Starting phenix.real_space_refine on Sun Apr 5 13:12:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ome_70611/04_2026/9ome_70611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ome_70611/04_2026/9ome_70611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ome_70611/04_2026/9ome_70611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ome_70611/04_2026/9ome_70611.map" model { file = "/net/cci-nas-00/data/ceres_data/9ome_70611/04_2026/9ome_70611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ome_70611/04_2026/9ome_70611.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 6786 2.51 5 N 1692 2.21 5 O 2124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "B" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "C" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "D" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "E" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "F" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "G" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "H" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "I" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "J" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "K" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "L" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "M" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "N" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "O" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "P" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "Q" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "R" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Time building chain proxies: 2.44, per 1000 atoms: 0.23 Number of scatterers: 10602 At special positions: 0 Unit cell: (105.6, 114.4, 106.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2124 8.00 N 1692 7.00 C 6786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 574.9 milliseconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 35.2% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 40 through 64 removed outlier: 3.517A pdb=" N LEU A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 64 removed outlier: 3.870A pdb=" N LEU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 64 removed outlier: 3.676A pdb=" N LEU C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 64 removed outlier: 3.569A pdb=" N LEU D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D 49 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS D 50 " --> pdb=" O ILE D 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 64 removed outlier: 4.090A pdb=" N LEU E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR E 49 " --> pdb=" O TYR E 45 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 64 removed outlier: 3.733A pdb=" N LYS F 50 " --> pdb=" O ILE F 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 64 removed outlier: 4.051A pdb=" N TYR G 49 " --> pdb=" O TYR G 45 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS G 50 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 64 removed outlier: 3.999A pdb=" N LEU H 44 " --> pdb=" O ASP H 40 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR H 49 " --> pdb=" O TYR H 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS H 50 " --> pdb=" O ILE H 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 63 removed outlier: 3.864A pdb=" N LEU I 44 " --> pdb=" O ASP I 40 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR I 45 " --> pdb=" O LYS I 41 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE I 46 " --> pdb=" O LYS I 42 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS I 47 " --> pdb=" O GLU I 43 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS I 50 " --> pdb=" O ILE I 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 64 removed outlier: 4.151A pdb=" N LEU J 44 " --> pdb=" O ASP J 40 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE J 46 " --> pdb=" O LYS J 42 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS J 50 " --> pdb=" O ILE J 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 64 removed outlier: 3.580A pdb=" N LYS K 50 " --> pdb=" O ILE K 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 64 removed outlier: 3.606A pdb=" N LEU L 44 " --> pdb=" O ASP L 40 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE L 46 " --> pdb=" O LYS L 42 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS L 47 " --> pdb=" O GLU L 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 64 removed outlier: 3.887A pdb=" N LYS M 50 " --> pdb=" O ILE M 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 64 removed outlier: 3.699A pdb=" N LYS N 50 " --> pdb=" O ILE N 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 64 Processing helix chain 'P' and resid 40 through 64 removed outlier: 3.592A pdb=" N LEU P 44 " --> pdb=" O ASP P 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS P 50 " --> pdb=" O ILE P 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 64 removed outlier: 4.404A pdb=" N LEU Q 44 " --> pdb=" O ASP Q 40 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR Q 49 " --> pdb=" O TYR Q 45 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 46 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU Q 51 " --> pdb=" O LYS Q 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 64 removed outlier: 3.558A pdb=" N LEU R 44 " --> pdb=" O ASP R 40 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR R 49 " --> pdb=" O TYR R 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS R 50 " --> pdb=" O ILE R 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 36 removed outlier: 4.773A pdb=" N ASN P 32 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS O 28 " --> pdb=" O ILE P 72 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE P 74 " --> pdb=" O HIS O 28 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER O 30 " --> pdb=" O PHE P 74 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N LYS P 76 " --> pdb=" O SER O 30 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ASN O 32 " --> pdb=" O LYS P 76 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL O 91 " --> pdb=" O ILE O 69 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE O 69 " --> pdb=" O VAL O 91 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN N 32 " --> pdb=" O PHE O 74 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LYS O 76 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 13.667A pdb=" N ASP N 34 " --> pdb=" O LYS O 76 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N VAL N 83 " --> pdb=" O LYS N 76 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS N 76 " --> pdb=" O VAL N 83 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR N 85 " --> pdb=" O PHE N 74 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE N 74 " --> pdb=" O THR N 85 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU N 87 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE N 72 " --> pdb=" O LEU N 87 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER N 89 " --> pdb=" O GLU N 70 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE N 72 " --> pdb=" O HIS E 28 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN E 32 " --> pdb=" O PHE N 74 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N LYS N 76 " --> pdb=" O ASN E 32 " (cutoff:3.500A) removed outlier: 13.541A pdb=" N ASP E 34 " --> pdb=" O LYS N 76 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL E 91 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE E 69 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N HIS L 28 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU E 70 " --> pdb=" O HIS L 28 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N SER L 30 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE E 72 " --> pdb=" O SER L 30 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ASN L 32 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N PHE E 74 " --> pdb=" O ASN L 32 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N ASP L 34 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 13.925A pdb=" N LYS E 76 " --> pdb=" O ASP L 34 " (cutoff:3.500A) removed outlier: 18.763A pdb=" N LYS L 36 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HIS J 28 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE L 74 " --> pdb=" O HIS J 28 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER J 30 " --> pdb=" O PHE L 74 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N LYS L 76 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N ASN J 32 " --> pdb=" O LYS L 76 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL J 91 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE J 69 " --> pdb=" O VAL J 91 " (cutoff:3.500A) removed outlier: 10.354A pdb=" N HIS Q 28 " --> pdb=" O GLN J 68 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU J 70 " --> pdb=" O HIS Q 28 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N SER Q 30 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE J 72 " --> pdb=" O SER Q 30 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N ASN Q 32 " --> pdb=" O ILE J 72 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N PHE J 74 " --> pdb=" O ASN Q 32 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASP Q 34 " --> pdb=" O PHE J 74 " (cutoff:3.500A) removed outlier: 13.478A pdb=" N LYS J 76 " --> pdb=" O ASP Q 34 " (cutoff:3.500A) removed outlier: 18.440A pdb=" N LYS Q 36 " --> pdb=" O LYS J 76 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL Q 91 " --> pdb=" O ILE Q 69 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE Q 69 " --> pdb=" O VAL Q 91 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N HIS B 28 " --> pdb=" O ILE Q 72 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N PHE Q 74 " --> pdb=" O HIS B 28 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER B 30 " --> pdb=" O PHE Q 74 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N LYS Q 76 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N ASN B 32 " --> pdb=" O LYS Q 76 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL B 91 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE B 69 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 30 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 74 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN A 32 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N LYS B 76 " --> pdb=" O ASN A 32 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N ASP A 34 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 36 removed outlier: 4.865A pdb=" N ASN I 32 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N LYS C 76 " --> pdb=" O ASN I 32 " (cutoff:3.500A) removed outlier: 13.570A pdb=" N ASP I 34 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL I 91 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE I 69 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 10.533A pdb=" N HIS M 28 " --> pdb=" O GLN I 68 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU I 70 " --> pdb=" O HIS M 28 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N SER M 30 " --> pdb=" O GLU I 70 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE I 72 " --> pdb=" O SER M 30 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ASN M 32 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N PHE I 74 " --> pdb=" O ASN M 32 " (cutoff:3.500A) removed outlier: 11.369A pdb=" N ASP M 34 " --> pdb=" O PHE I 74 " (cutoff:3.500A) removed outlier: 14.086A pdb=" N LYS I 76 " --> pdb=" O ASP M 34 " (cutoff:3.500A) removed outlier: 18.575A pdb=" N LYS M 36 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL M 91 " --> pdb=" O ILE M 69 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE M 69 " --> pdb=" O VAL M 91 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN K 32 " --> pdb=" O PHE M 74 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N LYS M 76 " --> pdb=" O ASN K 32 " (cutoff:3.500A) removed outlier: 13.421A pdb=" N ASP K 34 " --> pdb=" O LYS M 76 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS H 28 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N PHE K 74 " --> pdb=" O HIS H 28 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER H 30 " --> pdb=" O PHE K 74 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N LYS K 76 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N ASN H 32 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS G 28 " --> pdb=" O ILE H 72 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N PHE H 74 " --> pdb=" O HIS G 28 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER G 30 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N LYS H 76 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N ASN G 32 " --> pdb=" O LYS H 76 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS F 28 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N PHE G 74 " --> pdb=" O HIS F 28 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER F 30 " --> pdb=" O PHE G 74 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N LYS G 76 " --> pdb=" O SER F 30 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N ASN F 32 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN R 32 " --> pdb=" O PHE F 74 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N LYS F 76 " --> pdb=" O ASN R 32 " (cutoff:3.500A) removed outlier: 13.753A pdb=" N ASP R 34 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL R 91 " --> pdb=" O ILE R 69 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE R 69 " --> pdb=" O VAL R 91 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN D 32 " --> pdb=" O PHE R 74 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N LYS R 76 " --> pdb=" O ASN D 32 " (cutoff:3.500A) removed outlier: 13.735A pdb=" N ASP D 34 " --> pdb=" O LYS R 76 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL D 91 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE D 69 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS C 28 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N PHE D 74 " --> pdb=" O HIS C 28 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER C 30 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N LYS D 76 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N ASN C 32 " --> pdb=" O LYS D 76 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1833 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: 1.57 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1854 1.29 - 1.35: 1494 1.35 - 1.42: 1367 1.42 - 1.48: 1348 1.48 - 1.55: 4737 Bond restraints: 10800 Sorted by residual: bond pdb=" N ASN O 82 " pdb=" CA ASN O 82 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.12e+00 bond pdb=" CG1 ILE B 35 " pdb=" CD1 ILE B 35 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.92e+00 bond pdb=" N ASN D 82 " pdb=" CA ASN D 82 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.87e+00 bond pdb=" N ASN P 82 " pdb=" CA ASN P 82 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.64e+00 bond pdb=" CG1 ILE A 35 " pdb=" CD1 ILE A 35 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.46e+00 ... (remaining 10795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 13954 1.54 - 3.08: 451 3.08 - 4.61: 52 4.61 - 6.15: 11 6.15 - 7.69: 4 Bond angle restraints: 14472 Sorted by residual: angle pdb=" C GLU F 81 " pdb=" N ASN F 82 " pdb=" CA ASN F 82 " ideal model delta sigma weight residual 124.82 131.20 -6.38 1.78e+00 3.16e-01 1.28e+01 angle pdb=" C GLU L 81 " pdb=" N ASN L 82 " pdb=" CA ASN L 82 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C GLU Q 81 " pdb=" N ASN Q 82 " pdb=" CA ASN Q 82 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" CB LYS G 42 " pdb=" CG LYS G 42 " pdb=" CD LYS G 42 " ideal model delta sigma weight residual 111.30 103.61 7.69 2.30e+00 1.89e-01 1.12e+01 angle pdb=" C GLU M 81 " pdb=" N ASN M 82 " pdb=" CA ASN M 82 " ideal model delta sigma weight residual 122.07 126.67 -4.60 1.43e+00 4.89e-01 1.03e+01 ... (remaining 14467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5949 17.99 - 35.99: 490 35.99 - 53.98: 112 53.98 - 71.97: 23 71.97 - 89.97: 14 Dihedral angle restraints: 6588 sinusoidal: 2790 harmonic: 3798 Sorted by residual: dihedral pdb=" CA LYS G 41 " pdb=" C LYS G 41 " pdb=" N LYS G 42 " pdb=" CA LYS G 42 " ideal model delta harmonic sigma weight residual 180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LYS H 41 " pdb=" C LYS H 41 " pdb=" N LYS H 42 " pdb=" CA LYS H 42 " ideal model delta harmonic sigma weight residual 180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LYS D 41 " pdb=" C LYS D 41 " pdb=" N LYS D 42 " pdb=" CA LYS D 42 " ideal model delta harmonic sigma weight residual -180.00 -161.81 -18.19 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 6585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 960 0.036 - 0.072: 359 0.072 - 0.108: 131 0.108 - 0.144: 43 0.144 - 0.180: 19 Chirality restraints: 1512 Sorted by residual: chirality pdb=" CA ASN O 82 " pdb=" N ASN O 82 " pdb=" C ASN O 82 " pdb=" CB ASN O 82 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA ILE B 35 " pdb=" N ILE B 35 " pdb=" C ILE B 35 " pdb=" CB ILE B 35 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA ILE A 35 " pdb=" N ILE A 35 " pdb=" C ILE A 35 " pdb=" CB ILE A 35 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.08e-01 ... (remaining 1509 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 55 " -0.013 2.00e-02 2.50e+03 1.56e-02 4.88e+00 pdb=" CG TYR C 55 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 55 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR C 55 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR C 55 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 55 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 55 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 55 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 81 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C GLU A 81 " 0.030 2.00e-02 2.50e+03 pdb=" O GLU A 81 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN A 82 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 55 " -0.004 2.00e-02 2.50e+03 1.06e-02 2.24e+00 pdb=" CG TYR K 55 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR K 55 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR K 55 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR K 55 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR K 55 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR K 55 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 55 " 0.000 2.00e-02 2.50e+03 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 431 2.71 - 3.26: 10024 3.26 - 3.81: 15190 3.81 - 4.35: 18042 4.35 - 4.90: 32925 Nonbonded interactions: 76612 Sorted by model distance: nonbonded pdb=" OG SER F 77 " pdb=" O TYR F 80 " model vdw 2.165 3.040 nonbonded pdb=" NZ LYS C 48 " pdb=" OE1 GLU C 51 " model vdw 2.199 3.120 nonbonded pdb=" NZ LYS J 41 " pdb=" OH TYR J 45 " model vdw 2.223 3.120 nonbonded pdb=" O LYS J 42 " pdb=" OH TYR Q 55 " model vdw 2.237 3.040 nonbonded pdb=" OG SER R 77 " pdb=" O TYR R 80 " model vdw 2.256 3.040 ... (remaining 76607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.620 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10800 Z= 0.155 Angle : 0.645 7.690 14472 Z= 0.387 Chirality : 0.048 0.180 1512 Planarity : 0.003 0.028 1854 Dihedral : 14.651 89.966 4140 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.25 % Allowed : 0.08 % Favored : 99.67 % 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: 0.38 (0.23), residues: 1224 helix: 2.02 (0.25), residues: 414 sheet: 0.21 (0.21), residues: 504 loop : -2.13 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 71 TYR 0.038 0.001 TYR C 55 PHE 0.016 0.002 PHE L 59 HIS 0.001 0.000 HIS H 28 Details of bonding type rmsd covalent geometry : bond 0.00336 (10800) covalent geometry : angle 0.64512 (14472) hydrogen bonds : bond 0.13912 ( 637) hydrogen bonds : angle 5.64565 ( 1833) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 457 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 57 LYS cc_start: 0.8370 (ttmt) cc_final: 0.8068 (mtmt) REVERT: G 84 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8008 (mt-10) REVERT: K 48 LYS cc_start: 0.8069 (tptp) cc_final: 0.7748 (tttt) REVERT: K 92 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7330 (tm-30) REVERT: L 55 TYR cc_start: 0.8704 (t80) cc_final: 0.8435 (t80) REVERT: N 66 ASN cc_start: 0.8833 (t0) cc_final: 0.8412 (t0) outliers start: 3 outliers final: 0 residues processed: 458 average time/residue: 0.1114 time to fit residues: 70.0420 Evaluate side-chains 403 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 ASN F 38 ASN G 79 GLN G 82 ASN J 68 GLN L 66 ASN P 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108193 restraints weight = 15311.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111011 restraints weight = 10320.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.112977 restraints weight = 7920.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114319 restraints weight = 6623.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115229 restraints weight = 5860.308| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10800 Z= 0.150 Angle : 0.578 6.066 14472 Z= 0.334 Chirality : 0.048 0.155 1512 Planarity : 0.003 0.030 1854 Dihedral : 4.423 16.323 1368 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.07 % Allowed : 12.85 % Favored : 84.08 % 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: 0.53 (0.23), residues: 1224 helix: 2.25 (0.26), residues: 414 sheet: 0.20 (0.21), residues: 504 loop : -2.05 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 71 TYR 0.027 0.001 TYR M 55 PHE 0.013 0.002 PHE E 59 HIS 0.003 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00336 (10800) covalent geometry : angle 0.57771 (14472) hydrogen bonds : bond 0.04881 ( 637) hydrogen bonds : angle 4.82204 ( 1833) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 429 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: C 53 GLU cc_start: 0.8003 (tt0) cc_final: 0.7795 (tt0) REVERT: F 76 LYS cc_start: 0.8919 (mmtp) cc_final: 0.8686 (mmtm) REVERT: G 84 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8138 (mt-10) REVERT: K 92 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7343 (tm-30) REVERT: M 38 ASN cc_start: 0.8220 (t0) cc_final: 0.8010 (t0) REVERT: N 66 ASN cc_start: 0.8744 (t0) cc_final: 0.8410 (t0) REVERT: N 80 TYR cc_start: 0.7992 (m-80) cc_final: 0.7788 (m-10) REVERT: P 66 ASN cc_start: 0.8200 (p0) cc_final: 0.7776 (p0) REVERT: P 87 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8674 (tt) REVERT: Q 89 SER cc_start: 0.9354 (m) cc_final: 0.9142 (t) outliers start: 37 outliers final: 26 residues processed: 442 average time/residue: 0.1112 time to fit residues: 67.7916 Evaluate side-chains 432 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 405 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 ASN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 63 ASN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 82 ASN H 68 GLN J 68 GLN M 38 ASN P 32 ASN Q 38 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103037 restraints weight = 15564.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105830 restraints weight = 10273.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107770 restraints weight = 7818.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109092 restraints weight = 6514.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110010 restraints weight = 5752.164| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 10800 Z= 0.215 Angle : 0.616 6.484 14472 Z= 0.357 Chirality : 0.048 0.199 1512 Planarity : 0.003 0.024 1854 Dihedral : 4.540 18.313 1368 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.48 % Allowed : 15.75 % Favored : 79.77 % 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: 0.33 (0.23), residues: 1224 helix: 2.10 (0.26), residues: 414 sheet: 0.13 (0.21), residues: 504 loop : -2.23 (0.28), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 71 TYR 0.025 0.001 TYR D 55 PHE 0.019 0.002 PHE N 59 HIS 0.002 0.001 HIS P 28 Details of bonding type rmsd covalent geometry : bond 0.00523 (10800) covalent geometry : angle 0.61612 (14472) hydrogen bonds : bond 0.05621 ( 637) hydrogen bonds : angle 4.84689 ( 1833) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 410 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 48 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7505 (tttt) REVERT: F 76 LYS cc_start: 0.8899 (mmtp) cc_final: 0.8661 (mmtm) REVERT: K 51 GLU cc_start: 0.8319 (tt0) cc_final: 0.8043 (tt0) REVERT: K 92 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7463 (tm-30) REVERT: L 60 ASN cc_start: 0.9120 (t0) cc_final: 0.8882 (t0) REVERT: M 38 ASN cc_start: 0.8105 (t0) cc_final: 0.7685 (t0) REVERT: N 57 LYS cc_start: 0.8600 (tptp) cc_final: 0.8375 (tptp) REVERT: N 66 ASN cc_start: 0.8805 (t0) cc_final: 0.8459 (t0) REVERT: N 80 TYR cc_start: 0.8030 (m-80) cc_final: 0.7807 (m-10) REVERT: P 36 LYS cc_start: 0.7925 (pttp) cc_final: 0.7576 (pttp) REVERT: P 66 ASN cc_start: 0.8357 (p0) cc_final: 0.7852 (p0) REVERT: Q 57 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8258 (mtmt) REVERT: Q 66 ASN cc_start: 0.8524 (p0) cc_final: 0.8275 (p0) REVERT: Q 80 TYR cc_start: 0.7637 (m-80) cc_final: 0.7430 (m-80) REVERT: Q 89 SER cc_start: 0.9367 (m) cc_final: 0.9142 (t) REVERT: R 43 GLU cc_start: 0.8325 (mp0) cc_final: 0.8057 (mp0) outliers start: 54 outliers final: 40 residues processed: 430 average time/residue: 0.1119 time to fit residues: 66.1560 Evaluate side-chains 432 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 391 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain P residue 35 ILE Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 82 ASN Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN D 82 ASN G 82 ASN H 68 GLN I 32 ASN J 68 GLN P 32 ASN Q 38 ASN Q 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106543 restraints weight = 15565.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109448 restraints weight = 10233.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111454 restraints weight = 7737.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.112822 restraints weight = 6418.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113730 restraints weight = 5648.491| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10800 Z= 0.146 Angle : 0.565 5.900 14472 Z= 0.329 Chirality : 0.048 0.168 1512 Planarity : 0.002 0.023 1854 Dihedral : 4.452 17.924 1368 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.64 % Allowed : 18.08 % Favored : 77.28 % 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: 0.48 (0.24), residues: 1224 helix: 2.33 (0.27), residues: 414 sheet: 0.17 (0.21), residues: 504 loop : -2.26 (0.28), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 71 TYR 0.025 0.001 TYR K 55 PHE 0.014 0.002 PHE M 59 HIS 0.001 0.000 HIS H 28 Details of bonding type rmsd covalent geometry : bond 0.00337 (10800) covalent geometry : angle 0.56513 (14472) hydrogen bonds : bond 0.04594 ( 637) hydrogen bonds : angle 4.71317 ( 1833) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 413 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: B 35 ILE cc_start: 0.7857 (mt) cc_final: 0.7626 (mt) REVERT: D 47 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8541 (mtmm) REVERT: D 55 TYR cc_start: 0.8377 (t80) cc_final: 0.8159 (t80) REVERT: F 76 LYS cc_start: 0.8864 (mmtp) cc_final: 0.8619 (mmtm) REVERT: J 42 LYS cc_start: 0.7850 (mmtm) cc_final: 0.7610 (mmtp) REVERT: K 30 SER cc_start: 0.9211 (m) cc_final: 0.8977 (t) REVERT: K 92 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7379 (tm-30) REVERT: L 89 SER cc_start: 0.9056 (m) cc_final: 0.8707 (t) REVERT: M 38 ASN cc_start: 0.8286 (t0) cc_final: 0.7768 (t0) REVERT: N 66 ASN cc_start: 0.8714 (t0) cc_final: 0.8362 (t0) REVERT: N 80 TYR cc_start: 0.8065 (m-80) cc_final: 0.7844 (m-10) REVERT: P 36 LYS cc_start: 0.7953 (pttp) cc_final: 0.7637 (pttp) REVERT: P 66 ASN cc_start: 0.8190 (p0) cc_final: 0.7788 (p0) REVERT: Q 57 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8267 (mtmt) REVERT: Q 89 SER cc_start: 0.9349 (m) cc_final: 0.9086 (t) outliers start: 56 outliers final: 39 residues processed: 433 average time/residue: 0.1117 time to fit residues: 66.6050 Evaluate side-chains 443 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 403 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 ASN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 82 ASN Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN G 82 ASN H 68 GLN J 68 GLN N 63 ASN P 32 ASN Q 38 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107124 restraints weight = 15361.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.109945 restraints weight = 10090.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111980 restraints weight = 7636.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113346 restraints weight = 6319.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114222 restraints weight = 5552.002| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10800 Z= 0.141 Angle : 0.557 6.353 14472 Z= 0.324 Chirality : 0.047 0.162 1512 Planarity : 0.002 0.023 1854 Dihedral : 4.364 17.526 1368 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.73 % Allowed : 19.40 % Favored : 75.87 % 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: 0.49 (0.24), residues: 1224 helix: 2.40 (0.27), residues: 414 sheet: 0.14 (0.21), residues: 504 loop : -2.29 (0.28), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 71 TYR 0.026 0.001 TYR K 55 PHE 0.013 0.002 PHE L 59 HIS 0.001 0.000 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00325 (10800) covalent geometry : angle 0.55660 (14472) hydrogen bonds : bond 0.04409 ( 637) hydrogen bonds : angle 4.69325 ( 1833) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 411 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ILE cc_start: 0.7877 (mt) cc_final: 0.7629 (mt) REVERT: D 47 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8516 (mtmm) REVERT: D 55 TYR cc_start: 0.8458 (t80) cc_final: 0.8209 (t80) REVERT: F 76 LYS cc_start: 0.8853 (mmtp) cc_final: 0.8599 (mmtm) REVERT: K 30 SER cc_start: 0.9209 (m) cc_final: 0.8960 (t) REVERT: K 84 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8593 (mt-10) REVERT: K 92 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7327 (tm-30) REVERT: L 89 SER cc_start: 0.9050 (m) cc_final: 0.8686 (t) REVERT: M 38 ASN cc_start: 0.8298 (t0) cc_final: 0.7755 (t0) REVERT: N 80 TYR cc_start: 0.8051 (m-80) cc_final: 0.7831 (m-10) REVERT: P 36 LYS cc_start: 0.7997 (pttp) cc_final: 0.7740 (pttp) REVERT: P 66 ASN cc_start: 0.8261 (p0) cc_final: 0.7835 (p0) REVERT: Q 89 SER cc_start: 0.9332 (m) cc_final: 0.9113 (t) outliers start: 57 outliers final: 40 residues processed: 434 average time/residue: 0.1125 time to fit residues: 67.3519 Evaluate side-chains 441 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 400 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 77 SER Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 57 optimal weight: 0.0170 chunk 90 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN D 82 ASN G 82 ASN H 68 GLN M 82 ASN ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 38 ASN Q 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105304 restraints weight = 15511.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108178 restraints weight = 10259.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110180 restraints weight = 7785.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111501 restraints weight = 6470.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112446 restraints weight = 5712.843| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10800 Z= 0.171 Angle : 0.583 6.208 14472 Z= 0.340 Chirality : 0.048 0.165 1512 Planarity : 0.003 0.023 1854 Dihedral : 4.375 17.623 1368 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 5.22 % Allowed : 20.32 % Favored : 74.46 % 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: 0.39 (0.24), residues: 1224 helix: 2.34 (0.26), residues: 414 sheet: 0.09 (0.22), residues: 504 loop : -2.39 (0.27), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 71 TYR 0.028 0.001 TYR K 55 PHE 0.017 0.002 PHE L 59 HIS 0.001 0.000 HIS P 28 Details of bonding type rmsd covalent geometry : bond 0.00402 (10800) covalent geometry : angle 0.58286 (14472) hydrogen bonds : bond 0.04801 ( 637) hydrogen bonds : angle 4.70485 ( 1833) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 408 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ILE cc_start: 0.7911 (mt) cc_final: 0.7690 (mt) REVERT: D 47 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8552 (mtmm) REVERT: F 76 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8601 (mmtm) REVERT: G 57 LYS cc_start: 0.8505 (tppt) cc_final: 0.8277 (tmtt) REVERT: K 30 SER cc_start: 0.9229 (m) cc_final: 0.8992 (t) REVERT: K 92 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7310 (tm-30) REVERT: L 89 SER cc_start: 0.9071 (m) cc_final: 0.8718 (t) REVERT: M 38 ASN cc_start: 0.8349 (t0) cc_final: 0.7848 (t0) REVERT: N 80 TYR cc_start: 0.8058 (m-80) cc_final: 0.7830 (m-10) REVERT: P 36 LYS cc_start: 0.7975 (pttp) cc_final: 0.7728 (pttp) REVERT: P 66 ASN cc_start: 0.8338 (p0) cc_final: 0.7893 (p0) REVERT: Q 89 SER cc_start: 0.9349 (m) cc_final: 0.9117 (t) outliers start: 63 outliers final: 44 residues processed: 434 average time/residue: 0.1120 time to fit residues: 66.7970 Evaluate side-chains 443 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 398 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 82 ASN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 50 LYS Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 77 SER Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN D 82 ASN G 82 ASN H 68 GLN ** I 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 38 ASN Q 82 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106804 restraints weight = 15322.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109688 restraints weight = 10100.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111650 restraints weight = 7684.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113012 restraints weight = 6385.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113943 restraints weight = 5625.130| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10800 Z= 0.149 Angle : 0.575 6.284 14472 Z= 0.333 Chirality : 0.047 0.163 1512 Planarity : 0.002 0.022 1854 Dihedral : 4.337 15.453 1368 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.89 % Allowed : 20.90 % Favored : 74.21 % 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: 0.43 (0.24), residues: 1224 helix: 2.42 (0.27), residues: 414 sheet: 0.08 (0.22), residues: 504 loop : -2.39 (0.27), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 71 TYR 0.031 0.001 TYR K 55 PHE 0.015 0.002 PHE L 59 HIS 0.001 0.000 HIS N 28 Details of bonding type rmsd covalent geometry : bond 0.00343 (10800) covalent geometry : angle 0.57519 (14472) hydrogen bonds : bond 0.04461 ( 637) hydrogen bonds : angle 4.66452 ( 1833) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 410 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.8624 (p0) cc_final: 0.8396 (p0) REVERT: B 35 ILE cc_start: 0.7925 (mt) cc_final: 0.7681 (mt) REVERT: D 47 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8535 (mtmm) REVERT: F 76 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8579 (mmtm) REVERT: G 66 ASN cc_start: 0.8597 (p0) cc_final: 0.7925 (p0) REVERT: J 65 THR cc_start: 0.9045 (p) cc_final: 0.8840 (p) REVERT: K 30 SER cc_start: 0.9220 (m) cc_final: 0.8975 (t) REVERT: K 92 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7278 (tm-30) REVERT: L 89 SER cc_start: 0.9086 (m) cc_final: 0.8745 (t) REVERT: M 38 ASN cc_start: 0.8349 (t0) cc_final: 0.7827 (t0) REVERT: N 80 TYR cc_start: 0.8074 (m-80) cc_final: 0.7853 (m-10) REVERT: P 36 LYS cc_start: 0.7890 (pttp) cc_final: 0.7629 (pttp) REVERT: P 66 ASN cc_start: 0.8276 (p0) cc_final: 0.7839 (p0) REVERT: Q 57 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8298 (mtmt) REVERT: Q 89 SER cc_start: 0.9351 (m) cc_final: 0.9126 (t) outliers start: 59 outliers final: 45 residues processed: 435 average time/residue: 0.1100 time to fit residues: 65.9816 Evaluate side-chains 448 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 402 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 63 ASN Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 50 LYS Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 77 SER Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 82 ASN H 68 GLN ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 38 ASN Q 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103683 restraints weight = 15447.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106496 restraints weight = 10233.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108447 restraints weight = 7785.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109775 restraints weight = 6477.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110680 restraints weight = 5716.480| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10800 Z= 0.201 Angle : 0.620 6.300 14472 Z= 0.358 Chirality : 0.048 0.168 1512 Planarity : 0.003 0.024 1854 Dihedral : 4.452 16.397 1368 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.22 % Allowed : 21.23 % Favored : 73.55 % 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 (0.24), residues: 1224 helix: 2.26 (0.26), residues: 414 sheet: -0.02 (0.21), residues: 504 loop : -2.50 (0.27), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 71 TYR 0.032 0.001 TYR K 55 PHE 0.020 0.002 PHE L 59 HIS 0.002 0.000 HIS P 28 Details of bonding type rmsd covalent geometry : bond 0.00484 (10800) covalent geometry : angle 0.61979 (14472) hydrogen bonds : bond 0.05329 ( 637) hydrogen bonds : angle 4.73954 ( 1833) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 404 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.8710 (p0) cc_final: 0.8481 (p0) REVERT: B 35 ILE cc_start: 0.7992 (mt) cc_final: 0.7761 (mt) REVERT: D 47 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8546 (mtmm) REVERT: D 82 ASN cc_start: 0.8025 (p0) cc_final: 0.7732 (p0) REVERT: G 57 LYS cc_start: 0.8471 (tppt) cc_final: 0.8229 (tmtt) REVERT: L 89 SER cc_start: 0.9094 (m) cc_final: 0.8745 (t) REVERT: M 38 ASN cc_start: 0.8430 (t0) cc_final: 0.7845 (t0) REVERT: M 92 GLU cc_start: 0.7585 (tt0) cc_final: 0.7353 (tt0) REVERT: N 48 LYS cc_start: 0.8530 (tppp) cc_final: 0.8240 (tppt) REVERT: N 66 ASN cc_start: 0.8488 (t0) cc_final: 0.8258 (t0) REVERT: N 80 TYR cc_start: 0.8116 (m-80) cc_final: 0.7886 (m-10) REVERT: O 62 LYS cc_start: 0.7578 (ttmt) cc_final: 0.7363 (ttmt) REVERT: P 36 LYS cc_start: 0.7919 (pttp) cc_final: 0.7646 (pttp) REVERT: P 66 ASN cc_start: 0.8348 (p0) cc_final: 0.7881 (p0) REVERT: Q 57 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8302 (mtmt) outliers start: 63 outliers final: 50 residues processed: 431 average time/residue: 0.1103 time to fit residues: 65.1503 Evaluate side-chains 450 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 399 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 36 LYS Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 50 LYS Chi-restraints excluded: chain P residue 67 TYR Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 77 SER Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 82 ASN H 68 GLN ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 38 ASN Q 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.103704 restraints weight = 15471.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106498 restraints weight = 10238.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.108446 restraints weight = 7808.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109791 restraints weight = 6482.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110680 restraints weight = 5717.090| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10800 Z= 0.202 Angle : 0.633 6.407 14472 Z= 0.365 Chirality : 0.049 0.204 1512 Planarity : 0.003 0.023 1854 Dihedral : 4.556 16.287 1368 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.14 % Allowed : 21.64 % Favored : 73.22 % 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 (0.23), residues: 1224 helix: 2.16 (0.26), residues: 414 sheet: -0.13 (0.21), residues: 504 loop : -2.57 (0.27), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 71 TYR 0.032 0.002 TYR K 55 PHE 0.021 0.002 PHE N 59 HIS 0.001 0.000 HIS P 28 Details of bonding type rmsd covalent geometry : bond 0.00486 (10800) covalent geometry : angle 0.63326 (14472) hydrogen bonds : bond 0.05318 ( 637) hydrogen bonds : angle 4.77263 ( 1833) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 396 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.8630 (p0) cc_final: 0.8359 (p0) REVERT: B 35 ILE cc_start: 0.8003 (mt) cc_final: 0.7764 (mt) REVERT: D 47 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8581 (mtmm) REVERT: D 82 ASN cc_start: 0.7993 (p0) cc_final: 0.7672 (p0) REVERT: G 57 LYS cc_start: 0.8533 (tppt) cc_final: 0.8293 (tmtt) REVERT: G 66 ASN cc_start: 0.8634 (p0) cc_final: 0.7976 (p0) REVERT: L 89 SER cc_start: 0.9081 (m) cc_final: 0.8721 (t) REVERT: M 38 ASN cc_start: 0.8435 (t0) cc_final: 0.7837 (t0) REVERT: M 92 GLU cc_start: 0.7606 (tt0) cc_final: 0.7393 (tt0) REVERT: N 57 LYS cc_start: 0.8541 (tptp) cc_final: 0.8254 (tptp) REVERT: N 80 TYR cc_start: 0.8072 (m-80) cc_final: 0.7865 (m-10) REVERT: O 62 LYS cc_start: 0.7626 (ttmt) cc_final: 0.7386 (ttmt) REVERT: P 36 LYS cc_start: 0.7909 (pttp) cc_final: 0.7627 (pttp) REVERT: Q 57 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8337 (mtmt) outliers start: 62 outliers final: 53 residues processed: 423 average time/residue: 0.1090 time to fit residues: 63.0106 Evaluate side-chains 443 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 389 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 36 LYS Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 50 LYS Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain P residue 67 TYR Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 77 SER Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN G 82 ASN H 68 GLN ** I 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 38 ASN Q 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103618 restraints weight = 15460.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106435 restraints weight = 10238.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108379 restraints weight = 7795.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109709 restraints weight = 6482.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110454 restraints weight = 5718.134| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 10800 Z= 0.211 Angle : 0.885 59.168 14472 Z= 0.526 Chirality : 0.050 0.469 1512 Planarity : 0.003 0.057 1854 Dihedral : 4.622 32.703 1368 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.89 % Allowed : 22.14 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.07 (0.23), residues: 1224 helix: 2.16 (0.26), residues: 414 sheet: -0.14 (0.21), residues: 504 loop : -2.57 (0.27), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 71 TYR 0.027 0.001 TYR N 55 PHE 0.020 0.002 PHE N 59 HIS 0.001 0.000 HIS P 28 Details of bonding type rmsd covalent geometry : bond 0.00495 (10800) covalent geometry : angle 0.88533 (14472) hydrogen bonds : bond 0.05224 ( 637) hydrogen bonds : angle 4.76867 ( 1833) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 389 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASN cc_start: 0.8601 (p0) cc_final: 0.8347 (p0) REVERT: B 35 ILE cc_start: 0.8008 (mt) cc_final: 0.7761 (mt) REVERT: D 47 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8571 (mtmm) REVERT: D 82 ASN cc_start: 0.7982 (p0) cc_final: 0.7662 (p0) REVERT: G 57 LYS cc_start: 0.8521 (tppt) cc_final: 0.8295 (tmtt) REVERT: G 66 ASN cc_start: 0.8621 (p0) cc_final: 0.7960 (p0) REVERT: L 89 SER cc_start: 0.9082 (m) cc_final: 0.8725 (t) REVERT: M 38 ASN cc_start: 0.8426 (t0) cc_final: 0.7833 (t0) REVERT: M 92 GLU cc_start: 0.7577 (tt0) cc_final: 0.7362 (tt0) REVERT: N 57 LYS cc_start: 0.8537 (tptp) cc_final: 0.8237 (tptp) REVERT: N 80 TYR cc_start: 0.8068 (m-80) cc_final: 0.7858 (m-10) REVERT: O 62 LYS cc_start: 0.7618 (ttmt) cc_final: 0.7389 (ttmt) REVERT: P 36 LYS cc_start: 0.7909 (pttp) cc_final: 0.7628 (pttp) REVERT: Q 38 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6688 (p0) REVERT: Q 57 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8328 (mtmt) outliers start: 59 outliers final: 53 residues processed: 415 average time/residue: 0.1126 time to fit residues: 64.1357 Evaluate side-chains 442 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 387 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 36 LYS Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 50 LYS Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain P residue 67 TYR Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 77 SER Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 22 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN G 82 ASN H 68 GLN ** I 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 38 ASN Q 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103225 restraints weight = 15511.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106155 restraints weight = 10127.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108176 restraints weight = 7645.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109553 restraints weight = 6322.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110487 restraints weight = 5551.326| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.581 10800 Z= 0.460 Angle : 0.785 39.312 14472 Z= 0.525 Chirality : 0.049 0.200 1512 Planarity : 0.005 0.178 1854 Dihedral : 4.623 32.864 1368 Min Nonbonded Distance : 1.211 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.81 % Allowed : 22.31 % Favored : 72.89 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.07 (0.23), residues: 1224 helix: 2.16 (0.26), residues: 414 sheet: -0.14 (0.21), residues: 504 loop : -2.57 (0.27), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 71 TYR 0.027 0.001 TYR N 55 PHE 0.020 0.002 PHE N 59 HIS 0.001 0.000 HIS P 28 Details of bonding type rmsd covalent geometry : bond 0.00965 (10800) covalent geometry : angle 0.78522 (14472) hydrogen bonds : bond 0.05224 ( 637) hydrogen bonds : angle 4.76869 ( 1833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2009.31 seconds wall clock time: 35 minutes 33.17 seconds (2133.17 seconds total)