Starting phenix.real_space_refine on Mon Aug 25 14:34:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w8x_21579/08_2025/6w8x_21579.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w8x_21579/08_2025/6w8x_21579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6w8x_21579/08_2025/6w8x_21579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w8x_21579/08_2025/6w8x_21579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w8x_21579/08_2025/6w8x_21579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w8x_21579/08_2025/6w8x_21579.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 33 5.16 5 C 18876 2.51 5 N 4752 2.21 5 O 6105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29766 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "B" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "D" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "F" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "J" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "K" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "L" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "M" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "N" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "O" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "P" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "Q" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "R" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "S" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "T" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "U" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "V" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "W" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "X" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "Y" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "Z" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "a" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "b" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "c" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "d" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "e" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "f" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "g" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Time building chain proxies: 6.30, per 1000 atoms: 0.21 Number of scatterers: 29766 At special positions: 0 Unit cell: (90.72, 91.8, 258.12, 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 33 16.00 O 6105 8.00 N 4752 7.00 C 18876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7590 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 50 sheets defined 28.8% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 1 through 34 removed outlier: 3.695A pdb=" N VAL A 5 " --> pdb=" O LEU A 1 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.693A pdb=" N GLY A 106 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 34 removed outlier: 3.612A pdb=" N GLY B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.840A pdb=" N GLY B 106 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 34 removed outlier: 3.618A pdb=" N GLY C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.700A pdb=" N GLY C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 34 removed outlier: 3.606A pdb=" N GLY D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.683A pdb=" N GLY D 106 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 34 removed outlier: 3.636A pdb=" N GLY E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.718A pdb=" N GLY E 106 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 34 removed outlier: 3.622A pdb=" N GLY F 34 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 removed outlier: 3.762A pdb=" N GLY F 106 " --> pdb=" O THR F 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 34 removed outlier: 3.565A pdb=" N GLY G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.730A pdb=" N GLY G 106 " --> pdb=" O THR G 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 34 removed outlier: 3.610A pdb=" N GLY H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 107 removed outlier: 3.659A pdb=" N GLY H 106 " --> pdb=" O THR H 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 34 removed outlier: 3.642A pdb=" N GLY I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 107 removed outlier: 3.709A pdb=" N GLY I 106 " --> pdb=" O THR I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 34 removed outlier: 3.589A pdb=" N GLY J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 107 removed outlier: 3.693A pdb=" N GLY J 106 " --> pdb=" O THR J 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 34 removed outlier: 3.581A pdb=" N GLY K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 108 removed outlier: 3.805A pdb=" N GLY K 106 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL K 108 " --> pdb=" O ARG K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 34 removed outlier: 3.587A pdb=" N GLY L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.689A pdb=" N GLY L 106 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 34 removed outlier: 3.638A pdb=" N GLY M 34 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 107 removed outlier: 3.733A pdb=" N GLY M 106 " --> pdb=" O THR M 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 34 removed outlier: 3.588A pdb=" N GLY N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 107 removed outlier: 3.693A pdb=" N GLY N 106 " --> pdb=" O THR N 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 34 removed outlier: 3.603A pdb=" N GLY O 34 " --> pdb=" O GLY O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 107 removed outlier: 3.708A pdb=" N GLY O 106 " --> pdb=" O THR O 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 34 removed outlier: 3.649A pdb=" N GLY P 34 " --> pdb=" O GLY P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 107 removed outlier: 3.781A pdb=" N GLY P 106 " --> pdb=" O THR P 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 34 removed outlier: 3.658A pdb=" N GLY Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 107 removed outlier: 3.660A pdb=" N GLY Q 106 " --> pdb=" O THR Q 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 34 removed outlier: 3.655A pdb=" N GLY R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 107 removed outlier: 3.766A pdb=" N GLY R 106 " --> pdb=" O THR R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 34 removed outlier: 3.652A pdb=" N GLY S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 107 removed outlier: 3.661A pdb=" N GLY S 106 " --> pdb=" O THR S 103 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 34 removed outlier: 3.596A pdb=" N GLY T 34 " --> pdb=" O GLY T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 107 removed outlier: 3.739A pdb=" N GLY T 106 " --> pdb=" O THR T 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 34 removed outlier: 3.779A pdb=" N GLY U 34 " --> pdb=" O GLY U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 103 through 107 removed outlier: 3.702A pdb=" N GLY U 106 " --> pdb=" O THR U 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 34 removed outlier: 3.623A pdb=" N GLY V 34 " --> pdb=" O GLY V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 103 through 107 removed outlier: 3.674A pdb=" N GLY V 106 " --> pdb=" O THR V 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 34 removed outlier: 3.816A pdb=" N GLY W 34 " --> pdb=" O GLY W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 103 through 107 removed outlier: 3.750A pdb=" N GLY W 106 " --> pdb=" O THR W 103 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 34 removed outlier: 3.624A pdb=" N GLY X 34 " --> pdb=" O GLY X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 107 removed outlier: 3.675A pdb=" N GLY X 106 " --> pdb=" O THR X 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 34 removed outlier: 3.728A pdb=" N GLY Y 34 " --> pdb=" O GLY Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 107 removed outlier: 3.686A pdb=" N GLY Y 106 " --> pdb=" O THR Y 103 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 34 removed outlier: 3.670A pdb=" N GLY Z 34 " --> pdb=" O GLY Z 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 107 removed outlier: 3.735A pdb=" N GLY Z 106 " --> pdb=" O THR Z 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 34 removed outlier: 3.744A pdb=" N GLY a 34 " --> pdb=" O GLY a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 107 removed outlier: 3.670A pdb=" N GLY a 106 " --> pdb=" O THR a 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 34 removed outlier: 3.575A pdb=" N GLY b 34 " --> pdb=" O GLY b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 107 removed outlier: 3.636A pdb=" N GLY b 106 " --> pdb=" O THR b 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 34 removed outlier: 3.733A pdb=" N GLY c 34 " --> pdb=" O GLY c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 107 removed outlier: 3.692A pdb=" N GLY c 106 " --> pdb=" O THR c 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 34 removed outlier: 3.611A pdb=" N GLY d 34 " --> pdb=" O GLY d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 107 removed outlier: 3.687A pdb=" N GLY d 106 " --> pdb=" O THR d 103 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 34 removed outlier: 3.743A pdb=" N GLY e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 107 removed outlier: 3.700A pdb=" N GLY e 106 " --> pdb=" O THR e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 34 removed outlier: 3.579A pdb=" N GLY f 34 " --> pdb=" O GLY f 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 103 through 107 removed outlier: 3.733A pdb=" N GLY f 106 " --> pdb=" O THR f 103 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 34 removed outlier: 3.739A pdb=" N GLY g 34 " --> pdb=" O GLY g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 107 removed outlier: 3.687A pdb=" N GLY g 106 " --> pdb=" O THR g 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.644A pdb=" N THR A 64 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 5.236A pdb=" N VAL A 78 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR A 67 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 64 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 40 removed outlier: 5.150A pdb=" N VAL B 78 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR B 67 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.676A pdb=" N THR C 64 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 40 removed outlier: 5.133A pdb=" N VAL C 78 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N THR C 67 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 64 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 38 through 40 removed outlier: 5.078A pdb=" N VAL D 78 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N THR D 67 " --> pdb=" O VAL D 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 38 through 40 removed outlier: 3.715A pdb=" N THR E 64 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 38 through 40 removed outlier: 5.114A pdb=" N VAL E 78 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR E 67 " --> pdb=" O VAL E 78 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR E 64 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 38 through 40 removed outlier: 5.143A pdb=" N VAL F 78 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR F 67 " --> pdb=" O VAL F 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 38 through 40 removed outlier: 3.506A pdb=" N SER G 77 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL G 78 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR G 67 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA G 44 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N THR G 131 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU G 46 " --> pdb=" O THR G 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 38 through 40 removed outlier: 3.643A pdb=" N THR H 64 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 38 through 40 removed outlier: 5.005A pdb=" N VAL H 78 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR H 67 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR H 64 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 38 through 40 removed outlier: 3.575A pdb=" N SER I 77 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N VAL I 78 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N THR I 67 " --> pdb=" O VAL I 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 38 through 40 removed outlier: 5.153A pdb=" N VAL J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N THR J 67 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA J 44 " --> pdb=" O ILE J 129 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR J 131 " --> pdb=" O ALA J 44 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU J 46 " --> pdb=" O THR J 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 38 through 40 removed outlier: 5.133A pdb=" N VAL K 78 " --> pdb=" O THR K 67 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR K 67 " --> pdb=" O VAL K 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 38 through 40 removed outlier: 5.059A pdb=" N VAL L 78 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR L 67 " --> pdb=" O VAL L 78 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 38 through 40 removed outlier: 3.691A pdb=" N THR M 64 " --> pdb=" O ILE M 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 38 through 40 removed outlier: 5.069A pdb=" N VAL M 78 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR M 67 " --> pdb=" O VAL M 78 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR M 64 " --> pdb=" O ILE M 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 38 through 40 removed outlier: 5.311A pdb=" N VAL N 78 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N THR N 67 " --> pdb=" O VAL N 78 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 38 through 40 removed outlier: 3.643A pdb=" N THR O 64 " --> pdb=" O ILE O 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 38 through 40 removed outlier: 5.069A pdb=" N VAL O 78 " --> pdb=" O THR O 67 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR O 67 " --> pdb=" O VAL O 78 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR O 64 " --> pdb=" O ILE O 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 38 through 40 removed outlier: 3.665A pdb=" N THR P 64 " --> pdb=" O ILE P 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 38 through 40 removed outlier: 5.217A pdb=" N VAL P 78 " --> pdb=" O THR P 67 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR P 67 " --> pdb=" O VAL P 78 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR P 64 " --> pdb=" O ILE P 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Q' and resid 38 through 40 removed outlier: 4.999A pdb=" N VAL Q 78 " --> pdb=" O THR Q 67 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR Q 67 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 38 through 40 removed outlier: 3.708A pdb=" N THR R 64 " --> pdb=" O ILE R 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 38 through 40 removed outlier: 3.523A pdb=" N SER R 77 " --> pdb=" O SER R 96 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL R 78 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR R 67 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR R 64 " --> pdb=" O ILE R 84 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 38 through 40 removed outlier: 3.560A pdb=" N SER S 77 " --> pdb=" O SER S 96 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL S 78 " --> pdb=" O THR S 67 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N THR S 67 " --> pdb=" O VAL S 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 38 through 40 removed outlier: 5.007A pdb=" N VAL T 78 " --> pdb=" O THR T 67 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N THR T 67 " --> pdb=" O VAL T 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'U' and resid 38 through 40 removed outlier: 5.217A pdb=" N VAL U 78 " --> pdb=" O THR U 67 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR U 67 " --> pdb=" O VAL U 78 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 38 through 40 removed outlier: 3.575A pdb=" N THR V 64 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'V' and resid 38 through 40 removed outlier: 5.143A pdb=" N VAL V 78 " --> pdb=" O THR V 67 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N THR V 67 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR V 64 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 38 through 40 removed outlier: 3.707A pdb=" N THR W 64 " --> pdb=" O ILE W 84 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 38 through 40 removed outlier: 4.979A pdb=" N VAL W 78 " --> pdb=" O THR W 67 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR W 67 " --> pdb=" O VAL W 78 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR W 64 " --> pdb=" O ILE W 84 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 38 through 40 removed outlier: 5.038A pdb=" N VAL X 78 " --> pdb=" O THR X 67 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR X 67 " --> pdb=" O VAL X 78 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA X 44 " --> pdb=" O ILE X 129 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR X 131 " --> pdb=" O ALA X 44 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU X 46 " --> pdb=" O THR X 131 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Y' and resid 38 through 40 removed outlier: 3.722A pdb=" N THR Y 64 " --> pdb=" O ILE Y 84 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 38 through 40 removed outlier: 3.527A pdb=" N SER Y 77 " --> pdb=" O SER Y 96 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL Y 78 " --> pdb=" O THR Y 67 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N THR Y 67 " --> pdb=" O VAL Y 78 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR Y 64 " --> pdb=" O ILE Y 84 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 38 through 40 removed outlier: 3.678A pdb=" N THR Z 64 " --> pdb=" O ILE Z 84 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 38 through 40 removed outlier: 5.130A pdb=" N VAL Z 78 " --> pdb=" O THR Z 67 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR Z 67 " --> pdb=" O VAL Z 78 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR Z 64 " --> pdb=" O ILE Z 84 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 38 through 40 removed outlier: 3.652A pdb=" N THR a 64 " --> pdb=" O ILE a 84 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 38 through 40 removed outlier: 5.114A pdb=" N VAL a 78 " --> pdb=" O THR a 67 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR a 67 " --> pdb=" O VAL a 78 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR a 64 " --> pdb=" O ILE a 84 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'b' and resid 38 through 40 removed outlier: 5.066A pdb=" N VAL b 78 " --> pdb=" O THR b 67 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N THR b 67 " --> pdb=" O VAL b 78 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 38 through 40 removed outlier: 3.686A pdb=" N THR c 64 " --> pdb=" O ILE c 84 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 38 through 40 removed outlier: 3.506A pdb=" N SER c 77 " --> pdb=" O SER c 96 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL c 78 " --> pdb=" O THR c 67 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR c 67 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR c 64 " --> pdb=" O ILE c 84 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'd' and resid 38 through 40 removed outlier: 5.048A pdb=" N VAL d 78 " --> pdb=" O THR d 67 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR d 67 " --> pdb=" O VAL d 78 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'e' and resid 38 through 40 removed outlier: 3.661A pdb=" N THR e 64 " --> pdb=" O ILE e 84 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'e' and resid 38 through 40 removed outlier: 5.261A pdb=" N VAL e 78 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR e 67 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR e 64 " --> pdb=" O ILE e 84 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'f' and resid 38 through 40 removed outlier: 3.632A pdb=" N THR f 64 " --> pdb=" O ILE f 84 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'f' and resid 38 through 40 removed outlier: 5.059A pdb=" N VAL f 78 " --> pdb=" O THR f 67 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N THR f 67 " --> pdb=" O VAL f 78 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR f 64 " --> pdb=" O ILE f 84 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g' and resid 38 through 40 removed outlier: 3.659A pdb=" N THR g 64 " --> pdb=" O ILE g 84 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 38 through 40 removed outlier: 5.153A pdb=" N VAL g 78 " --> pdb=" O THR g 67 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR g 67 " --> pdb=" O VAL g 78 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR g 64 " --> pdb=" O ILE g 84 " (cutoff:3.500A) 2063 hydrogen bonds defined for protein. 5802 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: 7.01 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9405 1.34 - 1.46: 4901 1.46 - 1.57: 15526 1.57 - 1.69: 0 1.69 - 1.80: 66 Bond restraints: 29898 Sorted by residual: bond pdb=" CB ILE R 17 " pdb=" CG2 ILE R 17 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.42e+00 bond pdb=" CB ILE L 17 " pdb=" CG2 ILE L 17 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB THR K 43 " pdb=" CG2 THR K 43 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB ILE N 17 " pdb=" CG2 ILE N 17 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.29e+00 bond pdb=" CB ILE G 17 " pdb=" CG2 ILE G 17 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 ... (remaining 29893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 40199 1.79 - 3.59: 711 3.59 - 5.38: 70 5.38 - 7.17: 0 7.17 - 8.97: 6 Bond angle restraints: 40986 Sorted by residual: angle pdb=" C ILE E 71 " pdb=" N ASN E 72 " pdb=" CA ASN E 72 " ideal model delta sigma weight residual 120.82 124.82 -4.00 1.50e+00 4.44e-01 7.12e+00 angle pdb=" C ILE G 71 " pdb=" N ASN G 72 " pdb=" CA ASN G 72 " ideal model delta sigma weight residual 120.82 124.74 -3.92 1.50e+00 4.44e-01 6.84e+00 angle pdb=" CA LEU P 8 " pdb=" CB LEU P 8 " pdb=" CG LEU P 8 " ideal model delta sigma weight residual 116.30 107.33 8.97 3.50e+00 8.16e-02 6.56e+00 angle pdb=" CA LEU Z 8 " pdb=" CB LEU Z 8 " pdb=" CG LEU Z 8 " ideal model delta sigma weight residual 116.30 107.33 8.97 3.50e+00 8.16e-02 6.56e+00 angle pdb=" CA LEU T 8 " pdb=" CB LEU T 8 " pdb=" CG LEU T 8 " ideal model delta sigma weight residual 116.30 107.50 8.80 3.50e+00 8.16e-02 6.33e+00 ... (remaining 40981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16277 17.99 - 35.97: 804 35.97 - 53.96: 77 53.96 - 71.94: 3 71.94 - 89.93: 32 Dihedral angle restraints: 17193 sinusoidal: 5247 harmonic: 11946 Sorted by residual: dihedral pdb=" CA ILE b 71 " pdb=" C ILE b 71 " pdb=" N ASN b 72 " pdb=" CA ASN b 72 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ILE f 71 " pdb=" C ILE f 71 " pdb=" N ASN f 72 " pdb=" CA ASN f 72 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ILE Z 71 " pdb=" C ILE Z 71 " pdb=" N ASN Z 72 " pdb=" CA ASN Z 72 " ideal model delta harmonic sigma weight residual 180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 17190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3590 0.030 - 0.059: 1443 0.059 - 0.089: 470 0.089 - 0.119: 397 0.119 - 0.148: 172 Chirality restraints: 6072 Sorted by residual: chirality pdb=" CG LEU T 8 " pdb=" CB LEU T 8 " pdb=" CD1 LEU T 8 " pdb=" CD2 LEU T 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE a 112 " pdb=" N ILE a 112 " pdb=" C ILE a 112 " pdb=" CB ILE a 112 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CG LEU K 8 " pdb=" CB LEU K 8 " pdb=" CD1 LEU K 8 " pdb=" CD2 LEU K 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 6069 not shown) Planarity restraints: 4851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 29 " -0.011 2.00e-02 2.50e+03 8.44e-03 1.25e+00 pdb=" CG PHE L 29 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE L 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE L 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE L 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE L 29 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE L 29 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 29 " -0.011 2.00e-02 2.50e+03 8.34e-03 1.22e+00 pdb=" CG PHE F 29 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE F 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE F 29 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 29 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 29 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 29 " -0.011 2.00e-02 2.50e+03 8.23e-03 1.19e+00 pdb=" CG PHE B 29 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE B 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 29 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 29 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 29 " -0.006 2.00e-02 2.50e+03 ... (remaining 4848 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 274 2.61 - 3.18: 26448 3.18 - 3.76: 43390 3.76 - 4.33: 62257 4.33 - 4.90: 106639 Nonbonded interactions: 239008 Sorted by model distance: nonbonded pdb=" OG1 THR A 6 " pdb=" OG SER G 14 " model vdw 2.038 3.040 nonbonded pdb=" OG1 THR G 6 " pdb=" OG SER M 14 " model vdw 2.055 3.040 nonbonded pdb=" OG SER X 14 " pdb=" OG1 THR d 6 " model vdw 2.057 3.040 nonbonded pdb=" OG SER D 14 " pdb=" OG1 THR J 6 " model vdw 2.061 3.040 nonbonded pdb=" OG SER T 14 " pdb=" OG1 THR Z 6 " model vdw 2.062 3.040 ... (remaining 239003 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 27.620 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 29898 Z= 0.205 Angle : 0.590 8.968 40986 Z= 0.333 Chirality : 0.046 0.148 6072 Planarity : 0.002 0.010 4851 Dihedral : 11.443 89.926 9603 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.12), residues: 4290 helix: 0.68 (0.13), residues: 1353 sheet: -1.83 (0.12), residues: 1452 loop : -2.97 (0.13), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Z 105 TYR 0.004 0.001 TYR G 91 PHE 0.018 0.002 PHE L 29 Details of bonding type rmsd covalent geometry : bond 0.00459 (29898) covalent geometry : angle 0.58967 (40986) hydrogen bonds : bond 0.10178 ( 2012) hydrogen bonds : angle 5.12700 ( 5802) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.743 Fit side-chains REVERT: H 81 MET cc_start: 0.7726 (mtt) cc_final: 0.7518 (mtt) REVERT: e 58 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8529 (ttpt) REVERT: f 74 ASN cc_start: 0.8087 (m-40) cc_final: 0.7796 (m110) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2413 time to fit residues: 66.1114 Evaluate side-chains 130 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.0870 chunk 424 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 74 ASN G 65 GLN G 74 ASN H 74 ASN I 74 ASN K 65 GLN L 65 GLN L 74 ASN M 65 GLN N 74 ASN O 65 GLN Q 65 GLN R 65 GLN S 65 GLN S 74 ASN V 74 ASN W 74 ASN X 65 GLN Z 65 GLN c 65 GLN g 74 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.072716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.059066 restraints weight = 64205.584| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.84 r_work: 0.2709 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 29898 Z= 0.099 Angle : 0.485 7.785 40986 Z= 0.265 Chirality : 0.046 0.177 6072 Planarity : 0.002 0.027 4851 Dihedral : 3.993 18.941 4422 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.35 % Allowed : 8.18 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.12), residues: 4290 helix: 1.90 (0.14), residues: 1353 sheet: -0.62 (0.14), residues: 1188 loop : -2.50 (0.12), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG C 105 TYR 0.002 0.001 TYR W 91 PHE 0.012 0.001 PHE L 29 Details of bonding type rmsd covalent geometry : bond 0.00195 (29898) covalent geometry : angle 0.48536 (40986) hydrogen bonds : bond 0.03390 ( 2012) hydrogen bonds : angle 4.32934 ( 5802) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 1.212 Fit side-chains REVERT: A 74 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8302 (p0) REVERT: A 105 ARG cc_start: 0.8597 (ttm-80) cc_final: 0.8024 (ttm-80) REVERT: B 74 ASN cc_start: 0.8397 (m110) cc_final: 0.7994 (p0) REVERT: C 74 ASN cc_start: 0.8617 (m-40) cc_final: 0.8269 (p0) REVERT: D 74 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8159 (p0) REVERT: G 74 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8221 (p0) REVERT: G 105 ARG cc_start: 0.8747 (tpp80) cc_final: 0.8518 (ttm110) REVERT: H 29 PHE cc_start: 0.8258 (m-10) cc_final: 0.7985 (m-10) REVERT: H 74 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8231 (p0) REVERT: H 81 MET cc_start: 0.7868 (mtt) cc_final: 0.7597 (mtt) REVERT: I 74 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7930 (p0) REVERT: J 74 ASN cc_start: 0.8658 (m-40) cc_final: 0.8318 (p0) REVERT: J 105 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8117 (ttm-80) REVERT: K 74 ASN cc_start: 0.8513 (m-40) cc_final: 0.8229 (p0) REVERT: K 105 ARG cc_start: 0.8835 (ttm-80) cc_final: 0.8288 (ttm-80) REVERT: L 74 ASN cc_start: 0.8415 (m110) cc_final: 0.8163 (p0) REVERT: N 74 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8305 (p0) REVERT: Q 74 ASN cc_start: 0.8556 (m-40) cc_final: 0.8224 (p0) REVERT: R 29 PHE cc_start: 0.8451 (m-10) cc_final: 0.8205 (m-10) REVERT: R 74 ASN cc_start: 0.8438 (m-40) cc_final: 0.8067 (p0) REVERT: S 29 PHE cc_start: 0.8354 (m-10) cc_final: 0.8077 (m-10) REVERT: S 74 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.7997 (p0) REVERT: T 74 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8364 (p0) REVERT: V 35 GLN cc_start: 0.9323 (pt0) cc_final: 0.9106 (pt0) REVERT: V 74 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8045 (p0) REVERT: W 74 ASN cc_start: 0.8596 (m110) cc_final: 0.8145 (p0) REVERT: W 105 ARG cc_start: 0.8810 (tpp80) cc_final: 0.8536 (ttm-80) REVERT: X 74 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8270 (p0) REVERT: a 74 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8365 (p0) REVERT: c 74 ASN cc_start: 0.8436 (m-40) cc_final: 0.7936 (p0) REVERT: e 58 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8660 (ttpt) REVERT: e 74 ASN cc_start: 0.8541 (m-40) cc_final: 0.8119 (p0) REVERT: g 74 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8064 (p0) outliers start: 12 outliers final: 0 residues processed: 196 average time/residue: 0.2919 time to fit residues: 82.9513 Evaluate side-chains 167 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain S residue 74 ASN Chi-restraints excluded: chain T residue 74 ASN Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain X residue 74 ASN Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain g residue 74 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 33 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 366 optimal weight: 4.9990 chunk 295 optimal weight: 0.9990 chunk 425 optimal weight: 9.9990 chunk 360 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN J 74 ASN M 74 ASN ** M 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 ASN X 74 ASN ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 74 ASN b 74 ASN c 74 ASN e 74 ASN f 74 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.056830 restraints weight = 65624.288| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.87 r_work: 0.2648 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29898 Z= 0.169 Angle : 0.511 8.307 40986 Z= 0.276 Chirality : 0.046 0.156 6072 Planarity : 0.002 0.022 4851 Dihedral : 3.994 16.761 4422 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.79 % Allowed : 11.00 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.13), residues: 4290 helix: 2.15 (0.15), residues: 1353 sheet: -1.27 (0.12), residues: 1452 loop : -2.09 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG a 105 TYR 0.002 0.001 TYR G 91 PHE 0.009 0.001 PHE e 29 Details of bonding type rmsd covalent geometry : bond 0.00392 (29898) covalent geometry : angle 0.51075 (40986) hydrogen bonds : bond 0.03890 ( 2012) hydrogen bonds : angle 4.29548 ( 5802) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.231 Fit side-chains REVERT: B 74 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8065 (p0) REVERT: C 74 ASN cc_start: 0.8614 (m-40) cc_final: 0.8401 (p0) REVERT: D 74 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8249 (p0) REVERT: D 105 ARG cc_start: 0.8745 (ttm-80) cc_final: 0.8249 (ttm-80) REVERT: E 105 ARG cc_start: 0.8869 (tpp80) cc_final: 0.8436 (ttm-80) REVERT: G 105 ARG cc_start: 0.8771 (tpp80) cc_final: 0.8571 (ttm110) REVERT: H 29 PHE cc_start: 0.8386 (m-10) cc_final: 0.8083 (m-10) REVERT: H 81 MET cc_start: 0.7904 (mtt) cc_final: 0.7683 (mtt) REVERT: I 74 ASN cc_start: 0.8498 (m-40) cc_final: 0.8064 (p0) REVERT: J 74 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8446 (p0) REVERT: J 105 ARG cc_start: 0.8639 (ttm-80) cc_final: 0.8149 (ttm-80) REVERT: K 74 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8274 (p0) REVERT: K 105 ARG cc_start: 0.8825 (ttm-80) cc_final: 0.8341 (ttm-80) REVERT: L 74 ASN cc_start: 0.8458 (m110) cc_final: 0.8172 (p0) REVERT: L 105 ARG cc_start: 0.8689 (ttm-80) cc_final: 0.8359 (ttm110) REVERT: M 74 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8163 (p0) REVERT: N 105 ARG cc_start: 0.8528 (ttm-80) cc_final: 0.8192 (ttm110) REVERT: O 105 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8355 (ttm110) REVERT: Q 74 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8279 (p0) REVERT: R 29 PHE cc_start: 0.8549 (m-10) cc_final: 0.8272 (m-10) REVERT: R 74 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8192 (p0) REVERT: S 29 PHE cc_start: 0.8537 (m-10) cc_final: 0.8334 (m-80) REVERT: S 74 ASN cc_start: 0.8411 (m-40) cc_final: 0.8036 (p0) REVERT: T 74 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8286 (p0) REVERT: V 35 GLN cc_start: 0.9331 (pt0) cc_final: 0.9092 (pt0) REVERT: V 74 ASN cc_start: 0.8379 (m-40) cc_final: 0.7981 (p0) REVERT: W 74 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8183 (p0) REVERT: X 74 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8423 (p0) REVERT: Z 105 ARG cc_start: 0.8646 (ttm-80) cc_final: 0.8405 (ttm110) REVERT: a 74 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8436 (p0) REVERT: a 105 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8303 (ttm110) REVERT: c 74 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8106 (p0) REVERT: d 105 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8277 (ttm110) REVERT: e 58 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8702 (ttpt) REVERT: e 74 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8214 (p0) REVERT: g 74 ASN cc_start: 0.8611 (m-40) cc_final: 0.8232 (p0) outliers start: 27 outliers final: 9 residues processed: 165 average time/residue: 0.3086 time to fit residues: 72.2034 Evaluate side-chains 170 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain Q residue 74 ASN Chi-restraints excluded: chain R residue 74 ASN Chi-restraints excluded: chain T residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain W residue 74 ASN Chi-restraints excluded: chain W residue 122 GLU Chi-restraints excluded: chain X residue 74 ASN Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain e residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 59 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 346 optimal weight: 9.9990 chunk 377 optimal weight: 5.9990 chunk 365 optimal weight: 3.9990 chunk 386 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN J 74 ASN M 74 ASN M 120 ASN R 74 ASN R 120 ASN X 74 ASN ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 74 ASN d 74 ASN e 74 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.069010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.055677 restraints weight = 65871.513| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.85 r_work: 0.2619 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 29898 Z= 0.208 Angle : 0.534 8.361 40986 Z= 0.286 Chirality : 0.047 0.161 6072 Planarity : 0.002 0.032 4851 Dihedral : 4.144 20.346 4422 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.35 % Allowed : 12.92 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.13), residues: 4290 helix: 2.21 (0.15), residues: 1353 sheet: -1.23 (0.13), residues: 1452 loop : -2.09 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG X 105 TYR 0.003 0.001 TYR G 91 PHE 0.010 0.002 PHE C 29 Details of bonding type rmsd covalent geometry : bond 0.00487 (29898) covalent geometry : angle 0.53352 (40986) hydrogen bonds : bond 0.04135 ( 2012) hydrogen bonds : angle 4.35175 ( 5802) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 1.163 Fit side-chains REVERT: A 105 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8101 (ttm-80) REVERT: B 74 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8150 (p0) REVERT: D 105 ARG cc_start: 0.8743 (ttm-80) cc_final: 0.8265 (ttm-80) REVERT: E 105 ARG cc_start: 0.8874 (tpp80) cc_final: 0.8442 (ttm-80) REVERT: H 29 PHE cc_start: 0.8545 (m-10) cc_final: 0.8235 (m-10) REVERT: H 81 MET cc_start: 0.7925 (mtt) cc_final: 0.7707 (mtt) REVERT: I 74 ASN cc_start: 0.8491 (m-40) cc_final: 0.8071 (p0) REVERT: K 74 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8335 (p0) REVERT: K 105 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8230 (ttm-80) REVERT: L 74 ASN cc_start: 0.8550 (m110) cc_final: 0.8193 (p0) REVERT: M 74 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8270 (p0) REVERT: N 105 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.8037 (ttm110) REVERT: O 105 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8419 (ttm110) REVERT: Q 74 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8301 (p0) REVERT: R 29 PHE cc_start: 0.8621 (m-10) cc_final: 0.8304 (m-10) REVERT: R 74 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8321 (p0) REVERT: S 74 ASN cc_start: 0.8472 (m-40) cc_final: 0.8082 (p0) REVERT: T 74 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8386 (p0) REVERT: V 35 GLN cc_start: 0.9324 (pt0) cc_final: 0.9090 (pt0) REVERT: V 74 ASN cc_start: 0.8401 (m-40) cc_final: 0.7993 (p0) REVERT: W 74 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8175 (p0) REVERT: Z 74 ASN cc_start: 0.8395 (m-40) cc_final: 0.8075 (p0) REVERT: Z 105 ARG cc_start: 0.8673 (ttm-80) cc_final: 0.8422 (ttm110) REVERT: a 74 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8521 (p0) REVERT: a 105 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8320 (ttm110) REVERT: c 74 ASN cc_start: 0.8349 (m-40) cc_final: 0.8084 (p0) REVERT: d 105 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.8367 (ttm110) REVERT: e 58 LYS cc_start: 0.8903 (ttpt) cc_final: 0.8660 (ttpt) REVERT: e 74 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8405 (p0) REVERT: g 74 ASN cc_start: 0.8589 (m-40) cc_final: 0.8226 (p0) outliers start: 46 outliers final: 18 residues processed: 170 average time/residue: 0.3032 time to fit residues: 73.9836 Evaluate side-chains 163 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain Q residue 74 ASN Chi-restraints excluded: chain R residue 74 ASN Chi-restraints excluded: chain T residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain W residue 74 ASN Chi-restraints excluded: chain W residue 122 GLU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 155 optimal weight: 1.9990 chunk 311 optimal weight: 0.0980 chunk 335 optimal weight: 0.0270 chunk 283 optimal weight: 8.9990 chunk 342 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 221 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 74 ASN R 74 ASN U 65 GLN ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.071357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.057886 restraints weight = 64866.278| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.85 r_work: 0.2671 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29898 Z= 0.119 Angle : 0.469 7.222 40986 Z= 0.256 Chirality : 0.046 0.222 6072 Planarity : 0.002 0.026 4851 Dihedral : 3.851 18.491 4422 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.18 % Allowed : 14.15 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.13), residues: 4290 helix: 2.43 (0.15), residues: 1353 sheet: -0.86 (0.12), residues: 1518 loop : -1.76 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG I 105 TYR 0.002 0.001 TYR C 91 PHE 0.011 0.001 PHE F 32 Details of bonding type rmsd covalent geometry : bond 0.00264 (29898) covalent geometry : angle 0.46925 (40986) hydrogen bonds : bond 0.03527 ( 2012) hydrogen bonds : angle 4.19223 ( 5802) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 1.163 Fit side-chains REVERT: G 105 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8622 (ttm-80) REVERT: H 29 PHE cc_start: 0.8268 (m-10) cc_final: 0.7968 (m-10) REVERT: H 81 MET cc_start: 0.7906 (mtt) cc_final: 0.7633 (mtt) REVERT: I 74 ASN cc_start: 0.8491 (m-40) cc_final: 0.8148 (p0) REVERT: J 105 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8228 (ttm110) REVERT: K 74 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8315 (p0) REVERT: L 74 ASN cc_start: 0.8416 (m110) cc_final: 0.8213 (p0) REVERT: N 105 ARG cc_start: 0.8550 (ttm-80) cc_final: 0.8103 (ttm110) REVERT: O 105 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8338 (ttm110) REVERT: Q 74 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8272 (p0) REVERT: Q 105 ARG cc_start: 0.8690 (ttm-80) cc_final: 0.8403 (ttm110) REVERT: R 29 PHE cc_start: 0.8439 (m-10) cc_final: 0.8066 (m-10) REVERT: S 74 ASN cc_start: 0.8371 (m-40) cc_final: 0.8094 (p0) REVERT: V 35 GLN cc_start: 0.9334 (pt0) cc_final: 0.9098 (pt0) REVERT: W 74 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8321 (p0) REVERT: Y 74 ASN cc_start: 0.8520 (m110) cc_final: 0.7872 (p0) REVERT: b 74 ASN cc_start: 0.8325 (m110) cc_final: 0.8021 (p0) REVERT: c 74 ASN cc_start: 0.8335 (m-40) cc_final: 0.8053 (p0) REVERT: c 105 ARG cc_start: 0.8557 (ttm-80) cc_final: 0.8329 (ttm110) REVERT: g 74 ASN cc_start: 0.8500 (m-40) cc_final: 0.8250 (p0) outliers start: 40 outliers final: 18 residues processed: 182 average time/residue: 0.2912 time to fit residues: 76.5282 Evaluate side-chains 160 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain W residue 74 ASN Chi-restraints excluded: chain W residue 122 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 86 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 165 optimal weight: 0.0980 chunk 387 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 377 optimal weight: 1.9990 chunk 270 optimal weight: 9.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.055797 restraints weight = 66230.226| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.85 r_work: 0.2622 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 29898 Z= 0.200 Angle : 0.541 7.833 40986 Z= 0.287 Chirality : 0.047 0.190 6072 Planarity : 0.002 0.043 4851 Dihedral : 4.046 20.019 4422 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.59 % Allowed : 15.06 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.13), residues: 4290 helix: 2.36 (0.15), residues: 1353 sheet: -0.85 (0.12), residues: 1518 loop : -1.84 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG d 105 TYR 0.003 0.001 TYR W 91 PHE 0.014 0.002 PHE F 32 Details of bonding type rmsd covalent geometry : bond 0.00468 (29898) covalent geometry : angle 0.54068 (40986) hydrogen bonds : bond 0.04086 ( 2012) hydrogen bonds : angle 4.30314 ( 5802) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 124 time to evaluate : 1.156 Fit side-chains REVERT: A 105 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8362 (ttm110) REVERT: C 72 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8551 (p0) REVERT: G 105 ARG cc_start: 0.8857 (tpp80) cc_final: 0.8604 (ttm110) REVERT: H 29 PHE cc_start: 0.8445 (m-10) cc_final: 0.8101 (m-10) REVERT: H 81 MET cc_start: 0.7900 (mtt) cc_final: 0.7697 (mtt) REVERT: I 74 ASN cc_start: 0.8459 (m-40) cc_final: 0.8144 (p0) REVERT: J 105 ARG cc_start: 0.8627 (ttm-80) cc_final: 0.8104 (ttm-80) REVERT: K 74 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8331 (p0) REVERT: L 74 ASN cc_start: 0.8531 (m110) cc_final: 0.8253 (p0) REVERT: N 105 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8036 (ttm110) REVERT: O 105 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8410 (ttm110) REVERT: Q 74 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8192 (p0) REVERT: Q 105 ARG cc_start: 0.8749 (ttm-80) cc_final: 0.8433 (ttm110) REVERT: R 29 PHE cc_start: 0.8559 (m-10) cc_final: 0.8171 (m-10) REVERT: S 74 ASN cc_start: 0.8414 (m-40) cc_final: 0.8085 (p0) REVERT: W 74 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8307 (p0) REVERT: Y 74 ASN cc_start: 0.8519 (m110) cc_final: 0.8188 (p0) REVERT: b 74 ASN cc_start: 0.8282 (m110) cc_final: 0.7945 (p0) REVERT: c 74 ASN cc_start: 0.8367 (m-40) cc_final: 0.8044 (p0) REVERT: c 105 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8392 (ttm110) REVERT: g 74 ASN cc_start: 0.8479 (m-40) cc_final: 0.8256 (p0) outliers start: 54 outliers final: 24 residues processed: 173 average time/residue: 0.2810 time to fit residues: 71.1117 Evaluate side-chains 147 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain W residue 74 ASN Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 122 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 225 optimal weight: 7.9990 chunk 321 optimal weight: 6.9990 chunk 329 optimal weight: 8.9990 chunk 351 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 424 optimal weight: 0.7980 chunk 289 optimal weight: 9.9990 chunk 233 optimal weight: 8.9990 chunk 301 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.071109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.057692 restraints weight = 64908.332| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.85 r_work: 0.2675 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29898 Z= 0.124 Angle : 0.488 7.415 40986 Z= 0.263 Chirality : 0.046 0.243 6072 Planarity : 0.002 0.046 4851 Dihedral : 3.801 18.956 4422 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.32 % Allowed : 15.77 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.13), residues: 4290 helix: 2.53 (0.15), residues: 1353 sheet: -1.16 (0.12), residues: 1551 loop : -1.74 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG D 105 TYR 0.002 0.001 TYR W 91 PHE 0.017 0.001 PHE S 29 Details of bonding type rmsd covalent geometry : bond 0.00277 (29898) covalent geometry : angle 0.48822 (40986) hydrogen bonds : bond 0.03490 ( 2012) hydrogen bonds : angle 4.18814 ( 5802) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.8335 (ttm110) REVERT: B 58 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8600 (ttmt) REVERT: G 105 ARG cc_start: 0.8837 (tpp80) cc_final: 0.8627 (ttm-80) REVERT: H 81 MET cc_start: 0.7862 (mtt) cc_final: 0.7562 (mtt) REVERT: I 74 ASN cc_start: 0.8415 (m-40) cc_final: 0.8107 (p0) REVERT: J 105 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8256 (ttm110) REVERT: K 105 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8280 (ttm110) REVERT: N 105 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8113 (ttm110) REVERT: O 105 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8354 (ttm110) REVERT: Q 74 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8248 (p0) REVERT: Q 105 ARG cc_start: 0.8667 (ttm-80) cc_final: 0.8394 (ttm110) REVERT: R 29 PHE cc_start: 0.8428 (m-10) cc_final: 0.8006 (m-10) REVERT: T 105 ARG cc_start: 0.8502 (ttm110) cc_final: 0.8126 (ttm110) REVERT: V 35 GLN cc_start: 0.9335 (pt0) cc_final: 0.9110 (pt0) REVERT: Y 74 ASN cc_start: 0.8470 (m110) cc_final: 0.8047 (p0) REVERT: c 74 ASN cc_start: 0.8317 (m-40) cc_final: 0.8093 (p0) REVERT: c 105 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8386 (ttm110) outliers start: 45 outliers final: 23 residues processed: 183 average time/residue: 0.2846 time to fit residues: 75.8087 Evaluate side-chains 158 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 122 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 287 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 243 optimal weight: 9.9990 chunk 314 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 409 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 347 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.069385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.056203 restraints weight = 66361.638| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.86 r_work: 0.2637 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29898 Z= 0.177 Angle : 0.533 7.495 40986 Z= 0.285 Chirality : 0.047 0.225 6072 Planarity : 0.002 0.049 4851 Dihedral : 3.925 18.811 4422 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.27 % Allowed : 16.00 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.13), residues: 4290 helix: 2.44 (0.15), residues: 1353 sheet: -1.13 (0.12), residues: 1551 loop : -1.82 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG L 105 TYR 0.002 0.001 TYR G 91 PHE 0.016 0.001 PHE S 29 Details of bonding type rmsd covalent geometry : bond 0.00412 (29898) covalent geometry : angle 0.53266 (40986) hydrogen bonds : bond 0.03924 ( 2012) hydrogen bonds : angle 4.26502 ( 5802) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 1.180 Fit side-chains REVERT: A 105 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8354 (ttm110) REVERT: C 97 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8087 (tp) REVERT: G 105 ARG cc_start: 0.8886 (tpp80) cc_final: 0.8677 (ttm-80) REVERT: H 29 PHE cc_start: 0.8354 (m-10) cc_final: 0.8128 (m-10) REVERT: H 81 MET cc_start: 0.7945 (mtt) cc_final: 0.7667 (mtt) REVERT: I 74 ASN cc_start: 0.8485 (m-40) cc_final: 0.8151 (p0) REVERT: J 105 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8266 (ttm110) REVERT: K 105 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8247 (ttm110) REVERT: O 105 ARG cc_start: 0.8648 (ttm-80) cc_final: 0.8426 (ttm110) REVERT: Q 74 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8236 (p0) REVERT: Q 105 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8402 (ttm110) REVERT: R 29 PHE cc_start: 0.8514 (m-10) cc_final: 0.8110 (m-10) REVERT: T 105 ARG cc_start: 0.8524 (ttm110) cc_final: 0.8123 (ttm110) REVERT: V 35 GLN cc_start: 0.9323 (pt0) cc_final: 0.9071 (pt0) REVERT: Y 74 ASN cc_start: 0.8428 (m110) cc_final: 0.8190 (p0) REVERT: c 74 ASN cc_start: 0.8365 (m-40) cc_final: 0.8098 (p0) REVERT: c 105 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8399 (ttm110) outliers start: 43 outliers final: 28 residues processed: 167 average time/residue: 0.3012 time to fit residues: 72.4632 Evaluate side-chains 155 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain W residue 122 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 324 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 283 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 314 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 367 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 323 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.069410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.056287 restraints weight = 66116.787| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.85 r_work: 0.2638 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29898 Z= 0.179 Angle : 0.537 8.505 40986 Z= 0.286 Chirality : 0.047 0.203 6072 Planarity : 0.002 0.042 4851 Dihedral : 3.949 20.739 4422 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.06 % Allowed : 16.09 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.13), residues: 4290 helix: 2.44 (0.15), residues: 1353 sheet: -1.11 (0.12), residues: 1551 loop : -1.86 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG D 105 TYR 0.002 0.001 TYR W 91 PHE 0.014 0.001 PHE S 29 Details of bonding type rmsd covalent geometry : bond 0.00416 (29898) covalent geometry : angle 0.53670 (40986) hydrogen bonds : bond 0.03913 ( 2012) hydrogen bonds : angle 4.27915 ( 5802) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 1.087 Fit side-chains REVERT: A 105 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8335 (ttm110) REVERT: H 81 MET cc_start: 0.7880 (mtt) cc_final: 0.7577 (mtt) REVERT: I 74 ASN cc_start: 0.8466 (m-40) cc_final: 0.8112 (p0) REVERT: K 105 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8246 (ttm110) REVERT: N 105 ARG cc_start: 0.8561 (ttm110) cc_final: 0.8179 (ttm110) REVERT: O 105 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.8353 (ttm110) REVERT: Q 74 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8228 (p0) REVERT: Q 105 ARG cc_start: 0.8704 (ttm-80) cc_final: 0.8420 (ttm110) REVERT: R 29 PHE cc_start: 0.8513 (m-10) cc_final: 0.8090 (m-10) REVERT: T 105 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8141 (ttm110) REVERT: Y 74 ASN cc_start: 0.8384 (m110) cc_final: 0.8108 (p0) REVERT: c 74 ASN cc_start: 0.8348 (m-40) cc_final: 0.8067 (p0) REVERT: c 105 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8383 (ttm110) outliers start: 36 outliers final: 29 residues processed: 153 average time/residue: 0.3037 time to fit residues: 66.5990 Evaluate side-chains 151 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain W residue 122 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 28 optimal weight: 3.9990 chunk 304 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 360 optimal weight: 10.0000 chunk 369 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 207 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.069404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.056314 restraints weight = 66120.943| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.84 r_work: 0.2638 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29898 Z= 0.175 Angle : 0.535 8.410 40986 Z= 0.284 Chirality : 0.047 0.196 6072 Planarity : 0.002 0.035 4851 Dihedral : 3.939 18.964 4422 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.12 % Allowed : 16.06 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.13), residues: 4290 helix: 2.45 (0.15), residues: 1353 sheet: -0.85 (0.12), residues: 1617 loop : -2.07 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG D 105 TYR 0.002 0.001 TYR W 91 PHE 0.016 0.001 PHE H 29 Details of bonding type rmsd covalent geometry : bond 0.00408 (29898) covalent geometry : angle 0.53485 (40986) hydrogen bonds : bond 0.03893 ( 2012) hydrogen bonds : angle 4.27843 ( 5802) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 1.277 Fit side-chains REVERT: A 105 ARG cc_start: 0.8590 (ttm-80) cc_final: 0.8317 (ttm110) REVERT: E 74 ASN cc_start: 0.8417 (m110) cc_final: 0.8090 (p0) REVERT: H 81 MET cc_start: 0.7887 (mtt) cc_final: 0.7565 (mtt) REVERT: I 74 ASN cc_start: 0.8487 (m-40) cc_final: 0.8157 (p0) REVERT: J 105 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.8183 (ttm110) REVERT: K 105 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8339 (ttm110) REVERT: N 105 ARG cc_start: 0.8565 (ttm110) cc_final: 0.8127 (ttm110) REVERT: O 105 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8287 (ttm110) REVERT: Q 74 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8246 (p0) REVERT: Q 105 ARG cc_start: 0.8694 (ttm-80) cc_final: 0.8416 (ttm110) REVERT: R 29 PHE cc_start: 0.8524 (m-10) cc_final: 0.8111 (m-10) REVERT: T 105 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8115 (ttm110) REVERT: Y 74 ASN cc_start: 0.8391 (m110) cc_final: 0.8135 (p0) REVERT: c 74 ASN cc_start: 0.8359 (m-40) cc_final: 0.8089 (p0) REVERT: c 105 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8384 (ttm110) outliers start: 38 outliers final: 31 residues processed: 154 average time/residue: 0.3078 time to fit residues: 68.0580 Evaluate side-chains 152 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain W residue 122 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 71 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 301 optimal weight: 0.9980 chunk 225 optimal weight: 8.9990 chunk 356 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 382 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.070600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.057386 restraints weight = 65626.973| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.84 r_work: 0.2673 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29898 Z= 0.133 Angle : 0.503 8.938 40986 Z= 0.269 Chirality : 0.046 0.175 6072 Planarity : 0.002 0.060 4851 Dihedral : 3.782 18.268 4422 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.97 % Allowed : 16.42 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.13), residues: 4290 helix: 2.55 (0.15), residues: 1353 sheet: -0.81 (0.12), residues: 1617 loop : -1.99 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.003 ARG G 105 TYR 0.002 0.001 TYR W 91 PHE 0.015 0.001 PHE O 29 Details of bonding type rmsd covalent geometry : bond 0.00302 (29898) covalent geometry : angle 0.50331 (40986) hydrogen bonds : bond 0.03543 ( 2012) hydrogen bonds : angle 4.19568 ( 5802) =============================================================================== Job complete usr+sys time: 4340.10 seconds wall clock time: 77 minutes 1.35 seconds (4621.35 seconds total)