Starting phenix.real_space_refine on Wed Feb 21 06:45:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8x_21579/02_2024/6w8x_21579.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8x_21579/02_2024/6w8x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8x_21579/02_2024/6w8x_21579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8x_21579/02_2024/6w8x_21579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8x_21579/02_2024/6w8x_21579.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8x_21579/02_2024/6w8x_21579.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 15.19, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 11.43 Conformation dependent library (CDL) restraints added in 5.9 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: 4.39 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: 13.40 Time building geometry restraints manager: 12.25 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: 100.90 - 106.10: 65 106.10 - 111.29: 16575 111.29 - 116.49: 6283 116.49 - 121.68: 10932 121.68 - 126.88: 7131 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 2.440 nonbonded pdb=" OG1 THR G 6 " pdb=" OG SER M 14 " model vdw 2.055 2.440 nonbonded pdb=" OG SER X 14 " pdb=" OG1 THR d 6 " model vdw 2.057 2.440 nonbonded pdb=" OG SER D 14 " pdb=" OG1 THR J 6 " model vdw 2.061 2.440 nonbonded pdb=" OG SER T 14 " pdb=" OG1 THR Z 6 " model vdw 2.062 2.440 ... (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 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: 3.760 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: 8.620 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 80.690 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.160 ------------------------------------------------------------------------------- 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= 0.305 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 3.056 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: 0.5630 time to fit residues: 153.7818 Evaluate side-chains 130 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.005 ------------------------------------------------------------------------------- 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: 0.9980 chunk 325 optimal weight: 0.4980 chunk 180 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 chunk 336 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 389 optimal weight: 9.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 74 ASN B 74 ASN C 74 ASN D 74 ASN G 65 GLN G 74 ASN H 65 GLN H 74 ASN I 74 ASN J 74 ASN K 65 GLN L 65 GLN L 74 ASN M 65 GLN N 74 ASN O 65 GLN Q 65 GLN Q 74 ASN Q 89 ASN R 65 GLN R 74 ASN S 65 GLN S 74 ASN U 65 GLN V 74 ASN W 74 ASN Y 65 GLN Z 65 GLN Z 89 ASN a 74 ASN b 74 ASN c 74 ASN e 65 GLN g 74 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29898 Z= 0.182 Angle : 0.487 8.109 40986 Z= 0.263 Chirality : 0.045 0.175 6072 Planarity : 0.002 0.025 4851 Dihedral : 4.243 19.792 4422 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.26 % Allowed : 8.30 % Favored : 91.44 % 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: -1.03 (0.13), residues: 4290 helix: 1.90 (0.14), residues: 1353 sheet: -1.37 (0.12), residues: 1452 loop : -2.39 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE L 29 TYR 0.003 0.001 TYR W 91 ARG 0.007 0.002 ARG C 105 *********************** 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 178 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 3.251 Fit side-chains REVERT: C 74 ASN cc_start: 0.8573 (m110) cc_final: 0.8265 (p0) REVERT: D 74 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8173 (p0) REVERT: H 29 PHE cc_start: 0.8362 (m-10) cc_final: 0.8058 (m-10) REVERT: H 81 MET cc_start: 0.7761 (mtt) cc_final: 0.7523 (mtt) REVERT: I 74 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7940 (p0) REVERT: N 74 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8311 (p0) REVERT: Q 74 ASN cc_start: 0.8469 (m110) cc_final: 0.8246 (p0) REVERT: R 29 PHE cc_start: 0.8484 (m-10) cc_final: 0.8263 (m-10) REVERT: R 74 ASN cc_start: 0.8306 (m110) cc_final: 0.8055 (p0) REVERT: S 29 PHE cc_start: 0.8461 (m-10) cc_final: 0.8245 (m-80) REVERT: S 74 ASN cc_start: 0.8375 (m110) cc_final: 0.8078 (p0) REVERT: V 35 GLN cc_start: 0.9215 (pt0) cc_final: 0.8961 (pt0) REVERT: V 74 ASN cc_start: 0.8410 (m110) cc_final: 0.8058 (p0) REVERT: X 74 ASN cc_start: 0.8536 (m-40) cc_final: 0.8263 (p0) REVERT: a 74 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8395 (p0) REVERT: c 74 ASN cc_start: 0.8320 (m110) cc_final: 0.8047 (p0) REVERT: e 58 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8634 (ttpt) REVERT: e 74 ASN cc_start: 0.8510 (m-40) cc_final: 0.8222 (p0) REVERT: f 74 ASN cc_start: 0.8030 (m-40) cc_final: 0.7815 (m110) REVERT: g 74 ASN cc_start: 0.8383 (m110) cc_final: 0.8145 (p0) outliers start: 9 outliers final: 1 residues processed: 170 average time/residue: 0.5757 time to fit residues: 140.9392 Evaluate side-chains 147 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain N 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 216 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 324 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 390 optimal weight: 2.9990 chunk 421 optimal weight: 8.9990 chunk 347 optimal weight: 20.0000 chunk 387 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 313 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN C 89 ASN ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 74 ASN D 89 ASN E 89 ASN F 89 ASN G 89 ASN H 89 ASN J 89 ASN K 89 ASN L 89 ASN M 74 ASN M 89 ASN O 89 ASN P 89 ASN R 89 ASN ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN T 89 ASN U 89 ASN V 89 ASN W 89 ASN X 74 ASN Y 89 ASN Y 120 ASN a 74 ASN a 89 ASN b 74 ASN b 89 ASN d 74 ASN d 89 ASN e 74 ASN e 89 ASN f 89 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 29898 Z= 0.549 Angle : 0.679 10.174 40986 Z= 0.357 Chirality : 0.050 0.182 6072 Planarity : 0.003 0.025 4851 Dihedral : 4.925 23.209 4422 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.97 % Allowed : 13.12 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.33 (0.13), residues: 4290 helix: 1.83 (0.14), residues: 1353 sheet: -1.47 (0.12), residues: 1518 loop : -2.87 (0.14), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE O 32 TYR 0.005 0.001 TYR G 91 ARG 0.006 0.002 ARG a 105 *********************** 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 153 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 3.178 Fit side-chains REVERT: N 74 ASN cc_start: 0.8534 (m-40) cc_final: 0.8001 (p0) REVERT: R 74 ASN cc_start: 0.8500 (m110) cc_final: 0.8001 (p0) REVERT: T 32 PHE cc_start: 0.9219 (m-80) cc_final: 0.8694 (m-10) REVERT: Z 74 ASN cc_start: 0.8250 (m-40) cc_final: 0.7805 (p0) REVERT: c 74 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8031 (p0) REVERT: e 74 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8287 (p0) REVERT: f 74 ASN cc_start: 0.8183 (m-40) cc_final: 0.7946 (m-40) outliers start: 33 outliers final: 21 residues processed: 141 average time/residue: 0.6416 time to fit residues: 128.9526 Evaluate side-chains 137 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain F residue 74 ASN 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 O residue 37 THR Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain S residue 74 ASN Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 74 ASN Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 120 ASN Chi-restraints excluded: chain Z residue 12 ILE 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 385 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 chunk 391 optimal weight: 3.9990 chunk 414 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 371 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** D 74 ASN I 74 ASN M 74 ASN N 74 ASN ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN Y 120 ASN a 74 ASN b 65 GLN d 74 ASN e 74 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 29898 Z= 0.423 Angle : 0.596 8.903 40986 Z= 0.316 Chirality : 0.048 0.201 6072 Planarity : 0.002 0.032 4851 Dihedral : 4.809 23.397 4422 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.44 % Allowed : 16.56 % Favored : 81.99 % 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: -0.93 (0.13), residues: 4290 helix: 2.03 (0.14), residues: 1353 sheet: -0.79 (0.14), residues: 1254 loop : -2.80 (0.13), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE K 26 TYR 0.004 0.001 TYR W 91 ARG 0.009 0.002 ARG X 105 *********************** 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 174 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 125 time to evaluate : 3.413 Fit side-chains REVERT: C 74 ASN cc_start: 0.8660 (m110) cc_final: 0.8287 (p0) REVERT: D 74 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8368 (p0) REVERT: H 74 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8202 (p0) REVERT: N 74 ASN cc_start: 0.8568 (m110) cc_final: 0.8229 (p0) REVERT: Q 74 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8328 (p0) REVERT: R 74 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8090 (p0) REVERT: V 74 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8048 (p0) REVERT: X 74 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8296 (p0) REVERT: Y 74 ASN cc_start: 0.8494 (m110) cc_final: 0.8068 (p0) REVERT: c 74 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8066 (p0) REVERT: d 74 ASN cc_start: 0.8436 (m110) cc_final: 0.8181 (p0) REVERT: f 74 ASN cc_start: 0.8160 (m-40) cc_final: 0.7931 (m-40) outliers start: 49 outliers final: 29 residues processed: 155 average time/residue: 0.5985 time to fit residues: 135.1261 Evaluate side-chains 153 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 117 time to evaluate : 3.091 ------------------------------------------------------------------------------- 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 E residue 74 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 74 ASN 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 64 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain P residue 12 ILE 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 64 THR Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 74 ASN Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain X residue 74 ASN Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 120 ASN 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 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 345 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 308 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 353 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 chunk 372 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN I 65 GLN I 74 ASN c 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1333 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= 0.217 Angle : 0.492 7.604 40986 Z= 0.264 Chirality : 0.046 0.218 6072 Planarity : 0.002 0.025 4851 Dihedral : 4.293 21.048 4422 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.50 % Allowed : 17.71 % Favored : 80.79 % 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: -0.49 (0.13), residues: 4290 helix: 2.37 (0.15), residues: 1353 sheet: -0.47 (0.14), residues: 1188 loop : -2.51 (0.12), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE Q 32 TYR 0.003 0.001 TYR W 91 ARG 0.007 0.002 ARG N 105 *********************** 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 186 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 135 time to evaluate : 3.218 Fit side-chains REVERT: H 29 PHE cc_start: 0.8550 (m-10) cc_final: 0.8273 (m-10) REVERT: H 74 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8322 (p0) REVERT: N 74 ASN cc_start: 0.8497 (m110) cc_final: 0.8248 (p0) REVERT: Q 74 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8403 (p0) REVERT: R 29 PHE cc_start: 0.8600 (m-10) cc_final: 0.8195 (m-10) REVERT: R 74 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8248 (p0) REVERT: S 74 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8266 (p0) REVERT: V 74 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8186 (p0) REVERT: W 74 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8269 (p0) REVERT: Y 74 ASN cc_start: 0.8423 (m110) cc_final: 0.8198 (p0) outliers start: 51 outliers final: 22 residues processed: 168 average time/residue: 0.5654 time to fit residues: 139.0330 Evaluate side-chains 144 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain F 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 J residue 64 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 74 ASN 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 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 e residue 64 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 8.9990 chunk 373 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 415 optimal weight: 0.5980 chunk 344 optimal weight: 0.0570 chunk 192 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 217 optimal weight: 0.4980 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 120 ASN ** M 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29898 Z= 0.201 Angle : 0.489 6.869 40986 Z= 0.262 Chirality : 0.046 0.225 6072 Planarity : 0.002 0.032 4851 Dihedral : 4.081 20.546 4422 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.59 % Allowed : 18.03 % Favored : 80.38 % 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: -0.52 (0.13), residues: 4290 helix: 2.49 (0.15), residues: 1353 sheet: -1.32 (0.12), residues: 1551 loop : -1.99 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE C 29 TYR 0.002 0.001 TYR W 91 ARG 0.006 0.002 ARG O 105 *********************** 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 183 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 129 time to evaluate : 3.315 Fit side-chains REVERT: E 74 ASN cc_start: 0.8816 (p0) cc_final: 0.8592 (p0) REVERT: H 29 PHE cc_start: 0.8398 (m-10) cc_final: 0.8104 (m-10) REVERT: R 29 PHE cc_start: 0.8443 (m-10) cc_final: 0.8023 (m-10) REVERT: S 74 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8153 (p0) REVERT: V 35 GLN cc_start: 0.9227 (pt0) cc_final: 0.8912 (pt0) REVERT: Y 74 ASN cc_start: 0.8463 (m110) cc_final: 0.8245 (p0) outliers start: 54 outliers final: 29 residues processed: 175 average time/residue: 0.5422 time to fit residues: 143.2156 Evaluate side-chains 147 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 4.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H 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 64 THR Chi-restraints excluded: chain L residue 37 THR 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 S residue 74 ASN Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain U residue 37 THR 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 b residue 64 THR Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 0.9990 chunk 46 optimal weight: 0.0040 chunk 236 optimal weight: 5.9990 chunk 303 optimal weight: 0.7980 chunk 234 optimal weight: 1.9990 chunk 349 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 413 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN F 120 ASN P 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 29898 Z= 0.114 Angle : 0.453 9.319 40986 Z= 0.244 Chirality : 0.045 0.200 6072 Planarity : 0.002 0.048 4851 Dihedral : 3.677 18.033 4422 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.41 % Allowed : 18.27 % Favored : 80.32 % 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: 2.71 (0.15), residues: 1353 sheet: -1.19 (0.12), residues: 1551 loop : -1.82 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE C 29 TYR 0.001 0.000 TYR E 91 ARG 0.016 0.002 ARG T 105 *********************** 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 190 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 142 time to evaluate : 3.228 Fit side-chains REVERT: B 58 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8377 (ttmt) REVERT: F 29 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7757 (t80) REVERT: R 29 PHE cc_start: 0.8101 (m-10) cc_final: 0.7698 (m-10) REVERT: V 35 GLN cc_start: 0.9206 (pt0) cc_final: 0.8909 (pt0) outliers start: 48 outliers final: 23 residues processed: 186 average time/residue: 0.5468 time to fit residues: 151.1794 Evaluate side-chains 142 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 5.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR 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 Y residue 37 THR Chi-restraints excluded: chain Y residue 43 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 d residue 64 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** F 74 ASN ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 29898 Z= 0.303 Angle : 0.546 7.636 40986 Z= 0.290 Chirality : 0.047 0.230 6072 Planarity : 0.003 0.059 4851 Dihedral : 4.045 19.203 4422 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.09 % Allowed : 18.92 % Favored : 79.99 % 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: -0.28 (0.13), residues: 4290 helix: 2.48 (0.15), residues: 1353 sheet: -0.88 (0.12), residues: 1617 loop : -2.08 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE g 29 TYR 0.003 0.001 TYR G 91 ARG 0.010 0.002 ARG E 105 *********************** 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 149 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 112 time to evaluate : 3.563 Fit side-chains REVERT: B 58 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8468 (ttmt) REVERT: C 97 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7783 (tp) REVERT: R 29 PHE cc_start: 0.8421 (m-10) cc_final: 0.7983 (m-10) REVERT: V 35 GLN cc_start: 0.9240 (pt0) cc_final: 0.8930 (pt0) outliers start: 37 outliers final: 27 residues processed: 149 average time/residue: 0.5362 time to fit residues: 121.1251 Evaluate side-chains 134 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain L residue 37 THR 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 T residue 64 THR Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 8.9990 chunk 396 optimal weight: 8.9990 chunk 361 optimal weight: 8.9990 chunk 385 optimal weight: 20.0000 chunk 231 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 chunk 302 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 348 optimal weight: 0.8980 chunk 364 optimal weight: 0.8980 chunk 383 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 65 GLN Y 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29898 Z= 0.197 Angle : 0.498 8.942 40986 Z= 0.267 Chirality : 0.046 0.222 6072 Planarity : 0.002 0.040 4851 Dihedral : 3.877 18.563 4422 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.12 % Allowed : 18.92 % Favored : 79.96 % 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: -0.15 (0.13), residues: 4290 helix: 2.60 (0.15), residues: 1353 sheet: -0.82 (0.12), residues: 1617 loop : -2.00 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE H 29 TYR 0.002 0.001 TYR C 91 ARG 0.011 0.002 ARG E 105 *********************** 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 154 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 3.046 Fit side-chains REVERT: B 58 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8398 (ttmt) REVERT: C 97 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7757 (tp) REVERT: R 29 PHE cc_start: 0.8335 (m-10) cc_final: 0.7931 (m-10) REVERT: V 35 GLN cc_start: 0.9232 (pt0) cc_final: 0.8925 (pt0) outliers start: 38 outliers final: 31 residues processed: 154 average time/residue: 0.5408 time to fit residues: 124.7272 Evaluate side-chains 144 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 64 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 S residue 37 THR Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 120 ASN 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 e residue 64 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 5.9990 chunk 407 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 427 optimal weight: 0.9990 chunk 393 optimal weight: 10.0000 chunk 340 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 29898 Z= 0.204 Angle : 0.621 59.144 40986 Z= 0.351 Chirality : 0.046 0.365 6072 Planarity : 0.002 0.037 4851 Dihedral : 3.885 20.180 4422 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.97 % Allowed : 18.95 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.13), residues: 4290 helix: 2.61 (0.15), residues: 1353 sheet: -0.82 (0.12), residues: 1617 loop : -2.00 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE P 29 TYR 0.002 0.000 TYR C 91 ARG 0.018 0.003 ARG J 105 ********************** 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 148 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 3.223 Fit side-chains REVERT: B 58 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8396 (ttmt) REVERT: C 97 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7757 (tp) REVERT: R 29 PHE cc_start: 0.8334 (m-10) cc_final: 0.7931 (m-10) REVERT: V 35 GLN cc_start: 0.9228 (pt0) cc_final: 0.8945 (pt0) REVERT: Y 120 ASN cc_start: 0.9213 (p0) cc_final: 0.8901 (p0) outliers start: 33 outliers final: 31 residues processed: 147 average time/residue: 0.5313 time to fit residues: 118.2987 Evaluate side-chains 146 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 64 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 S residue 37 THR Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 43 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 e residue 64 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 37 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 0.3980 chunk 362 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 313 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 340 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 62 optimal weight: 0.1980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 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 = 0.3045 r_free = 0.3045 target = 0.070860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.057869 restraints weight = 65435.848| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.82 r_work: 0.2677 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 29898 Z= 0.204 Angle : 0.621 59.144 40986 Z= 0.351 Chirality : 0.046 0.365 6072 Planarity : 0.002 0.037 4851 Dihedral : 3.885 20.180 4422 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.94 % Allowed : 18.95 % Favored : 80.11 % 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: -0.15 (0.13), residues: 4290 helix: 2.61 (0.15), residues: 1353 sheet: -0.82 (0.12), residues: 1617 loop : -2.00 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE P 29 TYR 0.002 0.000 TYR C 91 ARG 0.018 0.003 ARG J 105 =============================================================================== Job complete usr+sys time: 4564.18 seconds wall clock time: 86 minutes 42.35 seconds (5202.35 seconds total)