Starting phenix.real_space_refine on Sat Jun 14 14:46:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dyy_27786/06_2025/8dyy_27786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dyy_27786/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dyy_27786/06_2025/8dyy_27786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dyy_27786/06_2025/8dyy_27786.map" model { file = "/net/cci-nas-00/data/ceres_data/8dyy_27786/06_2025/8dyy_27786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dyy_27786/06_2025/8dyy_27786.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.13, per 1000 atoms: 0.61 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: 4.15 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 3.63 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: 5.63 Time building geometry restraints manager: 4.93 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 41.120 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.002 TRP Q 52 HIS 0.004 0.001 HIS E 100B PHE 0.015 0.002 PHE M 29 TYR 0.023 0.002 TYR U 52A ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.26083 ( 589) hydrogen bonds : angle 10.72571 ( 1581) SS BOND : bond 0.00371 ( 18) SS BOND : angle 1.05396 ( 36) covalent geometry : bond 0.01132 (16912) covalent geometry : angle 0.95699 (22986) *********************** 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 : 1.741 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 204 average time/residue: 0.2799 time to fit residues: 86.6348 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 : 1.865 ------------------------------------------------------------------------------- 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 173 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 186 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 31 ASN O 39 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN Q 97 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.113898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089933 restraints weight = 30663.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091803 restraints weight = 20077.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.093083 restraints weight = 14912.063| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16930 Z= 0.160 Angle : 0.566 8.981 23022 Z= 0.301 Chirality : 0.043 0.166 2485 Planarity : 0.004 0.058 2933 Dihedral : 4.667 49.265 2337 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.71 % Allowed : 12.43 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.28 (0.18), residues: 945 loop : 0.15 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 52 HIS 0.003 0.001 HIS E 97 PHE 0.013 0.001 PHE M 29 TYR 0.015 0.001 TYR U 52A ARG 0.005 0.000 ARG E 71 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 589) hydrogen bonds : angle 6.77208 ( 1581) SS BOND : bond 0.00264 ( 18) SS BOND : angle 0.97233 ( 36) covalent geometry : bond 0.00374 (16912) covalent geometry : angle 0.56490 (22986) *********************** 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 278 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 1.703 Fit side-chains revert: symmetry clash REVERT: I 9 VAL cc_start: 0.8609 (m) cc_final: 0.8195 (t) REVERT: H 28 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8580 (p) REVERT: A 86 ASP cc_start: 0.7518 (m-30) cc_final: 0.7270 (m-30) REVERT: D 102 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.7932 (t) REVERT: E 72 ASP cc_start: 0.8200 (t0) cc_final: 0.7987 (t0) REVERT: P 6 GLN cc_start: 0.8027 (mt0) cc_final: 0.7812 (mt0) REVERT: R 100 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8463 (pt0) REVERT: S 108 LEU cc_start: 0.8365 (mt) cc_final: 0.8137 (mt) REVERT: U 72 ASP cc_start: 0.7997 (m-30) cc_final: 0.7793 (m-30) REVERT: U 79 TYR cc_start: 0.8232 (m-80) cc_final: 0.7909 (m-80) REVERT: V 74 THR cc_start: 0.8136 (m) cc_final: 0.7786 (p) REVERT: V 82 ASP cc_start: 0.8209 (m-30) cc_final: 0.7839 (m-30) outliers start: 49 outliers final: 34 residues processed: 257 average time/residue: 0.2778 time to fit residues: 109.2714 Evaluate side-chains 240 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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 68 THR 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 2 VAL 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 45 LYS 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 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 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 52 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 8 ASN I 20 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS M 97 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.113862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092085 restraints weight = 30441.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091928 restraints weight = 32606.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.092612 restraints weight = 27370.911| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16930 Z= 0.149 Angle : 0.533 8.343 23022 Z= 0.282 Chirality : 0.042 0.200 2485 Planarity : 0.004 0.052 2933 Dihedral : 4.466 55.737 2332 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.04 % Allowed : 12.76 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.44 (0.18), residues: 936 loop : 0.14 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 47 HIS 0.003 0.001 HIS E 100B PHE 0.012 0.001 PHE M 29 TYR 0.019 0.001 TYR M 52A ARG 0.005 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 589) hydrogen bonds : angle 6.12862 ( 1581) SS BOND : bond 0.00243 ( 18) SS BOND : angle 0.85948 ( 36) covalent geometry : bond 0.00350 (16912) covalent geometry : angle 0.53243 (22986) *********************** 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 273 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 1.750 Fit side-chains revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7626 (m-30) cc_final: 0.7398 (m-30) REVERT: D 102 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.7970 (t) REVERT: P 6 GLN cc_start: 0.7931 (mt0) cc_final: 0.7697 (mt0) REVERT: R 100 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8447 (pt0) REVERT: S 79 TYR cc_start: 0.8795 (m-80) cc_final: 0.8496 (m-80) REVERT: S 85 ASP cc_start: 0.7847 (t70) cc_final: 0.7588 (t0) REVERT: U 72 ASP cc_start: 0.7992 (m-30) cc_final: 0.7779 (m-30) REVERT: U 79 TYR cc_start: 0.8240 (m-80) cc_final: 0.7959 (m-80) REVERT: U 91 TYR cc_start: 0.8666 (m-80) cc_final: 0.8452 (m-10) REVERT: V 74 THR cc_start: 0.8295 (m) cc_final: 0.8024 (p) REVERT: V 82 ASP cc_start: 0.8201 (m-30) cc_final: 0.7887 (m-30) outliers start: 55 outliers final: 40 residues processed: 252 average time/residue: 0.2709 time to fit residues: 104.6560 Evaluate side-chains 234 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 1.761 ------------------------------------------------------------------------------- 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 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 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 22 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 75 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 17 SER 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 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 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 54 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 C 97 HIS E 97 HIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.109320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.089064 restraints weight = 31498.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.089682 restraints weight = 33588.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.090416 restraints weight = 29321.958| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 16930 Z= 0.366 Angle : 0.692 8.033 23022 Z= 0.368 Chirality : 0.047 0.213 2485 Planarity : 0.005 0.048 2933 Dihedral : 5.134 59.072 2332 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.36 % Allowed : 12.87 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.19 (0.16), residues: 1035 loop : -0.39 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 47 HIS 0.010 0.002 HIS E 100B PHE 0.024 0.002 PHE M 29 TYR 0.020 0.002 TYR U 52A ARG 0.005 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 589) hydrogen bonds : angle 6.33748 ( 1581) SS BOND : bond 0.00417 ( 18) SS BOND : angle 1.50267 ( 36) covalent geometry : bond 0.00868 (16912) covalent geometry : angle 0.68985 (22986) *********************** 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 275 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 196 time to evaluate : 1.877 Fit side-chains REVERT: H 97 HIS cc_start: 0.9006 (OUTLIER) cc_final: 0.8630 (m90) REVERT: A 4 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7040 (mp) REVERT: A 86 ASP cc_start: 0.7698 (m-30) cc_final: 0.7423 (m-30) REVERT: C 3 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7149 (tp40) REVERT: D 102 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8226 (t) REVERT: E 100 ARG cc_start: 0.7580 (tpp-160) cc_final: 0.7329 (tpp-160) REVERT: N 17 ASP cc_start: 0.8221 (t0) cc_final: 0.7825 (t0) REVERT: P 100 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: Q 16 ARG cc_start: 0.8362 (tpp80) cc_final: 0.8060 (tpp-160) REVERT: Q 52 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.7894 (t80) REVERT: R 100 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: U 72 ASP cc_start: 0.7822 (m-30) cc_final: 0.7585 (m-30) REVERT: U 79 TYR cc_start: 0.8305 (m-80) cc_final: 0.8052 (m-80) REVERT: V 82 ASP cc_start: 0.8207 (m-30) cc_final: 0.7917 (m-30) outliers start: 79 outliers final: 56 residues processed: 255 average time/residue: 0.2731 time to fit residues: 106.2614 Evaluate side-chains 247 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 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 40 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 78 LEU 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 6 GLU 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 72 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 53 ASP Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 102 THR 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 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 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 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 193 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 201 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 HIS Q 35 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 = 0.3682 r_free = 0.3682 target = 0.114943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092465 restraints weight = 31256.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.093056 restraints weight = 21460.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093357 restraints weight = 17651.672| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16930 Z= 0.108 Angle : 0.524 8.879 23022 Z= 0.279 Chirality : 0.042 0.245 2485 Planarity : 0.004 0.047 2933 Dihedral : 4.518 57.933 2332 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.93 % Allowed : 13.76 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.41 (0.18), residues: 936 loop : -0.04 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.012 0.001 HIS C 97 PHE 0.010 0.001 PHE H 29 TYR 0.018 0.001 TYR U 52A ARG 0.006 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02791 ( 589) hydrogen bonds : angle 5.62726 ( 1581) SS BOND : bond 0.00241 ( 18) SS BOND : angle 0.72542 ( 36) covalent geometry : bond 0.00249 (16912) covalent geometry : angle 0.52387 (22986) *********************** 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 263 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 1.760 Fit side-chains revert: symmetry clash REVERT: A 4 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6741 (mp) REVERT: A 86 ASP cc_start: 0.7590 (m-30) cc_final: 0.7298 (m-30) REVERT: D 102 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8055 (t) REVERT: E 100 ARG cc_start: 0.7511 (tpp-160) cc_final: 0.7293 (tpp-160) REVERT: N 17 ASP cc_start: 0.8054 (t0) cc_final: 0.7670 (t0) REVERT: P 100 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: Q 16 ARG cc_start: 0.8290 (tpp80) cc_final: 0.7910 (mpp-170) REVERT: Q 52 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7751 (t80) REVERT: R 100 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8357 (pt0) REVERT: U 72 ASP cc_start: 0.8124 (m-30) cc_final: 0.7904 (m-30) REVERT: U 79 TYR cc_start: 0.8241 (m-80) cc_final: 0.7945 (m-80) REVERT: V 82 ASP cc_start: 0.8341 (m-30) cc_final: 0.8011 (m-30) outliers start: 53 outliers final: 38 residues processed: 246 average time/residue: 0.2726 time to fit residues: 102.6113 Evaluate side-chains 231 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 28 THR 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 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 M residue 6 GLU 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 17 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** O 97 HIS Q 97 HIS ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.113164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.092958 restraints weight = 31087.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.092680 restraints weight = 29549.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.093357 restraints weight = 27675.253| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16930 Z= 0.159 Angle : 0.548 8.777 23022 Z= 0.289 Chirality : 0.043 0.268 2485 Planarity : 0.004 0.046 2933 Dihedral : 4.498 56.075 2332 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.31 % Allowed : 13.98 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.36 (0.18), residues: 945 loop : -0.14 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 47 HIS 0.004 0.001 HIS E 100B PHE 0.012 0.001 PHE H 29 TYR 0.020 0.001 TYR M 52A ARG 0.007 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02815 ( 589) hydrogen bonds : angle 5.52215 ( 1581) SS BOND : bond 0.00229 ( 18) SS BOND : angle 0.92303 ( 36) covalent geometry : bond 0.00378 (16912) covalent geometry : angle 0.54692 (22986) *********************** 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 263 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 1.891 Fit side-chains REVERT: H 97 HIS cc_start: 0.8971 (OUTLIER) cc_final: 0.8605 (m90) REVERT: A 4 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6964 (mp) REVERT: A 86 ASP cc_start: 0.7639 (m-30) cc_final: 0.7315 (m-30) REVERT: B 90 GLN cc_start: 0.7528 (pp30) cc_final: 0.6889 (pp30) REVERT: C 83 ARG cc_start: 0.7558 (mpp80) cc_final: 0.7324 (mpp80) REVERT: D 102 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8196 (t) REVERT: N 17 ASP cc_start: 0.8177 (t0) cc_final: 0.7706 (t0) REVERT: P 100 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: Q 16 ARG cc_start: 0.8405 (tpp80) cc_final: 0.7949 (mpp-170) REVERT: Q 52 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7919 (t80) REVERT: R 100 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8399 (pt0) REVERT: S 79 TYR cc_start: 0.8802 (m-80) cc_final: 0.8322 (m-10) REVERT: U 79 TYR cc_start: 0.8162 (m-80) cc_final: 0.7950 (m-80) REVERT: V 82 ASP cc_start: 0.8244 (m-30) cc_final: 0.7948 (m-30) outliers start: 60 outliers final: 43 residues processed: 246 average time/residue: 0.2790 time to fit residues: 104.9902 Evaluate side-chains 244 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 28 THR 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 40 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 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 106 ILE Chi-restraints excluded: chain M residue 6 GLU 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 17 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 86 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 119 optimal weight: 0.0170 chunk 11 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 overall best weight: 4.4026 ------------------------------------------------------------------------------- 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 81 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS S 97 HIS ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.091970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.066107 restraints weight = 32709.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.069537 restraints weight = 18261.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.070246 restraints weight = 10549.326| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 16930 Z= 0.284 Angle : 0.640 8.696 23022 Z= 0.339 Chirality : 0.045 0.264 2485 Planarity : 0.004 0.046 2933 Dihedral : 4.902 56.293 2332 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.59 % Allowed : 14.20 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.24 (0.17), residues: 1035 loop : -0.42 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 52 HIS 0.008 0.001 HIS E 100B PHE 0.018 0.002 PHE C 29 TYR 0.019 0.002 TYR M 52A ARG 0.006 0.000 ARG S 16 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 589) hydrogen bonds : angle 5.84829 ( 1581) SS BOND : bond 0.00333 ( 18) SS BOND : angle 1.30127 ( 36) covalent geometry : bond 0.00675 (16912) covalent geometry : angle 0.63807 (22986) *********************** 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 259 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 194 time to evaluate : 1.902 Fit side-chains REVERT: H 97 HIS cc_start: 0.9024 (OUTLIER) cc_final: 0.8455 (m90) REVERT: A 4 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6218 (mp) REVERT: A 86 ASP cc_start: 0.7311 (m-30) cc_final: 0.6891 (m-30) REVERT: C 3 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7710 (tp40) REVERT: C 83 ARG cc_start: 0.7454 (mpp80) cc_final: 0.7219 (mpp80) REVERT: C 100 HIS cc_start: 0.7924 (t-90) cc_final: 0.7612 (t70) REVERT: D 18 ARG cc_start: 0.9005 (mmm-85) cc_final: 0.8785 (ttt-90) REVERT: N 17 ASP cc_start: 0.8392 (t0) cc_final: 0.7699 (t0) REVERT: P 3 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7177 (mm-40) REVERT: P 100 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8466 (pm20) REVERT: Q 52 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.7845 (t80) REVERT: R 100 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8457 (pt0) REVERT: U 79 TYR cc_start: 0.8235 (m-80) cc_final: 0.7817 (m-80) REVERT: V 82 ASP cc_start: 0.8540 (m-30) cc_final: 0.8049 (m-30) outliers start: 65 outliers final: 52 residues processed: 240 average time/residue: 0.3022 time to fit residues: 112.5375 Evaluate side-chains 243 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 2.047 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 40 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 6 GLU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 81 GLN 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 6 GLU 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 17 SER Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 80 LEU 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 40 THR 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 67 optimal weight: 0.0970 chunk 168 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 O 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092593 restraints weight = 30741.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.093599 restraints weight = 21465.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.094174 restraints weight = 15458.984| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16930 Z= 0.106 Angle : 0.533 9.234 23022 Z= 0.280 Chirality : 0.042 0.299 2485 Planarity : 0.003 0.046 2933 Dihedral : 4.428 55.785 2332 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.98 % Allowed : 15.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.42 (0.18), residues: 936 loop : -0.10 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS C 35 PHE 0.009 0.001 PHE H 29 TYR 0.018 0.001 TYR U 52A ARG 0.006 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02659 ( 589) hydrogen bonds : angle 5.32743 ( 1581) SS BOND : bond 0.00262 ( 18) SS BOND : angle 0.66856 ( 36) covalent geometry : bond 0.00245 (16912) covalent geometry : angle 0.53230 (22986) *********************** 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 258 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 1.860 Fit side-chains revert: symmetry clash REVERT: H 97 HIS cc_start: 0.8971 (OUTLIER) cc_final: 0.8658 (m90) REVERT: A 4 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6757 (mp) REVERT: A 86 ASP cc_start: 0.7552 (m-30) cc_final: 0.7210 (m-30) REVERT: B 90 GLN cc_start: 0.7365 (pp30) cc_final: 0.6671 (pp30) REVERT: C 13 GLN cc_start: 0.7959 (pm20) cc_final: 0.7626 (pm20) REVERT: C 108 LEU cc_start: 0.8090 (tp) cc_final: 0.7310 (mp) REVERT: D 102 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8148 (t) REVERT: N 17 ASP cc_start: 0.8051 (t0) cc_final: 0.7571 (t0) REVERT: P 3 GLN cc_start: 0.7362 (mm-40) cc_final: 0.6940 (mm-40) REVERT: Q 52 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7731 (t80) REVERT: R 100 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8455 (pt0) REVERT: S 13 GLN cc_start: 0.8838 (mp10) cc_final: 0.8443 (mp10) REVERT: S 79 TYR cc_start: 0.8722 (m-80) cc_final: 0.8265 (m-10) REVERT: S 97 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7550 (m90) outliers start: 54 outliers final: 44 residues processed: 243 average time/residue: 0.2714 time to fit residues: 101.2275 Evaluate side-chains 240 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 2.084 ------------------------------------------------------------------------------- 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 28 THR 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 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 6 GLU 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 6 GLU 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 17 SER 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 S residue 97 HIS 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 33 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** E 81 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.093521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.068124 restraints weight = 32535.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.070690 restraints weight = 18747.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.071820 restraints weight = 11414.437| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16930 Z= 0.205 Angle : 0.594 9.121 23022 Z= 0.312 Chirality : 0.043 0.297 2485 Planarity : 0.004 0.045 2933 Dihedral : 4.623 56.510 2332 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.26 % Allowed : 15.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.34 (0.17), residues: 1035 loop : -0.34 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 52 HIS 0.008 0.001 HIS C 100B PHE 0.013 0.001 PHE H 29 TYR 0.019 0.001 TYR U 52A ARG 0.006 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 589) hydrogen bonds : angle 5.50169 ( 1581) SS BOND : bond 0.00258 ( 18) SS BOND : angle 1.03169 ( 36) covalent geometry : bond 0.00486 (16912) covalent geometry : angle 0.59306 (22986) *********************** 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 247 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 188 time to evaluate : 1.740 Fit side-chains revert: symmetry clash REVERT: H 97 HIS cc_start: 0.9027 (OUTLIER) cc_final: 0.8510 (m90) REVERT: A 4 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6197 (mp) REVERT: A 86 ASP cc_start: 0.7271 (m-30) cc_final: 0.6842 (m-30) REVERT: B 90 GLN cc_start: 0.7043 (pp30) cc_final: 0.6281 (pp30) REVERT: C 3 GLN cc_start: 0.8197 (tp-100) cc_final: 0.7645 (tp40) REVERT: N 17 ASP cc_start: 0.8346 (t0) cc_final: 0.7618 (t0) REVERT: P 3 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7096 (mm-40) REVERT: P 100 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: Q 52 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7944 (t80) REVERT: R 100 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8482 (pt0) REVERT: S 79 TYR cc_start: 0.8767 (m-80) cc_final: 0.8262 (m-10) REVERT: S 97 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7340 (m90) REVERT: U 79 TYR cc_start: 0.8009 (m-80) cc_final: 0.7477 (m-10) outliers start: 59 outliers final: 48 residues processed: 232 average time/residue: 0.2567 time to fit residues: 92.1037 Evaluate side-chains 239 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 28 THR 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 D residue 106 ILE Chi-restraints excluded: chain E residue 6 GLU 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 6 GLU Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 72 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 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 97 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 198 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 169 optimal weight: 0.5980 chunk 161 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 97 HIS ** C 100BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** 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 = 0.3707 r_free = 0.3707 target = 0.115804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094555 restraints weight = 30857.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094811 restraints weight = 28450.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095433 restraints weight = 26315.206| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16930 Z= 0.104 Angle : 0.532 9.509 23022 Z= 0.279 Chirality : 0.042 0.307 2485 Planarity : 0.004 0.045 2933 Dihedral : 4.287 56.872 2332 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.76 % Allowed : 15.14 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.47 (0.18), residues: 936 loop : -0.02 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 96 HIS 0.006 0.001 HIS C 100B PHE 0.008 0.001 PHE B 98 TYR 0.018 0.001 TYR U 52A ARG 0.008 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02579 ( 589) hydrogen bonds : angle 5.09746 ( 1581) SS BOND : bond 0.00276 ( 18) SS BOND : angle 0.58622 ( 36) covalent geometry : bond 0.00237 (16912) covalent geometry : angle 0.53216 (22986) ********************** 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 260 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 1.857 Fit side-chains revert: symmetry clash REVERT: H 97 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8695 (m90) REVERT: A 86 ASP cc_start: 0.7588 (m-30) cc_final: 0.7290 (m-30) REVERT: B 90 GLN cc_start: 0.7470 (pp30) cc_final: 0.6888 (pp30) REVERT: C 13 GLN cc_start: 0.7958 (pm20) cc_final: 0.7488 (pm20) REVERT: C 32 TYR cc_start: 0.8147 (m-80) cc_final: 0.7910 (m-80) REVERT: C 108 LEU cc_start: 0.8002 (tp) cc_final: 0.7260 (mp) REVERT: D 102 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8208 (t) REVERT: N 17 ASP cc_start: 0.8083 (t0) cc_final: 0.7574 (t0) REVERT: O 79 TYR cc_start: 0.9058 (m-80) cc_final: 0.8827 (m-80) REVERT: P 3 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7027 (mm-40) REVERT: P 92 ASN cc_start: 0.7943 (t0) cc_final: 0.7641 (t0) REVERT: Q 52 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7673 (t80) REVERT: R 100 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8468 (pt0) REVERT: S 13 GLN cc_start: 0.8829 (mp10) cc_final: 0.8508 (mp10) REVERT: S 79 TYR cc_start: 0.8730 (m-80) cc_final: 0.8289 (m-10) REVERT: S 97 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7475 (m90) REVERT: U 6 GLU cc_start: 0.7785 (pm20) cc_final: 0.7499 (pm20) REVERT: U 96 ARG cc_start: 0.8621 (ttp80) cc_final: 0.8113 (ttm-80) outliers start: 50 outliers final: 42 residues processed: 245 average time/residue: 0.2689 time to fit residues: 101.2870 Evaluate side-chains 243 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 28 THR 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 6 GLU 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 102 THR 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 S residue 97 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 34 optimal weight: 0.0010 chunk 155 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 43 optimal weight: 50.0000 overall best weight: 1.6992 ------------------------------------------------------------------------------- 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** E 81 GLN Q 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.069873 restraints weight = 32342.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.073604 restraints weight = 17981.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.074502 restraints weight = 10138.244| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16930 Z= 0.138 Angle : 0.554 9.314 23022 Z= 0.290 Chirality : 0.043 0.294 2485 Planarity : 0.004 0.046 2933 Dihedral : 4.307 54.044 2332 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.98 % Allowed : 15.47 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.44 (0.18), residues: 945 loop : -0.10 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 47 HIS 0.004 0.001 HIS C 97 PHE 0.009 0.001 PHE H 29 TYR 0.019 0.001 TYR M 52A ARG 0.009 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02682 ( 589) hydrogen bonds : angle 5.14283 ( 1581) SS BOND : bond 0.00207 ( 18) SS BOND : angle 0.74420 ( 36) covalent geometry : bond 0.00326 (16912) covalent geometry : angle 0.55373 (22986) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4437.34 seconds wall clock time: 79 minutes 17.32 seconds (4757.32 seconds total)