Starting phenix.real_space_refine on Sun Aug 24 02:10:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dyy_27786/08_2025/8dyy_27786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dyy_27786/08_2025/8dyy_27786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dyy_27786/08_2025/8dyy_27786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dyy_27786/08_2025/8dyy_27786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dyy_27786/08_2025/8dyy_27786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dyy_27786/08_2025/8dyy_27786.map" } resolution = 3.62 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= 0.005 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 10379 2.51 5 N 2833 2.21 5 O 3224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16499 Number of models: 1 Model: "" Number of chains: 19 Chain: "I" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 506 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 18, 'TRANS': 53} Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "F" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "M" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "N" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "O" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "P" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "Q" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "R" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "S" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "T" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "U" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "V" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Time building chain proxies: 4.40, per 1000 atoms: 0.27 Number of scatterers: 16499 At special positions: 0 Unit cell: (110.4, 115, 156.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 3224 8.00 N 2833 7.00 C 10379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.04 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 807.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 56 sheets defined 4.5% alpha, 48.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.655A pdb=" N ASN H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.735A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.705A pdb=" N ASN A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.039A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.591A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.701A pdb=" N THR E 87 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.915A pdb=" N ASN M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.655A pdb=" N THR M 87 " --> pdb=" O VAL M 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.552A pdb=" N ASN O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.971A pdb=" N THR Q 87 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 removed outlier: 4.236A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.735A pdb=" N THR S 87 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.636A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 87 removed outlier: 3.640A pdb=" N THR U 87 " --> pdb=" O VAL U 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.091A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.091A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.597A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AA7, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.535A pdb=" N LEU A 80 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.427A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 58 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.427A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.618A pdb=" N GLU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.723A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.699A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.583A pdb=" N VAL C 89 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.509A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.700A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 67 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.468A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.504A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.541A pdb=" N LEU E 20 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.250A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.250A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 4 through 7 removed outlier: 4.047A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER F 67 " --> pdb=" O GLU F 70 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.522A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.522A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.619A pdb=" N SER M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.389A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR M 58 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.389A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.795A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.607A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.127A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET O 34 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR O 58 " --> pdb=" O ILE O 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.127A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.827A pdb=" N GLU P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.577A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR P 49 " --> pdb=" O SER P 53 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.532A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.810A pdb=" N SER Q 21 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 10 through 12 removed outlier: 3.524A pdb=" N THR Q 107 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET Q 34 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR Q 58 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 3.524A pdb=" N THR Q 107 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 103 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP Q 103 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 4 through 7 removed outlier: 4.165A pdb=" N GLU R 70 " --> pdb=" O SER R 67 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER R 67 " --> pdb=" O GLU R 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.692A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR R 85 " --> pdb=" O GLN R 38 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.692A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR R 97 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.511A pdb=" N CYS S 22 " --> pdb=" O LEU S 78 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.210A pdb=" N GLY S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET S 34 " --> pdb=" O ILE S 50 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.210A pdb=" N GLY S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N CYS S 92 " --> pdb=" O TRP S 103 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TRP S 103 " --> pdb=" O CYS S 92 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG S 94 " --> pdb=" O ASP S 101 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 4 through 7 removed outlier: 4.259A pdb=" N GLU T 70 " --> pdb=" O SER T 67 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER T 67 " --> pdb=" O GLU T 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.489A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 10 through 13 Processing sheet with id=AF6, first strand: chain 'U' and resid 3 through 7 removed outlier: 3.633A pdb=" N LEU U 20 " --> pdb=" O LEU U 80 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU U 80 " --> pdb=" O LEU U 20 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.798A pdb=" N MET U 34 " --> pdb=" O ILE U 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR U 58 " --> pdb=" O ILE U 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.978A pdb=" N LEU U 102 " --> pdb=" O ARG U 94 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 4 through 7 removed outlier: 3.929A pdb=" N GLU V 70 " --> pdb=" O SER V 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER V 67 " --> pdb=" O GLU V 70 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.535A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.535A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1581 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: 3.28 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.31: 2630 1.31 - 1.60: 14191 1.60 - 1.89: 90 1.89 - 2.18: 0 2.18 - 2.47: 1 Bond restraints: 16912 Sorted by residual: bond pdb=" CB PRO I 3 " pdb=" CG PRO I 3 " ideal model delta sigma weight residual 1.492 2.467 -0.975 5.00e-02 4.00e+02 3.80e+02 bond pdb=" CG PRO I 3 " pdb=" CD PRO I 3 " ideal model delta sigma weight residual 1.503 1.024 0.479 3.40e-02 8.65e+02 1.98e+02 bond pdb=" N PRO I 3 " pdb=" CA PRO I 3 " ideal model delta sigma weight residual 1.472 1.398 0.073 1.34e-02 5.57e+03 2.99e+01 bond pdb=" N PRO I 3 " pdb=" CD PRO I 3 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" CA PRO I 3 " pdb=" CB PRO I 3 " ideal model delta sigma weight residual 1.534 1.477 0.056 1.52e-02 4.33e+03 1.38e+01 ... (remaining 16907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 22984 21.21 - 42.42: 1 42.42 - 63.63: 0 63.63 - 84.85: 0 84.85 - 106.06: 1 Bond angle restraints: 22986 Sorted by residual: angle pdb=" CB PRO I 3 " pdb=" CG PRO I 3 " pdb=" CD PRO I 3 " ideal model delta sigma weight residual 106.10 0.04 106.06 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO I 3 " pdb=" N PRO I 3 " pdb=" CD PRO I 3 " ideal model delta sigma weight residual 112.00 92.60 19.40 1.40e+00 5.10e-01 1.92e+02 angle pdb=" N PRO I 3 " pdb=" CA PRO I 3 " pdb=" CB PRO I 3 " ideal model delta sigma weight residual 103.26 87.76 15.50 1.14e+00 7.69e-01 1.85e+02 angle pdb=" CA PRO I 3 " pdb=" CB PRO I 3 " pdb=" CG PRO I 3 " ideal model delta sigma weight residual 104.50 93.75 10.75 1.90e+00 2.77e-01 3.20e+01 angle pdb=" C ASP I 2 " pdb=" N PRO I 3 " pdb=" CD PRO I 3 " ideal model delta sigma weight residual 125.00 147.48 -22.48 4.10e+00 5.95e-02 3.01e+01 ... (remaining 22981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 9206 23.61 - 47.21: 545 47.21 - 70.82: 64 70.82 - 94.42: 21 94.42 - 118.03: 1 Dihedral angle restraints: 9837 sinusoidal: 3736 harmonic: 6101 Sorted by residual: dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 174.54 -81.54 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS U 22 " pdb=" SG CYS U 22 " pdb=" SG CYS U 92 " pdb=" CB CYS U 92 " ideal model delta sinusoidal sigma weight residual -86.00 -164.76 78.76 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 92 " pdb=" CB CYS E 92 " ideal model delta sinusoidal sigma weight residual 93.00 166.86 -73.86 1 1.00e+01 1.00e-02 6.93e+01 ... (remaining 9834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1952 0.050 - 0.100: 407 0.100 - 0.150: 123 0.150 - 0.200: 2 0.200 - 0.250: 1 Chirality restraints: 2485 Sorted by residual: chirality pdb=" CA PRO I 3 " pdb=" N PRO I 3 " pdb=" C PRO I 3 " pdb=" CB PRO I 3 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB THR A 28 " pdb=" CA THR A 28 " pdb=" OG1 THR A 28 " pdb=" CG2 THR A 28 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CB THR E 28 " pdb=" CA THR E 28 " pdb=" OG1 THR E 28 " pdb=" CG2 THR E 28 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 2482 not shown) Planarity restraints: 2933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO I 3 " 0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C PRO I 3 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO I 3 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN I 4 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS V 39 " 0.051 5.00e-02 4.00e+02 7.73e-02 9.57e+00 pdb=" N PRO V 40 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO V 40 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO V 40 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 40 " -0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO A 41 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " -0.040 5.00e-02 4.00e+02 ... (remaining 2930 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 243 2.65 - 3.21: 14490 3.21 - 3.77: 24459 3.77 - 4.34: 34295 4.34 - 4.90: 60507 Nonbonded interactions: 133994 Sorted by model distance: nonbonded pdb=" OE1 GLN A 3 " pdb=" N LEU A 4 " model vdw 2.085 3.120 nonbonded pdb=" OD1 ASP V 17 " pdb=" N ARG V 18 " model vdw 2.093 3.120 nonbonded pdb=" O HIS C 100B" pdb=" ND1 HIS C 100B" model vdw 2.161 3.120 nonbonded pdb=" OD1 ASP N 17 " pdb=" N ARG N 18 " model vdw 2.185 3.120 nonbonded pdb=" N GLN A 105 " pdb=" OE1 GLN A 105 " model vdw 2.199 3.120 ... (remaining 133989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.790 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.011 0.975 16930 Z= 0.379 Angle : 0.957 106.058 23022 Z= 0.416 Chirality : 0.045 0.250 2485 Planarity : 0.005 0.077 2933 Dihedral : 14.400 118.025 5913 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.33 % Allowed : 14.48 % Favored : 85.19 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.11 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.01 (0.17), residues: 1062 loop : 0.00 (0.21), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.023 0.002 TYR U 52A PHE 0.015 0.002 PHE M 29 TRP 0.015 0.002 TRP Q 52 HIS 0.004 0.001 HIS E 100B Details of bonding type rmsd covalent geometry : bond 0.01132 (16912) covalent geometry : angle 0.95699 (22986) SS BOND : bond 0.00371 ( 18) SS BOND : angle 1.05396 ( 36) hydrogen bonds : bond 0.26083 ( 589) hydrogen bonds : angle 10.72571 ( 1581) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 202 time to evaluate : 0.764 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 204 average time/residue: 0.1416 time to fit residues: 43.6891 Evaluate side-chains 205 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain U residue 72 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 24 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS O 39 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN Q 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.091283 restraints weight = 30641.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.093298 restraints weight = 19900.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094613 restraints weight = 14750.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095458 restraints weight = 12014.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095938 restraints weight = 10446.712| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16930 Z= 0.127 Angle : 0.547 9.510 23022 Z= 0.291 Chirality : 0.042 0.162 2485 Planarity : 0.004 0.057 2933 Dihedral : 4.546 48.027 2337 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.32 % Allowed : 12.60 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.42 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.43 (0.17), residues: 999 loop : 0.28 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 71 TYR 0.016 0.001 TYR U 52A PHE 0.011 0.001 PHE M 29 TRP 0.011 0.001 TRP A 52 HIS 0.003 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00291 (16912) covalent geometry : angle 0.54658 (22986) SS BOND : bond 0.00244 ( 18) SS BOND : angle 0.82998 ( 36) hydrogen bonds : bond 0.03562 ( 589) hydrogen bonds : angle 6.80458 ( 1581) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: I 9 VAL cc_start: 0.8484 (m) cc_final: 0.8229 (t) REVERT: H 28 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8570 (p) REVERT: A 3 GLN cc_start: 0.7523 (tp-100) cc_final: 0.7252 (tp-100) REVERT: A 86 ASP cc_start: 0.7535 (m-30) cc_final: 0.7314 (m-30) REVERT: B 11 LEU cc_start: 0.8252 (pt) cc_final: 0.8032 (tt) REVERT: D 102 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.7905 (t) REVERT: E 100 ARG cc_start: 0.7395 (tpp-160) cc_final: 0.7192 (tpp-160) REVERT: F 17 ASP cc_start: 0.7623 (t0) cc_final: 0.7414 (t0) REVERT: O 79 TYR cc_start: 0.9153 (m-80) cc_final: 0.8895 (m-80) REVERT: P 3 GLN cc_start: 0.7507 (tp40) cc_final: 0.7301 (mm-40) REVERT: P 6 GLN cc_start: 0.7985 (mt0) cc_final: 0.7784 (mt0) REVERT: R 100 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8462 (pt0) REVERT: S 108 LEU cc_start: 0.8392 (mt) cc_final: 0.8173 (mt) REVERT: U 72 ASP cc_start: 0.8011 (m-30) cc_final: 0.7789 (m-30) REVERT: U 79 TYR cc_start: 0.8171 (m-80) cc_final: 0.7819 (m-80) REVERT: U 82 MET cc_start: 0.6715 (mtm) cc_final: 0.6488 (mtm) REVERT: V 74 THR cc_start: 0.8063 (m) cc_final: 0.7707 (p) outliers start: 42 outliers final: 30 residues processed: 256 average time/residue: 0.1272 time to fit residues: 50.3227 Evaluate side-chains 235 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 88 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 176 optimal weight: 0.8980 chunk 191 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 8 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS E 97 HIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.110395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.086712 restraints weight = 31709.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087761 restraints weight = 24070.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088407 restraints weight = 17202.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088642 restraints weight = 15602.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.088859 restraints weight = 14624.210| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 16930 Z= 0.322 Angle : 0.663 8.137 23022 Z= 0.352 Chirality : 0.046 0.188 2485 Planarity : 0.005 0.052 2933 Dihedral : 5.032 57.944 2332 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.54 % Allowed : 12.43 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: -0.07 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.26 (0.17), residues: 1035 loop : -0.26 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.021 0.002 TYR M 52A PHE 0.023 0.002 PHE M 29 TRP 0.016 0.002 TRP O 47 HIS 0.009 0.002 HIS E 100B Details of bonding type rmsd covalent geometry : bond 0.00764 (16912) covalent geometry : angle 0.66141 (22986) SS BOND : bond 0.00361 ( 18) SS BOND : angle 1.37687 ( 36) hydrogen bonds : bond 0.03811 ( 589) hydrogen bonds : angle 6.52722 ( 1581) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 197 time to evaluate : 0.684 Fit side-chains REVERT: I 9 VAL cc_start: 0.8976 (m) cc_final: 0.8638 (t) REVERT: A 4 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6837 (mp) REVERT: A 86 ASP cc_start: 0.7614 (m-30) cc_final: 0.7321 (m-30) REVERT: D 102 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8092 (t) REVERT: F 17 ASP cc_start: 0.7762 (t0) cc_final: 0.7509 (t0) REVERT: N 17 ASP cc_start: 0.8146 (t0) cc_final: 0.7768 (t0) REVERT: P 3 GLN cc_start: 0.7427 (tp40) cc_final: 0.7162 (mm-40) REVERT: P 100 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: Q 16 ARG cc_start: 0.8334 (tpp80) cc_final: 0.8024 (tpp-160) REVERT: Q 52 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.7969 (t80) REVERT: R 100 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8344 (pt0) REVERT: S 108 LEU cc_start: 0.8545 (mt) cc_final: 0.8309 (mt) REVERT: U 72 ASP cc_start: 0.8097 (m-30) cc_final: 0.7730 (m-30) REVERT: U 79 TYR cc_start: 0.8342 (m-80) cc_final: 0.7938 (m-80) REVERT: V 82 ASP cc_start: 0.8376 (m-30) cc_final: 0.8010 (m-30) REVERT: V 92 ASN cc_start: 0.8257 (t0) cc_final: 0.8050 (t0) outliers start: 64 outliers final: 48 residues processed: 244 average time/residue: 0.1262 time to fit residues: 47.1279 Evaluate side-chains 239 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 17 SER Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 90 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 20 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.114660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090835 restraints weight = 30843.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.092807 restraints weight = 20126.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094075 restraints weight = 14977.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.094958 restraints weight = 12211.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095464 restraints weight = 10659.146| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16930 Z= 0.107 Angle : 0.523 8.779 23022 Z= 0.277 Chirality : 0.042 0.220 2485 Planarity : 0.004 0.049 2933 Dihedral : 4.533 58.750 2332 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.04 % Allowed : 13.48 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.27 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.45 (0.18), residues: 936 loop : 0.05 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.019 0.001 TYR U 52A PHE 0.010 0.001 PHE H 29 TRP 0.010 0.001 TRP E 47 HIS 0.020 0.001 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00247 (16912) covalent geometry : angle 0.52239 (22986) SS BOND : bond 0.00236 ( 18) SS BOND : angle 0.72885 ( 36) hydrogen bonds : bond 0.02848 ( 589) hydrogen bonds : angle 5.81785 ( 1581) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 0.637 Fit side-chains REVERT: I 10 ASP cc_start: 0.8619 (t0) cc_final: 0.8349 (t0) REVERT: H 97 HIS cc_start: 0.8953 (OUTLIER) cc_final: 0.8578 (m90) REVERT: A 4 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6522 (mp) REVERT: A 86 ASP cc_start: 0.7530 (m-30) cc_final: 0.7251 (m-30) REVERT: D 102 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.7979 (t) REVERT: F 17 ASP cc_start: 0.7587 (t0) cc_final: 0.7338 (t0) REVERT: N 17 ASP cc_start: 0.8070 (t0) cc_final: 0.7686 (t0) REVERT: P 3 GLN cc_start: 0.7390 (tp40) cc_final: 0.7002 (mm-40) REVERT: P 6 GLN cc_start: 0.7785 (mt0) cc_final: 0.7555 (mt0) REVERT: Q 52 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7764 (t80) REVERT: R 100 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: U 72 ASP cc_start: 0.8022 (m-30) cc_final: 0.7803 (m-30) REVERT: U 79 TYR cc_start: 0.8211 (m-80) cc_final: 0.7866 (m-80) REVERT: V 82 ASP cc_start: 0.8292 (m-30) cc_final: 0.8008 (m-30) outliers start: 55 outliers final: 32 residues processed: 257 average time/residue: 0.1191 time to fit residues: 47.0374 Evaluate side-chains 229 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 187 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 133 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.112808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.090579 restraints weight = 31290.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091037 restraints weight = 20515.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090904 restraints weight = 18348.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091326 restraints weight = 18879.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.091733 restraints weight = 15815.766| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16930 Z= 0.199 Angle : 0.569 8.442 23022 Z= 0.300 Chirality : 0.043 0.240 2485 Planarity : 0.004 0.047 2933 Dihedral : 4.609 56.484 2332 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.43 % Allowed : 13.70 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.07 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.39 (0.17), residues: 1035 loop : -0.21 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 24 TYR 0.019 0.002 TYR M 52A PHE 0.014 0.001 PHE H 29 TRP 0.012 0.001 TRP S 103 HIS 0.005 0.001 HIS E 100B Details of bonding type rmsd covalent geometry : bond 0.00473 (16912) covalent geometry : angle 0.56786 (22986) SS BOND : bond 0.00260 ( 18) SS BOND : angle 1.02126 ( 36) hydrogen bonds : bond 0.02999 ( 589) hydrogen bonds : angle 5.74657 ( 1581) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 204 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: H 97 HIS cc_start: 0.8984 (OUTLIER) cc_final: 0.8651 (m90) REVERT: A 4 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6839 (mp) REVERT: A 86 ASP cc_start: 0.7590 (m-30) cc_final: 0.7252 (m-30) REVERT: D 102 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8179 (t) REVERT: F 17 ASP cc_start: 0.7717 (t0) cc_final: 0.7461 (t0) REVERT: N 17 ASP cc_start: 0.8168 (t0) cc_final: 0.7774 (t0) REVERT: P 6 GLN cc_start: 0.7947 (mt0) cc_final: 0.7679 (mt0) REVERT: Q 16 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7876 (mpp-170) REVERT: Q 52 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7927 (t80) REVERT: R 100 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8361 (pt0) REVERT: U 72 ASP cc_start: 0.8080 (m-30) cc_final: 0.7807 (m-30) REVERT: U 79 TYR cc_start: 0.8230 (m-80) cc_final: 0.7921 (m-80) REVERT: V 82 ASP cc_start: 0.8340 (m-30) cc_final: 0.8013 (m-30) REVERT: V 92 ASN cc_start: 0.8214 (t0) cc_final: 0.7994 (t0) outliers start: 62 outliers final: 44 residues processed: 246 average time/residue: 0.1208 time to fit residues: 45.4016 Evaluate side-chains 239 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 4 MET Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 35 optimal weight: 0.0570 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS B 79 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS S 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.114898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092401 restraints weight = 30721.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.093035 restraints weight = 22770.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.093457 restraints weight = 16817.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.094000 restraints weight = 15396.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.094374 restraints weight = 13343.738| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16930 Z= 0.113 Angle : 0.516 8.900 23022 Z= 0.273 Chirality : 0.042 0.259 2485 Planarity : 0.003 0.045 2933 Dihedral : 4.355 56.377 2332 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.09 % Allowed : 14.03 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.31 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.52 (0.18), residues: 936 loop : 0.04 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 24 TYR 0.020 0.001 TYR S 79 PHE 0.009 0.001 PHE H 29 TRP 0.009 0.001 TRP Q 52 HIS 0.002 0.001 HIS C 100B Details of bonding type rmsd covalent geometry : bond 0.00263 (16912) covalent geometry : angle 0.51614 (22986) SS BOND : bond 0.00217 ( 18) SS BOND : angle 0.68804 ( 36) hydrogen bonds : bond 0.02680 ( 589) hydrogen bonds : angle 5.40254 ( 1581) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 0.618 Fit side-chains REVERT: H 97 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.8624 (m90) REVERT: A 4 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6422 (mp) REVERT: A 86 ASP cc_start: 0.7525 (m-30) cc_final: 0.7197 (m-30) REVERT: B 90 GLN cc_start: 0.7387 (pp30) cc_final: 0.6698 (pp30) REVERT: C 108 LEU cc_start: 0.8009 (tp) cc_final: 0.7193 (mp) REVERT: D 102 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8132 (t) REVERT: F 17 ASP cc_start: 0.7649 (t0) cc_final: 0.7388 (t0) REVERT: N 17 ASP cc_start: 0.8202 (t0) cc_final: 0.7754 (t0) REVERT: P 100 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8307 (pm20) REVERT: Q 16 ARG cc_start: 0.8290 (tpp80) cc_final: 0.7898 (mpp-170) REVERT: Q 52 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7731 (t80) REVERT: R 100 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8453 (pt0) REVERT: U 72 ASP cc_start: 0.8149 (m-30) cc_final: 0.7886 (m-30) REVERT: U 79 TYR cc_start: 0.8148 (m-80) cc_final: 0.7880 (m-80) REVERT: V 82 ASP cc_start: 0.8354 (m-30) cc_final: 0.8035 (m-30) outliers start: 56 outliers final: 38 residues processed: 246 average time/residue: 0.1113 time to fit residues: 42.3526 Evaluate side-chains 236 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 124 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 50.0000 chunk 170 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 195 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN A 100BHIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS Q 97 HIS S 97 HIS ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.111990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089557 restraints weight = 31006.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.090196 restraints weight = 22764.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.090432 restraints weight = 17715.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.090541 restraints weight = 16747.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090739 restraints weight = 15761.020| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16930 Z= 0.216 Angle : 0.584 8.875 23022 Z= 0.308 Chirality : 0.044 0.216 2485 Planarity : 0.004 0.045 2933 Dihedral : 4.614 56.934 2332 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.43 % Allowed : 14.14 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.07 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.38 (0.18), residues: 945 loop : -0.15 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 16 TYR 0.018 0.002 TYR U 52A PHE 0.014 0.002 PHE H 29 TRP 0.010 0.001 TRP Q 52 HIS 0.006 0.001 HIS E 100B Details of bonding type rmsd covalent geometry : bond 0.00515 (16912) covalent geometry : angle 0.58251 (22986) SS BOND : bond 0.00265 ( 18) SS BOND : angle 1.07751 ( 36) hydrogen bonds : bond 0.02987 ( 589) hydrogen bonds : angle 5.60628 ( 1581) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: H 97 HIS cc_start: 0.8956 (OUTLIER) cc_final: 0.8570 (m90) REVERT: A 4 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6686 (mp) REVERT: A 86 ASP cc_start: 0.7541 (m-30) cc_final: 0.7145 (m-30) REVERT: B 90 GLN cc_start: 0.7455 (pp30) cc_final: 0.6796 (pp30) REVERT: C 3 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7062 (tp40) REVERT: D 102 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8200 (t) REVERT: F 17 ASP cc_start: 0.7687 (t0) cc_final: 0.7430 (t0) REVERT: N 17 ASP cc_start: 0.8259 (t0) cc_final: 0.7763 (t0) REVERT: P 3 GLN cc_start: 0.7349 (mm-40) cc_final: 0.7044 (mm-40) REVERT: P 100 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: Q 16 ARG cc_start: 0.8344 (tpp80) cc_final: 0.7959 (mpp-170) REVERT: Q 52 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7923 (t80) REVERT: R 100 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8334 (pt0) REVERT: S 79 TYR cc_start: 0.8753 (m-80) cc_final: 0.8295 (m-10) REVERT: U 72 ASP cc_start: 0.8162 (m-30) cc_final: 0.7867 (m-30) REVERT: U 79 TYR cc_start: 0.8197 (m-80) cc_final: 0.7876 (m-80) REVERT: V 82 ASP cc_start: 0.8378 (m-30) cc_final: 0.8016 (m-30) REVERT: V 92 ASN cc_start: 0.8166 (t0) cc_final: 0.7900 (t0) outliers start: 62 outliers final: 47 residues processed: 240 average time/residue: 0.1173 time to fit residues: 43.2505 Evaluate side-chains 243 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 101 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS ** C 100BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.115269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091438 restraints weight = 30778.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.093414 restraints weight = 20064.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.094732 restraints weight = 14926.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.095478 restraints weight = 12179.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.096157 restraints weight = 10664.137| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16930 Z= 0.108 Angle : 0.523 9.255 23022 Z= 0.275 Chirality : 0.042 0.318 2485 Planarity : 0.003 0.046 2933 Dihedral : 4.310 57.200 2332 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.82 % Allowed : 15.19 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.35 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.56 (0.18), residues: 936 loop : 0.05 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 16 TYR 0.017 0.001 TYR U 52A PHE 0.009 0.001 PHE H 29 TRP 0.009 0.001 TRP E 47 HIS 0.008 0.001 HIS C 100B Details of bonding type rmsd covalent geometry : bond 0.00251 (16912) covalent geometry : angle 0.52316 (22986) SS BOND : bond 0.00248 ( 18) SS BOND : angle 0.67053 ( 36) hydrogen bonds : bond 0.02581 ( 589) hydrogen bonds : angle 5.23525 ( 1581) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: H 97 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8610 (m90) REVERT: A 4 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6592 (mp) REVERT: A 86 ASP cc_start: 0.7466 (m-30) cc_final: 0.7128 (m-30) REVERT: B 90 GLN cc_start: 0.7194 (pp30) cc_final: 0.6518 (pp30) REVERT: C 108 LEU cc_start: 0.8057 (tp) cc_final: 0.7305 (mp) REVERT: D 102 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8184 (t) REVERT: E 100 ARG cc_start: 0.7593 (tpp-160) cc_final: 0.7348 (tpp-160) REVERT: F 17 ASP cc_start: 0.7563 (t0) cc_final: 0.7362 (t0) REVERT: N 17 ASP cc_start: 0.8210 (t0) cc_final: 0.7726 (t0) REVERT: P 3 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7061 (mm-40) REVERT: P 92 ASN cc_start: 0.7986 (t0) cc_final: 0.7696 (t0) REVERT: Q 16 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7859 (mpp-170) REVERT: Q 52 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7707 (t80) REVERT: R 100 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: S 13 GLN cc_start: 0.8724 (mp10) cc_final: 0.8432 (mp10) REVERT: S 79 TYR cc_start: 0.8716 (m-80) cc_final: 0.8260 (m-10) REVERT: V 82 ASP cc_start: 0.8253 (m-30) cc_final: 0.8011 (m-30) outliers start: 51 outliers final: 42 residues processed: 251 average time/residue: 0.1121 time to fit residues: 43.2706 Evaluate side-chains 241 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 77 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS ** C 100BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.067402 restraints weight = 32481.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.071107 restraints weight = 18113.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.072127 restraints weight = 10220.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.071945 restraints weight = 8509.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.072436 restraints weight = 9015.697| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16930 Z= 0.227 Angle : 0.606 9.126 23022 Z= 0.318 Chirality : 0.044 0.291 2485 Planarity : 0.004 0.045 2933 Dihedral : 4.608 53.926 2332 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.04 % Allowed : 15.25 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.04 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.36 (0.18), residues: 945 loop : -0.17 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 24 TYR 0.022 0.002 TYR O 79 PHE 0.014 0.002 PHE M 29 TRP 0.011 0.002 TRP S 52 HIS 0.009 0.001 HIS C 100B Details of bonding type rmsd covalent geometry : bond 0.00539 (16912) covalent geometry : angle 0.60486 (22986) SS BOND : bond 0.00279 ( 18) SS BOND : angle 1.07768 ( 36) hydrogen bonds : bond 0.02993 ( 589) hydrogen bonds : angle 5.52212 ( 1581) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 0.624 Fit side-chains REVERT: H 97 HIS cc_start: 0.9014 (OUTLIER) cc_final: 0.8436 (m90) REVERT: A 4 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.6116 (mp) REVERT: A 86 ASP cc_start: 0.7243 (m-30) cc_final: 0.6827 (m-30) REVERT: B 90 GLN cc_start: 0.6996 (pp30) cc_final: 0.6269 (pp30) REVERT: C 3 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7650 (tp40) REVERT: C 13 GLN cc_start: 0.7995 (pm20) cc_final: 0.7534 (pm20) REVERT: F 17 ASP cc_start: 0.7890 (t0) cc_final: 0.7523 (t0) REVERT: N 17 ASP cc_start: 0.8596 (t0) cc_final: 0.7877 (t0) REVERT: P 3 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7149 (mm-40) REVERT: P 100 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: Q 16 ARG cc_start: 0.8506 (tpp80) cc_final: 0.8034 (mpp-170) REVERT: Q 52 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.8043 (t80) REVERT: R 100 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8465 (pt0) REVERT: S 13 GLN cc_start: 0.8863 (mp10) cc_final: 0.8497 (mp10) REVERT: V 92 ASN cc_start: 0.8090 (t0) cc_final: 0.7771 (t0) outliers start: 55 outliers final: 46 residues processed: 228 average time/residue: 0.1043 time to fit residues: 36.8145 Evaluate side-chains 237 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 186 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 163 optimal weight: 4.9990 chunk 42 optimal weight: 40.0000 chunk 109 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 189 optimal weight: 0.0030 chunk 121 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS ** C 100BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS Q 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.113568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089799 restraints weight = 30939.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091701 restraints weight = 20232.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.093036 restraints weight = 15100.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093866 restraints weight = 12329.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094433 restraints weight = 10722.470| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16930 Z= 0.141 Angle : 0.559 9.457 23022 Z= 0.293 Chirality : 0.043 0.307 2485 Planarity : 0.004 0.045 2933 Dihedral : 4.450 53.066 2332 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.82 % Allowed : 15.30 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.21 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.47 (0.18), residues: 936 loop : -0.05 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 24 TYR 0.019 0.001 TYR M 52A PHE 0.010 0.001 PHE H 29 TRP 0.009 0.001 TRP S 52 HIS 0.007 0.001 HIS C 100B Details of bonding type rmsd covalent geometry : bond 0.00333 (16912) covalent geometry : angle 0.55800 (22986) SS BOND : bond 0.00234 ( 18) SS BOND : angle 0.82755 ( 36) hydrogen bonds : bond 0.02713 ( 589) hydrogen bonds : angle 5.34117 ( 1581) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.655 Fit side-chains REVERT: H 97 HIS cc_start: 0.8998 (OUTLIER) cc_final: 0.8624 (m90) REVERT: A 4 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6602 (mp) REVERT: A 86 ASP cc_start: 0.7439 (m-30) cc_final: 0.7045 (m-30) REVERT: B 90 GLN cc_start: 0.7212 (pp30) cc_final: 0.6523 (pp30) REVERT: C 13 GLN cc_start: 0.7953 (pm20) cc_final: 0.7633 (pm20) REVERT: C 108 LEU cc_start: 0.8043 (tp) cc_final: 0.7257 (mp) REVERT: D 102 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8213 (t) REVERT: E 100 ARG cc_start: 0.7590 (tpp-160) cc_final: 0.7325 (tpp-160) REVERT: F 17 ASP cc_start: 0.7595 (t0) cc_final: 0.7349 (t0) REVERT: N 17 ASP cc_start: 0.8293 (t0) cc_final: 0.7802 (t0) REVERT: P 3 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7072 (mm-40) REVERT: Q 16 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7869 (mpp-170) REVERT: Q 52 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7759 (t80) REVERT: R 100 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8334 (pt0) REVERT: S 13 GLN cc_start: 0.8768 (mp10) cc_final: 0.8477 (mp10) REVERT: S 79 TYR cc_start: 0.8717 (m-80) cc_final: 0.8262 (m-10) REVERT: U 6 GLU cc_start: 0.7950 (pm20) cc_final: 0.7505 (pm20) REVERT: V 92 ASN cc_start: 0.8156 (t0) cc_final: 0.7905 (t0) outliers start: 51 outliers final: 43 residues processed: 233 average time/residue: 0.1213 time to fit residues: 43.2414 Evaluate side-chains 241 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 187 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 43 optimal weight: 30.0000 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS ** C 100BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS Q 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.114937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091156 restraints weight = 30895.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.093112 restraints weight = 20177.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.094404 restraints weight = 15050.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095165 restraints weight = 12304.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.095828 restraints weight = 10772.894| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16930 Z= 0.122 Angle : 0.546 9.416 23022 Z= 0.285 Chirality : 0.043 0.308 2485 Planarity : 0.004 0.045 2933 Dihedral : 4.323 53.043 2332 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.87 % Allowed : 15.47 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.20 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.46 (0.18), residues: 945 loop : -0.05 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 24 TYR 0.019 0.001 TYR M 52A PHE 0.009 0.001 PHE H 29 TRP 0.008 0.001 TRP E 47 HIS 0.002 0.001 HIS E 100B Details of bonding type rmsd covalent geometry : bond 0.00287 (16912) covalent geometry : angle 0.54581 (22986) SS BOND : bond 0.00226 ( 18) SS BOND : angle 0.68936 ( 36) hydrogen bonds : bond 0.02630 ( 589) hydrogen bonds : angle 5.20909 ( 1581) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2215.64 seconds wall clock time: 39 minutes 24.19 seconds (2364.19 seconds total)