Starting phenix.real_space_refine on Tue Jun 24 18:49:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w8x_21579/06_2025/6w8x_21579.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w8x_21579/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6w8x_21579/06_2025/6w8x_21579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w8x_21579/06_2025/6w8x_21579.map" model { file = "/net/cci-nas-00/data/ceres_data/6w8x_21579/06_2025/6w8x_21579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w8x_21579/06_2025/6w8x_21579.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.40, per 1000 atoms: 0.58 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: 8.14 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 5.85 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: 13.46 Time building geometry restraints manager: 9.40 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: 0.06 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 73.990 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.800 ------------------------------------------------------------------------------- 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 : 8.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 PHE 0.018 0.002 PHE L 29 TYR 0.004 0.001 TYR G 91 ARG 0.001 0.000 ARG Z 105 Details of bonding type rmsd hydrogen bonds : bond 0.10178 ( 2012) hydrogen bonds : angle 5.12700 ( 5802) covalent geometry : bond 0.00459 (29898) covalent geometry : angle 0.58967 (40986) *********************** 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 : 3.217 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: 0.5611 time to fit residues: 153.2291 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 : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 0.8980 chunk 325 optimal weight: 0.3980 chunk 180 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 173 optimal weight: 20.0000 chunk 336 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 389 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 C 74 ASN D 74 ASN G 65 GLN G 74 ASN H 74 ASN I 74 ASN J 74 ASN K 65 GLN K 74 ASN L 65 GLN L 74 ASN M 65 GLN N 74 ASN O 65 GLN Q 65 GLN Q 74 ASN R 65 GLN R 74 ASN ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 GLN S 74 ASN T 74 ASN V 74 ASN W 74 ASN X 74 ASN Z 65 GLN a 74 ASN c 65 GLN c 74 ASN e 65 GLN e 74 ASN g 74 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.069412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.056054 restraints weight = 65462.456| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.84 r_work: 0.2625 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0881 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 : 0.541 9.035 40986 Z= 0.291 Chirality : 0.047 0.181 6072 Planarity : 0.002 0.026 4851 Dihedral : 4.328 20.474 4422 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.18 % Allowed : 9.59 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.13), residues: 4290 helix: 1.74 (0.14), residues: 1353 sheet: -1.38 (0.13), residues: 1452 loop : -2.41 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE L 29 TYR 0.003 0.001 TYR G 91 ARG 0.007 0.002 ARG C 105 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 2012) hydrogen bonds : angle 4.51392 ( 5802) covalent geometry : bond 0.00410 (29898) covalent geometry : angle 0.54147 (40986) *********************** 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 161 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 3.460 Fit side-chains REVERT: A 74 ASN cc_start: 0.8643 (m110) cc_final: 0.8351 (p0) REVERT: A 105 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.7988 (ttm-80) REVERT: B 74 ASN cc_start: 0.8492 (m110) cc_final: 0.7966 (p0) REVERT: C 74 ASN cc_start: 0.8730 (m110) cc_final: 0.8207 (p0) REVERT: D 74 ASN cc_start: 0.8568 (m110) cc_final: 0.8137 (p0) REVERT: G 74 ASN cc_start: 0.8623 (m110) cc_final: 0.8167 (p0) REVERT: H 29 PHE cc_start: 0.8592 (m-10) cc_final: 0.8306 (m-10) REVERT: H 81 MET cc_start: 0.7894 (mtt) cc_final: 0.7665 (mtt) REVERT: I 74 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.7835 (p0) REVERT: J 74 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8316 (p0) REVERT: J 105 ARG cc_start: 0.8638 (ttm-80) cc_final: 0.8150 (ttm-80) REVERT: K 74 ASN cc_start: 0.8623 (m110) cc_final: 0.8311 (p0) REVERT: K 105 ARG cc_start: 0.8858 (ttm-80) cc_final: 0.8223 (ttm-80) REVERT: N 74 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8243 (p0) REVERT: Q 74 ASN cc_start: 0.8647 (m110) cc_final: 0.8212 (p0) REVERT: R 74 ASN cc_start: 0.8477 (m110) cc_final: 0.8042 (p0) REVERT: S 29 PHE cc_start: 0.8536 (m-10) cc_final: 0.8325 (m-10) REVERT: S 74 ASN cc_start: 0.8550 (m110) cc_final: 0.8100 (p0) REVERT: T 74 ASN cc_start: 0.8711 (m110) cc_final: 0.8361 (p0) REVERT: V 35 GLN cc_start: 0.9310 (pt0) cc_final: 0.9096 (pt0) REVERT: V 74 ASN cc_start: 0.8436 (m110) cc_final: 0.7912 (p0) REVERT: X 74 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8253 (p0) REVERT: a 74 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8382 (p0) REVERT: a 105 ARG cc_start: 0.8674 (tpp80) cc_final: 0.8169 (ttm-80) REVERT: c 74 ASN cc_start: 0.8494 (m110) cc_final: 0.7899 (p0) REVERT: e 58 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8592 (ttpt) REVERT: e 74 ASN cc_start: 0.8572 (m110) cc_final: 0.8138 (p0) REVERT: g 74 ASN cc_start: 0.8507 (m110) cc_final: 0.7984 (p0) outliers start: 6 outliers final: 0 residues processed: 156 average time/residue: 0.6481 time to fit residues: 146.1058 Evaluate side-chains 142 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain X residue 74 ASN Chi-restraints excluded: chain a residue 74 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 74 optimal weight: 0.0970 chunk 219 optimal weight: 6.9990 chunk 279 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 304 optimal weight: 9.9990 chunk 407 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 369 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 chunk 235 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN ** M 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 74 ASN f 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.067153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.054110 restraints weight = 67469.145| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 2.80 r_work: 0.2582 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 29898 Z= 0.280 Angle : 0.613 9.541 40986 Z= 0.325 Chirality : 0.048 0.168 6072 Planarity : 0.002 0.023 4851 Dihedral : 4.522 20.509 4422 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.97 % Allowed : 13.00 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 4290 helix: 1.93 (0.14), residues: 1353 sheet: -1.35 (0.13), residues: 1452 loop : -2.38 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE R 29 TYR 0.004 0.001 TYR G 91 ARG 0.006 0.002 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 2012) hydrogen bonds : angle 4.59428 ( 5802) covalent geometry : bond 0.00661 (29898) covalent geometry : angle 0.61284 (40986) *********************** 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 169 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 3.129 Fit side-chains REVERT: A 74 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8359 (p0) REVERT: A 105 ARG cc_start: 0.8677 (ttm-80) cc_final: 0.8044 (ttm-80) REVERT: B 74 ASN cc_start: 0.8619 (m110) cc_final: 0.8032 (p0) REVERT: C 74 ASN cc_start: 0.8774 (m110) cc_final: 0.8191 (p0) REVERT: D 74 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8140 (p0) REVERT: D 105 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8418 (ttm110) REVERT: H 29 PHE cc_start: 0.8774 (m-10) cc_final: 0.8463 (m-10) REVERT: H 74 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8168 (p0) REVERT: J 74 ASN cc_start: 0.8627 (m-40) cc_final: 0.8308 (p0) REVERT: J 105 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8170 (ttm-80) REVERT: K 74 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8263 (p0) REVERT: K 105 ARG cc_start: 0.8851 (ttm-80) cc_final: 0.8248 (ttm-80) REVERT: N 74 ASN cc_start: 0.8631 (m-40) cc_final: 0.8185 (p0) REVERT: N 105 ARG cc_start: 0.8579 (ttm-80) cc_final: 0.8174 (ttm110) REVERT: Q 74 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8177 (p0) REVERT: R 74 ASN cc_start: 0.8581 (m110) cc_final: 0.8025 (p0) REVERT: T 74 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8280 (p0) REVERT: U 74 ASN cc_start: 0.8653 (m-40) cc_final: 0.8126 (p0) REVERT: X 74 ASN cc_start: 0.8600 (m-40) cc_final: 0.8230 (p0) REVERT: Z 105 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8414 (ttm110) REVERT: a 74 ASN cc_start: 0.8651 (m-40) cc_final: 0.8262 (p0) REVERT: c 74 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.7915 (p0) REVERT: e 74 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8148 (p0) REVERT: g 74 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.7976 (p0) outliers start: 33 outliers final: 17 residues processed: 155 average time/residue: 0.6349 time to fit residues: 141.2179 Evaluate side-chains 153 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain B residue 37 THR 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 H residue 74 ASN Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain L residue 74 ASN Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain Q residue 74 ASN Chi-restraints excluded: chain S residue 74 ASN Chi-restraints excluded: chain T residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 74 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 393 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 358 optimal weight: 3.9990 chunk 48 optimal weight: 0.0170 chunk 145 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 74 ASN M 74 ASN T 65 GLN U 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.071022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.057614 restraints weight = 65151.602| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.85 r_work: 0.2663 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29898 Z= 0.127 Angle : 0.476 7.252 40986 Z= 0.258 Chirality : 0.045 0.188 6072 Planarity : 0.002 0.027 4851 Dihedral : 4.022 19.318 4422 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.12 % Allowed : 14.65 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 4290 helix: 2.36 (0.15), residues: 1353 sheet: -0.51 (0.14), residues: 1188 loop : -2.38 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE M 29 TYR 0.002 0.001 TYR W 91 ARG 0.006 0.002 ARG G 105 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 2012) hydrogen bonds : angle 4.26627 ( 5802) covalent geometry : bond 0.00281 (29898) covalent geometry : angle 0.47610 (40986) *********************** 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 203 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 3.579 Fit side-chains REVERT: A 105 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8078 (ttm-80) REVERT: B 74 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8255 (p0) REVERT: D 74 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8290 (p0) REVERT: D 105 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.8479 (ttm110) REVERT: G 74 ASN cc_start: 0.8577 (m110) cc_final: 0.8374 (p0) REVERT: G 105 ARG cc_start: 0.8577 (ttm-80) cc_final: 0.8351 (ttm110) REVERT: H 29 PHE cc_start: 0.8440 (m-10) cc_final: 0.8144 (m-10) REVERT: H 74 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8310 (p0) REVERT: I 74 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8195 (p0) REVERT: K 74 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8331 (p0) REVERT: K 105 ARG cc_start: 0.8820 (ttm-80) cc_final: 0.8197 (ttm-80) REVERT: L 74 ASN cc_start: 0.8631 (m110) cc_final: 0.8276 (p0) REVERT: M 74 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8294 (p0) REVERT: N 105 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8022 (ttm110) REVERT: O 105 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8290 (ttm110) REVERT: P 74 ASN cc_start: 0.8488 (m-40) cc_final: 0.8093 (p0) REVERT: Q 74 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8332 (p0) REVERT: R 74 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8279 (p0) REVERT: S 74 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8129 (p0) REVERT: T 74 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8396 (p0) REVERT: V 35 GLN cc_start: 0.9327 (pt0) cc_final: 0.9065 (pt0) REVERT: V 74 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8265 (p0) REVERT: W 74 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8333 (p0) REVERT: Y 74 ASN cc_start: 0.8534 (m110) cc_final: 0.7740 (p0) REVERT: Z 29 PHE cc_start: 0.8572 (m-10) cc_final: 0.8371 (m-80) REVERT: c 74 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8094 (p0) REVERT: e 74 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8270 (p0) REVERT: g 74 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8281 (p0) REVERT: g 105 ARG cc_start: 0.8670 (ttm-80) cc_final: 0.8432 (ttm110) outliers start: 38 outliers final: 13 residues processed: 186 average time/residue: 0.5842 time to fit residues: 159.5500 Evaluate side-chains 173 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 3.634 ------------------------------------------------------------------------------- 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 D residue 37 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain I residue 74 ASN 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 M 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 R residue 74 ASN Chi-restraints excluded: chain S residue 74 ASN Chi-restraints excluded: chain T residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain W residue 74 ASN Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain g residue 74 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 127 optimal weight: 9.9990 chunk 368 optimal weight: 5.9990 chunk 374 optimal weight: 10.0000 chunk 422 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 277 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 74 ASN ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN M 74 ASN M 120 ASN d 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.069008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.055782 restraints weight = 66138.186| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.85 r_work: 0.2624 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1331 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= 0.188 Angle : 0.527 7.900 40986 Z= 0.281 Chirality : 0.047 0.233 6072 Planarity : 0.002 0.032 4851 Dihedral : 4.089 20.032 4422 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.56 % Allowed : 16.06 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4290 helix: 2.34 (0.15), residues: 1353 sheet: -1.21 (0.13), residues: 1452 loop : -2.13 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE R 29 TYR 0.003 0.001 TYR G 91 ARG 0.008 0.002 ARG d 105 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 2012) hydrogen bonds : angle 4.32262 ( 5802) covalent geometry : bond 0.00440 (29898) covalent geometry : angle 0.52746 (40986) *********************** 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 188 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 3.190 Fit side-chains REVERT: A 105 ARG cc_start: 0.8639 (ttm-80) cc_final: 0.8072 (ttm-80) REVERT: B 74 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8243 (p0) REVERT: D 74 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8248 (p0) REVERT: E 74 ASN cc_start: 0.8752 (p0) cc_final: 0.8461 (p0) REVERT: H 29 PHE cc_start: 0.8515 (m-10) cc_final: 0.8178 (m-10) REVERT: H 74 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8308 (p0) REVERT: K 74 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8274 (p0) REVERT: K 105 ARG cc_start: 0.8827 (ttm-80) cc_final: 0.8207 (ttm-80) REVERT: L 74 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8233 (p0) REVERT: N 105 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8032 (ttm110) REVERT: O 105 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8272 (ttm110) REVERT: P 74 ASN cc_start: 0.8483 (m-40) cc_final: 0.8063 (p0) REVERT: Q 74 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8317 (p0) REVERT: Q 105 ARG cc_start: 0.8783 (ttm-80) cc_final: 0.8431 (ttm110) REVERT: R 74 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8265 (p0) REVERT: S 74 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8122 (p0) REVERT: T 74 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8349 (p0) REVERT: V 74 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8214 (p0) REVERT: W 74 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8340 (p0) REVERT: Y 74 ASN cc_start: 0.8578 (m110) cc_final: 0.8162 (p0) REVERT: a 105 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8396 (ttm110) REVERT: c 74 ASN cc_start: 0.8431 (m110) cc_final: 0.8086 (p0) REVERT: c 105 ARG cc_start: 0.8581 (ttm-80) cc_final: 0.8366 (ttm110) REVERT: e 74 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8286 (p0) REVERT: g 74 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8210 (p0) REVERT: g 105 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8416 (ttm110) outliers start: 53 outliers final: 21 residues processed: 171 average time/residue: 0.5593 time to fit residues: 139.6377 Evaluate side-chains 161 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 3.318 ------------------------------------------------------------------------------- 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 D residue 37 THR Chi-restraints excluded: chain D residue 74 ASN 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 H residue 74 ASN 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 L 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 74 ASN Chi-restraints excluded: chain R residue 74 ASN Chi-restraints excluded: chain S residue 74 ASN Chi-restraints excluded: chain T residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain W residue 74 ASN Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 74 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 106 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 291 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 350 optimal weight: 0.9990 chunk 378 optimal weight: 0.9980 chunk 374 optimal weight: 1.9990 chunk 397 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.057021 restraints weight = 65693.638| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.82 r_work: 0.2657 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29898 Z= 0.143 Angle : 0.499 7.841 40986 Z= 0.268 Chirality : 0.046 0.232 6072 Planarity : 0.002 0.039 4851 Dihedral : 3.942 21.293 4422 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.65 % Allowed : 16.74 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 4290 helix: 2.47 (0.15), residues: 1353 sheet: -1.27 (0.12), residues: 1551 loop : -1.85 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE C 29 TYR 0.002 0.001 TYR W 91 ARG 0.011 0.002 ARG L 105 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 2012) hydrogen bonds : angle 4.24647 ( 5802) covalent geometry : bond 0.00325 (29898) covalent geometry : angle 0.49886 (40986) *********************** 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 199 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 3.450 Fit side-chains REVERT: A 105 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8088 (ttm-80) REVERT: C 29 PHE cc_start: 0.8315 (m-10) cc_final: 0.8109 (m-10) REVERT: D 74 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8317 (p0) REVERT: E 74 ASN cc_start: 0.8727 (p0) cc_final: 0.8504 (p0) REVERT: H 29 PHE cc_start: 0.8355 (m-10) cc_final: 0.8057 (m-10) REVERT: H 74 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8300 (p0) REVERT: J 105 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8145 (ttm110) REVERT: K 74 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8310 (p0) REVERT: L 74 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8222 (p0) REVERT: N 105 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8061 (ttm110) REVERT: O 105 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8282 (ttm110) REVERT: P 74 ASN cc_start: 0.8393 (m-40) cc_final: 0.7988 (p0) REVERT: Q 74 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8304 (p0) REVERT: Q 105 ARG cc_start: 0.8753 (ttm-80) cc_final: 0.8395 (ttm110) REVERT: S 74 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8103 (p0) REVERT: T 105 ARG cc_start: 0.8520 (ttm110) cc_final: 0.8129 (ttm110) REVERT: V 35 GLN cc_start: 0.9320 (pt0) cc_final: 0.9031 (pt0) REVERT: V 74 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8223 (p0) REVERT: W 74 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8352 (p0) REVERT: Y 74 ASN cc_start: 0.8468 (m110) cc_final: 0.7888 (p0) REVERT: a 105 ARG cc_start: 0.8583 (ttm-80) cc_final: 0.8343 (ttm110) REVERT: b 74 ASN cc_start: 0.8317 (m110) cc_final: 0.8075 (p0) REVERT: c 74 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8038 (p0) REVERT: c 105 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.8364 (ttm110) REVERT: d 105 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8022 (ttm110) REVERT: e 74 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8250 (p0) REVERT: g 74 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8256 (p0) REVERT: g 105 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8388 (ttm110) outliers start: 56 outliers final: 26 residues processed: 183 average time/residue: 0.5884 time to fit residues: 158.9675 Evaluate side-chains 173 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 3.633 ------------------------------------------------------------------------------- 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 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 H residue 14 SER Chi-restraints excluded: chain H residue 74 ASN 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 K residue 74 ASN Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 74 ASN Chi-restraints excluded: chain M residue 14 SER 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 S residue 74 ASN Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain W residue 74 ASN Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain X residue 114 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 74 ASN Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 74 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 213 optimal weight: 4.9990 chunk 335 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 338 optimal weight: 0.0000 chunk 425 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 chunk 333 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.055820 restraints weight = 66228.243| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.84 r_work: 0.2625 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1477 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= 0.188 Angle : 0.537 7.726 40986 Z= 0.286 Chirality : 0.047 0.256 6072 Planarity : 0.002 0.040 4851 Dihedral : 4.023 19.969 4422 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.77 % Allowed : 17.18 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4290 helix: 2.38 (0.15), residues: 1353 sheet: -0.81 (0.14), residues: 1221 loop : -2.35 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE S 29 TYR 0.003 0.001 TYR G 91 ARG 0.012 0.002 ARG D 105 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 2012) hydrogen bonds : angle 4.31777 ( 5802) covalent geometry : bond 0.00438 (29898) covalent geometry : angle 0.53692 (40986) *********************** 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 187 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 127 time to evaluate : 3.612 Fit side-chains REVERT: A 105 ARG cc_start: 0.8661 (ttm-80) cc_final: 0.8073 (ttm-80) REVERT: B 58 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8635 (ttmt) REVERT: D 74 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8307 (p0) REVERT: H 29 PHE cc_start: 0.8516 (m-10) cc_final: 0.8174 (m-10) REVERT: H 74 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8310 (p0) REVERT: J 105 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.8182 (ttm110) REVERT: K 74 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8331 (p0) REVERT: L 74 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8189 (p0) REVERT: O 105 ARG cc_start: 0.8574 (ttm-80) cc_final: 0.8188 (ttm110) REVERT: P 74 ASN cc_start: 0.8411 (m-40) cc_final: 0.7988 (p0) REVERT: Q 74 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8279 (p0) REVERT: Q 105 ARG cc_start: 0.8755 (ttm-80) cc_final: 0.8396 (ttm110) REVERT: S 74 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8059 (p0) REVERT: T 105 ARG cc_start: 0.8520 (ttm110) cc_final: 0.8133 (ttm110) REVERT: V 74 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8252 (p0) REVERT: W 74 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8365 (p0) REVERT: Y 74 ASN cc_start: 0.8457 (m110) cc_final: 0.8195 (p0) REVERT: a 105 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8366 (ttm110) REVERT: b 74 ASN cc_start: 0.8299 (m110) cc_final: 0.8077 (p0) REVERT: c 74 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8064 (p0) REVERT: c 105 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8379 (ttm110) REVERT: e 74 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8248 (p0) REVERT: g 74 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8235 (p0) REVERT: g 105 ARG cc_start: 0.8673 (ttm-80) cc_final: 0.8428 (ttm110) outliers start: 60 outliers final: 31 residues processed: 175 average time/residue: 0.5812 time to fit residues: 149.7363 Evaluate side-chains 163 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 3.387 ------------------------------------------------------------------------------- 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 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 H residue 14 SER Chi-restraints excluded: chain H residue 74 ASN 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 K residue 74 ASN Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 74 ASN Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 37 THR 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 S residue 37 THR Chi-restraints excluded: chain S residue 74 ASN Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 97 ILE Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain W residue 74 ASN Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain X residue 114 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 c residue 43 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 74 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 169 optimal weight: 3.9990 chunk 389 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 392 optimal weight: 2.9990 chunk 321 optimal weight: 0.4980 chunk 236 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 189 optimal weight: 0.0980 chunk 61 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.071393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.057990 restraints weight = 64857.658| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.85 r_work: 0.2688 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1681 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= 0.114 Angle : 0.486 8.833 40986 Z= 0.262 Chirality : 0.046 0.187 6072 Planarity : 0.002 0.050 4851 Dihedral : 3.764 19.604 4422 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.62 % Allowed : 17.21 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4290 helix: 2.57 (0.15), residues: 1353 sheet: -0.89 (0.12), residues: 1617 loop : -1.98 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE S 29 TYR 0.002 0.000 TYR C 91 ARG 0.014 0.002 ARG K 105 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 2012) hydrogen bonds : angle 4.16966 ( 5802) covalent geometry : bond 0.00251 (29898) covalent geometry : angle 0.48630 (40986) *********************** 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 198 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 143 time to evaluate : 3.118 Fit side-chains REVERT: A 105 ARG cc_start: 0.8660 (ttm-80) cc_final: 0.8065 (ttm-80) REVERT: B 58 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8582 (ttmt) REVERT: F 29 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7607 (t80) REVERT: J 105 ARG cc_start: 0.8579 (ttm-80) cc_final: 0.8151 (ttm110) REVERT: K 74 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8320 (p0) REVERT: N 105 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8206 (ttm110) REVERT: O 105 ARG cc_start: 0.8573 (ttm-80) cc_final: 0.8289 (ttm110) REVERT: P 74 ASN cc_start: 0.8373 (m-40) cc_final: 0.7875 (p0) REVERT: Q 74 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8219 (p0) REVERT: Q 105 ARG cc_start: 0.8717 (ttm-80) cc_final: 0.8387 (ttm110) REVERT: S 74 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8091 (p0) REVERT: T 105 ARG cc_start: 0.8496 (ttm110) cc_final: 0.8210 (ttm110) REVERT: V 35 GLN cc_start: 0.9306 (pt0) cc_final: 0.9019 (pt0) REVERT: V 74 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8201 (p0) REVERT: Y 74 ASN cc_start: 0.8478 (m110) cc_final: 0.8103 (p0) REVERT: a 105 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.8370 (ttm110) REVERT: c 74 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8135 (p0) REVERT: c 105 ARG cc_start: 0.8596 (ttm-80) cc_final: 0.8387 (ttm110) REVERT: e 74 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8250 (p0) REVERT: g 105 ARG cc_start: 0.8657 (ttm-80) cc_final: 0.8402 (ttm110) outliers start: 55 outliers final: 29 residues processed: 186 average time/residue: 0.5341 time to fit residues: 147.3412 Evaluate side-chains 167 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 3.269 ------------------------------------------------------------------------------- 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 E residue 37 THR Chi-restraints excluded: chain F residue 29 PHE 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 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 K residue 74 ASN Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 37 THR 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 R residue 37 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain V residue 74 ASN 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 c residue 43 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 97 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 145 optimal weight: 0.9980 chunk 214 optimal weight: 10.0000 chunk 326 optimal weight: 2.9990 chunk 303 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 378 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 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 = 0.3006 r_free = 0.3006 target = 0.068868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.055606 restraints weight = 66067.288| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.84 r_work: 0.2632 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29898 Z= 0.187 Angle : 0.545 7.621 40986 Z= 0.289 Chirality : 0.048 0.246 6072 Planarity : 0.002 0.052 4851 Dihedral : 3.938 17.784 4422 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.21 % Allowed : 17.68 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4290 helix: 2.45 (0.15), residues: 1353 sheet: -0.87 (0.12), residues: 1617 loop : -2.06 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE S 29 TYR 0.003 0.001 TYR G 91 ARG 0.012 0.002 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 2012) hydrogen bonds : angle 4.27854 ( 5802) covalent geometry : bond 0.00437 (29898) covalent geometry : angle 0.54501 (40986) *********************** 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 162 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 3.553 Fit side-chains REVERT: A 105 ARG cc_start: 0.8642 (ttm-80) cc_final: 0.8041 (ttm-80) REVERT: J 105 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8151 (ttm110) REVERT: K 74 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8273 (p0) REVERT: N 105 ARG cc_start: 0.8552 (ttm110) cc_final: 0.8034 (ttm110) REVERT: O 105 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8221 (ttm110) REVERT: P 74 ASN cc_start: 0.8357 (m-40) cc_final: 0.7974 (p0) REVERT: Q 74 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8207 (p0) REVERT: Q 105 ARG cc_start: 0.8755 (ttm-80) cc_final: 0.8406 (ttm110) REVERT: S 74 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8107 (p0) REVERT: T 105 ARG cc_start: 0.8503 (ttm110) cc_final: 0.8113 (ttm110) REVERT: V 74 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8207 (p0) REVERT: Y 74 ASN cc_start: 0.8463 (m110) cc_final: 0.8192 (p0) REVERT: a 105 ARG cc_start: 0.8592 (ttm-80) cc_final: 0.8344 (ttm110) REVERT: c 74 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8083 (p0) REVERT: c 105 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8380 (ttm110) REVERT: e 74 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8261 (p0) REVERT: g 105 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8411 (ttm110) outliers start: 41 outliers final: 31 residues processed: 156 average time/residue: 0.5716 time to fit residues: 131.8279 Evaluate side-chains 156 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 3.366 ------------------------------------------------------------------------------- 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 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 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 K residue 74 ASN Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 37 THR 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 R residue 37 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 74 ASN Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Z residue 37 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 c residue 74 ASN Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain f residue 71 ILE 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 74 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 369 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 425 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.066911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.053953 restraints weight = 67919.983| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.87 r_work: 0.2578 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 29898 Z= 0.288 Angle : 0.641 8.704 40986 Z= 0.335 Chirality : 0.050 0.237 6072 Planarity : 0.003 0.055 4851 Dihedral : 4.395 20.894 4422 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.15 % Allowed : 17.86 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 4290 helix: 2.23 (0.14), residues: 1353 sheet: -1.01 (0.12), residues: 1650 loop : -2.19 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE H 29 TYR 0.004 0.001 TYR G 91 ARG 0.012 0.003 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04640 ( 2012) hydrogen bonds : angle 4.51982 ( 5802) covalent geometry : bond 0.00682 (29898) covalent geometry : angle 0.64071 (40986) ********************** 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 152 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 3.174 Fit side-chains REVERT: J 105 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8163 (ttm110) REVERT: K 74 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8316 (p0) REVERT: N 105 ARG cc_start: 0.8598 (ttm110) cc_final: 0.8048 (ttm110) REVERT: O 105 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8309 (ttm110) REVERT: Q 74 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8303 (p0) REVERT: Q 105 ARG cc_start: 0.8764 (ttm-80) cc_final: 0.8388 (ttm110) REVERT: S 74 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8188 (p0) REVERT: T 105 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8173 (ttm110) REVERT: V 74 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8121 (p0) REVERT: Y 74 ASN cc_start: 0.8386 (m110) cc_final: 0.8096 (p0) REVERT: a 105 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.8402 (ttm110) REVERT: c 74 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8119 (p0) REVERT: c 105 ARG cc_start: 0.8646 (ttm-80) cc_final: 0.8432 (ttm110) REVERT: e 74 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8271 (p0) outliers start: 39 outliers final: 28 residues processed: 146 average time/residue: 0.5942 time to fit residues: 127.8212 Evaluate side-chains 145 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 3.506 ------------------------------------------------------------------------------- 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 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 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 K residue 74 ASN Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N 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 R residue 37 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 74 ASN Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Z residue 37 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 c residue 74 ASN Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain f residue 71 ILE 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 8 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 412 optimal weight: 0.5980 chunk 272 optimal weight: 2.9990 chunk 318 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 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 = 0.3031 r_free = 0.3031 target = 0.070213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.056992 restraints weight = 65576.431| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.84 r_work: 0.2660 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1680 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= 0.132 Angle : 0.513 8.912 40986 Z= 0.273 Chirality : 0.047 0.224 6072 Planarity : 0.002 0.050 4851 Dihedral : 3.915 19.507 4422 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.06 % Allowed : 18.18 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4290 helix: 2.51 (0.15), residues: 1353 sheet: -0.85 (0.12), residues: 1617 loop : -2.12 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.001 PHE C 29 TYR 0.002 0.001 TYR G 91 ARG 0.011 0.003 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 2012) hydrogen bonds : angle 4.27948 ( 5802) covalent geometry : bond 0.00297 (29898) covalent geometry : angle 0.51263 (40986) =============================================================================== Job complete usr+sys time: 9356.62 seconds wall clock time: 164 minutes 43.52 seconds (9883.52 seconds total)