angle 4.47108 / 3.15 ( 2319) link_BETA1-4 : bond 0.01027 / 0.46 ( 6) link_BETA1-4 : angle 2.83785 / 1.82 ( 18) link_NAG-ASN : bond 0.00558 / 0.24 ( 9) link_NAG-ASN : angle 4.15755 / 3.03 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 436 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8332 (p0) cc_final: 0.7943 (p0) REVERT: B 171 MET cc_start: 0.7840 (tpt) cc_final: 0.7520 (tpp) REVERT: B 176 GLN cc_start: 0.8136 (tp40) cc_final: 0.7612 (tm-30) REVERT: B 261 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6256 (tp30) REVERT: B 305 ASN cc_start: 0.7127 (m110) cc_final: 0.6648 (m-40) REVERT: B 407 ASP cc_start: 0.3830 (OUTLIER) cc_final: 0.3258 (m-30) REVERT: B 425 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7709 (m) REVERT: B 428 VAL cc_start: 0.7875 (t) cc_final: 0.7469 (m) REVERT: D 158 ASN cc_start: 0.8449 (p0) cc_final: 0.8082 (p0) REVERT: D 176 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7877 (tm-30) REVERT: D 212 GLU cc_start: 0.8170 (tp30) cc_final: 0.7932 (tp30) REVERT: D 221 LEU cc_start: 0.8494 (tp) cc_final: 0.8276 (mt) REVERT: D 232 GLN cc_start: 0.8580 (mp10) cc_final: 0.8157 (mt0) REVERT: D 261 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6269 (mp0) REVERT: D 268 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7725 (ptp90) REVERT: D 300 GLU cc_start: 0.6168 (tp30) cc_final: 0.5875 (tp30) REVERT: D 305 ASN cc_start: 0.7443 (m110) cc_final: 0.6878 (m-40) REVERT: D 377 ASN cc_start: 0.7474 (t0) cc_final: 0.6980 (t0) REVERT: D 398 TYR cc_start: 0.8433 (t80) cc_final: 0.8062 (t80) REVERT: D 428 VAL cc_start: 0.8249 (t) cc_final: 0.7943 (m) REVERT: F 158 ASN cc_start: 0.8334 (p0) cc_final: 0.8030 (p0) REVERT: F 222 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7544 (ptm-80) REVERT: F 261 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.5950 (tp30) REVERT: F 283 ILE cc_start: 0.8632 (mm) cc_final: 0.8417 (mp) REVERT: F 305 ASN cc_start: 0.7252 (m110) cc_final: 0.6849 (m-40) REVERT: F 356 GLN cc_start: 0.7654 (mt0) cc_final: 0.7168 (mp10) REVERT: F 378 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7258 (tpp80) REVERT: F 389 ASN cc_start: 0.7838 (t0) cc_final: 0.6969 (t0) REVERT: F 398 TYR cc_start: 0.7846 (t80) cc_final: 0.7364 (t80) REVERT: G 48 MET cc_start: 0.8172 (mtp) cc_final: 0.7902 (mtm) REVERT: G 102 SER cc_start: 0.8898 (m) cc_final: 0.8684 (t) REVERT: G 106 TYR cc_start: 0.8843 (m-80) cc_final: 0.8581 (m-80) REVERT: H 4 MET cc_start: 0.8108 (mtp) cc_final: 0.7596 (mmm) REVERT: H 55 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: H 56 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.7846 (t) REVERT: H 61 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8364 (mpp-170) REVERT: M 5 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8182 (m) REVERT: M 21 SER cc_start: 0.8386 (m) cc_final: 0.7941 (p) REVERT: M 83 MET cc_start: 0.8709 (mtm) cc_final: 0.8413 (mtm) REVERT: N 22 THR cc_start: 0.8312 (m) cc_final: 0.7938 (t) REVERT: N 31 ASN cc_start: 0.6112 (OUTLIER) cc_final: 0.5838 (p0) REVERT: O 17 SER cc_start: 0.7993 (p) cc_final: 0.7727 (t) REVERT: P 61 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7741 (ptt-90) REVERT: P 70 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: P 77 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7470 (p) REVERT: P 79 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7111 (mp10) REVERT: P 95 SER cc_start: 0.8730 (m) cc_final: 0.8502 (p) REVERT: P 102 THR cc_start: 0.8862 (m) cc_final: 0.8504 (p) outliers start: 86 outliers final: 56 residues processed: 498 average time/residue: 0.4740 time to fit residues: 274.1141 Evaluate side-chains 504 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 432 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 59 ASN Chi-restraints excluded: chain O residue 120 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain R residue 76 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [166, 33, 217, 159, 50, 5, 116, 255, 239, 173, 20] chunk 166 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 255 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 ASN C 97 ASN D 191 ASN D 328 ASN D 385 ASN D 462 ASN F 130 GLN I 6 GLN O 84 ASN P 96 GLN Q 84 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.131042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108923 restraints weight = 31664.264| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.28 r_work: 0.3297 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21132 Z= 0.197 Angle : 0.614 12.373 28731 Z= 0.305 Chirality : 0.049 0.539 3294 Planarity : 0.004 0.056 3636 Dihedral : 6.265 58.186 3270 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.65 % Allowed : 30.40 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2616 helix: 1.16 (0.25), residues: 447 sheet: 0.41 (0.19), residues: 771 loop : -0.55 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG O 58 TYR 0.023 0.002 TYR O 50 PHE 0.020 0.002 PHE F 278 TRP 0.011 0.001 TRP M 113 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (21093) covalent geometry : angle 0.59172 / 0.30 (28638) SS BOND : bond 0.00409 / 0.28 ( 24) SS BOND : angle 1.21920 / 0.93 ( 48) hydrogen bonds : bond 0.03863 / 2.67 ( 813) hydrogen bonds : angle 4.59921 / 3.23 ( 2319) link_BETA1-4 : bond 0.01230 / 0.57 ( 6) link_BETA1-4 : angle 3.48511 / 2.23 ( 18) link_NAG-ASN : bond 0.00426 / 0.19 ( 9) link_NAG-ASN : angle 4.29496 / 3.12 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 436 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8377 (p0) cc_final: 0.7963 (p0) REVERT: B 171 MET cc_start: 0.7868 (tpt) cc_final: 0.7546 (tpp) REVERT: B 176 GLN cc_start: 0.8192 (tp40) cc_final: 0.7624 (tm-30) REVERT: B 222 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8143 (ptm-80) REVERT: B 261 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6244 (tp30) REVERT: B 305 ASN cc_start: 0.7114 (m110) cc_final: 0.6621 (m-40) REVERT: B 407 ASP cc_start: 0.3999 (OUTLIER) cc_final: 0.3359 (m-30) REVERT: B 428 VAL cc_start: 0.7892 (t) cc_final: 0.7483 (m) REVERT: D 158 ASN cc_start: 0.8454 (p0) cc_final: 0.8086 (p0) REVERT: D 176 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7882 (tm-30) REVERT: D 212 GLU cc_start: 0.8152 (tp30) cc_final: 0.7898 (tp30) REVERT: D 232 GLN cc_start: 0.8593 (mp10) cc_final: 0.8169 (mt0) REVERT: D 261 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: D 268 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7704 (ptp90) REVERT: D 300 GLU cc_start: 0.6136 (tp30) cc_final: 0.5849 (tp30) REVERT: D 305 ASN cc_start: 0.7413 (m110) cc_final: 0.6817 (m-40) REVERT: D 377 ASN cc_start: 0.7485 (t0) cc_final: 0.6976 (t0) REVERT: D 398 TYR cc_start: 0.8457 (t80) cc_final: 0.8088 (t80) REVERT: D 428 VAL cc_start: 0.8285 (t) cc_final: 0.7986 (m) REVERT: F 158 ASN cc_start: 0.8350 (p0) cc_final: 0.8019 (p0) REVERT: F 165 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8140 (mmm-85) REVERT: F 222 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7585 (ptm-80) REVERT: F 261 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5923 (tp30) REVERT: F 283 ILE cc_start: 0.8658 (mm) cc_final: 0.8451 (mp) REVERT: F 305 ASN cc_start: 0.7250 (m110) cc_final: 0.6824 (m-40) REVERT: F 356 GLN cc_start: 0.7693 (mt0) cc_final: 0.7188 (mp10) REVERT: F 378 ARG cc_start: 0.8053 (mmt90) cc_final: 0.7304 (tpp80) REVERT: F 389 ASN cc_start: 0.7877 (t0) cc_final: 0.7027 (t0) REVERT: G 48 MET cc_start: 0.8198 (mtp) cc_final: 0.7941 (mtm) REVERT: G 102 SER cc_start: 0.8913 (m) cc_final: 0.8692 (t) REVERT: H 4 MET cc_start: 0.8151 (mtp) cc_final: 0.7644 (mmm) REVERT: H 55 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: H 61 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8378 (mpp-170) REVERT: M 5 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8197 (m) REVERT: M 21 SER cc_start: 0.8474 (m) cc_final: 0.8023 (p) REVERT: M 83 MET cc_start: 0.8718 (mtm) cc_final: 0.8423 (mtm) REVERT: N 22 THR cc_start: 0.8303 (m) cc_final: 0.7928 (t) REVERT: N 31 ASN cc_start: 0.6229 (OUTLIER) cc_final: 0.5977 (p0) REVERT: O 17 SER cc_start: 0.8049 (p) cc_final: 0.7775 (t) REVERT: P 61 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7756 (ptt-90) REVERT: P 77 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7427 (p) REVERT: P 79 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: P 95 SER cc_start: 0.8773 (m) cc_final: 0.8539 (p) REVERT: P 102 THR cc_start: 0.8885 (m) cc_final: 0.8520 (p) outliers start: 82 outliers final: 57 residues processed: 495 average time/residue: 0.4914 time to fit residues: 281.5602 Evaluate side-chains 506 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 434 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 120 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 45 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [185, 139, 254, 24, 212, 17, 57, 18, 112, 137, 249] chunk 185 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 254 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 212 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 18 optimal weight: 0.0470 chunk 112 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 249 optimal weight: 0.1980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 271 HIS B 328 ASN C 97 ASN D 191 ASN D 328 ASN D 385 ASN F 130 GLN I 6 GLN O 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.132859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110731 restraints weight = 31769.042| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.30 r_work: 0.3338 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21132 Z= 0.099 Angle : 0.550 9.930 28731 Z= 0.275 Chirality : 0.046 0.496 3294 Planarity : 0.004 0.051 3636 Dihedral : 6.109 58.653 3268 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.34 % Allowed : 30.93 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2616 helix: 1.31 (0.25), residues: 456 sheet: 0.46 (0.19), residues: 813 loop : -0.45 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 208 TYR 0.014 0.001 TYR O 50 PHE 0.013 0.001 PHE F 278 TRP 0.012 0.001 TRP K 105 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (21093) covalent geometry : angle 0.53136 / 0.27 (28638) SS BOND : bond 0.00244 / 0.16 ( 24) SS BOND : angle 0.75746 / 0.56 ( 48) hydrogen bonds : bond 0.03158 / 2.19 ( 813) hydrogen bonds : angle 4.34937 / 3.07 ( 2319) link_BETA1-4 : bond 0.00900 / 0.42 ( 6) link_BETA1-4 : angle 2.66756 / 1.71 ( 18) link_NAG-ASN : bond 0.00570 / 0.25 ( 9) link_NAG-ASN : angle 4.05258 / 2.96 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7926.67 seconds wall clock time: 135 minutes 32.12 seconds (8132.12 seconds total)