Starting phenix.real_space_refine on Thu Sep 26 12:11:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/09_2024/6vfe_21160.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/09_2024/6vfe_21160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/09_2024/6vfe_21160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/09_2024/6vfe_21160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/09_2024/6vfe_21160.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/09_2024/6vfe_21160.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 165 5.16 5 C 38709 2.51 5 N 11187 2.21 5 O 11847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 61908 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "B" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "C" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "D" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "E" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "F" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "G" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "H" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "I" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "J" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "K" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "L" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "M" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "N" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "O" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "P" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "Q" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "R" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "S" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "T" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "U" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "V" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "W" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "X" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "Y" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "Z" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "a" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "b" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "c" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "d" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "e" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "f" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "g" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Time building chain proxies: 27.27, per 1000 atoms: 0.44 Number of scatterers: 61908 At special positions: 0 Unit cell: (334.9, 334.9, 91.8, 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 165 16.00 O 11847 8.00 N 11187 7.00 C 38709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.30 Conformation dependent library (CDL) restraints added in 6.1 seconds 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14652 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 0 sheets defined 15.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 27 through 32 removed outlier: 4.239A pdb=" N THR A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 removed outlier: 3.545A pdb=" N ARG A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.805A pdb=" N THR B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 27 through 32 removed outlier: 4.267A pdb=" N THR C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 137 removed outlier: 3.670A pdb=" N ARG C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 154 Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 27 through 34 removed outlier: 4.266A pdb=" N THR D 32 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY D 33 " --> pdb=" O GLN D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 27 through 34 removed outlier: 4.293A pdb=" N THR E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 147 through 154 Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 27 through 32 removed outlier: 3.817A pdb=" N THR F 32 " --> pdb=" O LEU F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 27 through 32 removed outlier: 4.176A pdb=" N THR G 32 " --> pdb=" O LEU G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 136 Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 27 through 34 removed outlier: 4.287A pdb=" N THR H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY H 33 " --> pdb=" O GLN H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 126 through 137 removed outlier: 3.522A pdb=" N ARG I 137 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 154 Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 126 through 137 removed outlier: 3.515A pdb=" N ARG J 137 " --> pdb=" O LEU J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 154 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 29 through 34 removed outlier: 3.597A pdb=" N GLY K 33 " --> pdb=" O GLN K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 147 through 154 Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 147 through 154 Processing helix chain 'M' and resid 5 through 15 Processing helix chain 'M' and resid 27 through 32 removed outlier: 4.427A pdb=" N THR M 32 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 137 removed outlier: 3.745A pdb=" N ARG M 137 " --> pdb=" O LEU M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 154 Processing helix chain 'N' and resid 5 through 15 Processing helix chain 'N' and resid 27 through 34 removed outlier: 4.046A pdb=" N THR N 32 " --> pdb=" O LEU N 28 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY N 33 " --> pdb=" O GLN N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 147 through 154 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 27 through 34 removed outlier: 4.344A pdb=" N THR O 32 " --> pdb=" O LEU O 28 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY O 33 " --> pdb=" O GLN O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 147 through 154 Processing helix chain 'P' and resid 5 through 15 Processing helix chain 'P' and resid 126 through 137 removed outlier: 3.567A pdb=" N ARG P 137 " --> pdb=" O LEU P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 154 Processing helix chain 'Q' and resid 5 through 15 Processing helix chain 'Q' and resid 29 through 34 removed outlier: 3.990A pdb=" N GLY Q 33 " --> pdb=" O GLN Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 137 removed outlier: 3.781A pdb=" N ARG Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 154 Processing helix chain 'R' and resid 5 through 15 Processing helix chain 'R' and resid 27 through 34 removed outlier: 4.342A pdb=" N THR R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY R 33 " --> pdb=" O GLN R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 137 removed outlier: 3.701A pdb=" N ARG R 137 " --> pdb=" O LEU R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 154 Processing helix chain 'S' and resid 5 through 15 Processing helix chain 'S' and resid 29 through 34 removed outlier: 4.014A pdb=" N GLY S 33 " --> pdb=" O GLN S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 137 removed outlier: 3.882A pdb=" N ARG S 137 " --> pdb=" O LEU S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 154 Processing helix chain 'T' and resid 5 through 15 Processing helix chain 'T' and resid 27 through 31 removed outlier: 3.596A pdb=" N SER T 31 " --> pdb=" O LEU T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 147 through 154 Processing helix chain 'U' and resid 5 through 15 Processing helix chain 'U' and resid 29 through 34 removed outlier: 4.122A pdb=" N GLY U 33 " --> pdb=" O GLN U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 137 removed outlier: 3.617A pdb=" N ARG U 137 " --> pdb=" O LEU U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 154 Processing helix chain 'V' and resid 5 through 15 Processing helix chain 'V' and resid 27 through 34 removed outlier: 3.951A pdb=" N THR V 32 " --> pdb=" O LEU V 28 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY V 33 " --> pdb=" O GLN V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 147 through 154 Processing helix chain 'W' and resid 5 through 15 Processing helix chain 'W' and resid 126 through 137 removed outlier: 3.864A pdb=" N ARG W 137 " --> pdb=" O LEU W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 154 Processing helix chain 'X' and resid 5 through 15 Processing helix chain 'X' and resid 27 through 32 removed outlier: 4.175A pdb=" N THR X 32 " --> pdb=" O LEU X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 126 through 136 Processing helix chain 'X' and resid 147 through 154 Processing helix chain 'Y' and resid 5 through 15 Processing helix chain 'Y' and resid 126 through 136 Processing helix chain 'Y' and resid 147 through 154 Processing helix chain 'Z' and resid 5 through 15 Processing helix chain 'Z' and resid 27 through 32 removed outlier: 4.210A pdb=" N THR Z 32 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 126 through 137 removed outlier: 3.531A pdb=" N ARG Z 137 " --> pdb=" O LEU Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 154 Processing helix chain 'a' and resid 5 through 15 Processing helix chain 'a' and resid 28 through 32 removed outlier: 3.625A pdb=" N SER a 31 " --> pdb=" O LEU a 28 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR a 32 " --> pdb=" O GLN a 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 28 through 32' Processing helix chain 'a' and resid 126 through 137 Processing helix chain 'a' and resid 147 through 154 Processing helix chain 'b' and resid 5 through 15 Processing helix chain 'b' and resid 27 through 32 removed outlier: 4.090A pdb=" N THR b 32 " --> pdb=" O LEU b 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 137 removed outlier: 3.657A pdb=" N ARG b 137 " --> pdb=" O LEU b 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 154 Processing helix chain 'c' and resid 5 through 15 Processing helix chain 'c' and resid 27 through 31 Processing helix chain 'c' and resid 126 through 137 Processing helix chain 'c' and resid 147 through 154 Processing helix chain 'd' and resid 5 through 15 Processing helix chain 'd' and resid 27 through 32 removed outlier: 3.915A pdb=" N THR d 32 " --> pdb=" O LEU d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 137 Processing helix chain 'd' and resid 147 through 154 Processing helix chain 'e' and resid 5 through 15 Processing helix chain 'e' and resid 27 through 34 removed outlier: 4.286A pdb=" N THR e 32 " --> pdb=" O LEU e 28 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY e 33 " --> pdb=" O GLN e 29 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 137 Processing helix chain 'e' and resid 147 through 154 Processing helix chain 'f' and resid 5 through 15 Processing helix chain 'f' and resid 27 through 34 removed outlier: 4.295A pdb=" N THR f 32 " --> pdb=" O LEU f 28 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY f 33 " --> pdb=" O GLN f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 137 removed outlier: 3.595A pdb=" N ARG f 137 " --> pdb=" O LEU f 133 " (cutoff:3.500A) Processing helix chain 'f' and resid 147 through 154 Processing helix chain 'g' and resid 5 through 15 Processing helix chain 'g' and resid 27 through 34 removed outlier: 4.302A pdb=" N THR g 32 " --> pdb=" O LEU g 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY g 33 " --> pdb=" O GLN g 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 126 through 137 removed outlier: 3.637A pdb=" N ARG g 137 " --> pdb=" O LEU g 133 " (cutoff:3.500A) Processing helix chain 'g' and resid 147 through 154 646 hydrogen bonds defined for protein. 1929 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: 11.25 Time building geometry restraints manager: 13.61 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: 20980 1.34 - 1.46: 12423 1.46 - 1.58: 29549 1.58 - 1.69: 12 1.69 - 1.81: 231 Bond restraints: 63195 Sorted by residual: bond pdb=" CA GLN N 167 " pdb=" CB GLN N 167 " ideal model delta sigma weight residual 1.527 1.602 -0.075 2.48e-02 1.63e+03 9.10e+00 bond pdb=" C GLN W 141 " pdb=" N PRO W 142 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.58e+00 bond pdb=" C ALA d 98 " pdb=" N PRO d 99 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.12e+00 bond pdb=" CA GLN Z 167 " pdb=" CB GLN Z 167 " ideal model delta sigma weight residual 1.531 1.599 -0.069 3.12e-02 1.03e+03 4.84e+00 bond pdb=" C ALA S 98 " pdb=" N PRO S 99 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.72e+00 ... (remaining 63190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 84359 2.60 - 5.20: 1071 5.20 - 7.80: 90 7.80 - 10.40: 14 10.40 - 13.00: 35 Bond angle restraints: 85569 Sorted by residual: angle pdb=" C GLN L 167 " pdb=" N LYS L 168 " pdb=" CA LYS L 168 " ideal model delta sigma weight residual 122.09 134.39 -12.30 1.86e+00 2.89e-01 4.38e+01 angle pdb=" C GLN K 167 " pdb=" N LYS K 168 " pdb=" CA LYS K 168 " ideal model delta sigma weight residual 121.54 132.62 -11.08 1.91e+00 2.74e-01 3.36e+01 angle pdb=" C GLN B 167 " pdb=" N LYS B 168 " pdb=" CA LYS B 168 " ideal model delta sigma weight residual 121.63 132.74 -11.11 1.92e+00 2.71e-01 3.35e+01 angle pdb=" C GLN V 167 " pdb=" N LYS V 168 " pdb=" CA LYS V 168 " ideal model delta sigma weight residual 122.19 134.99 -12.80 2.30e+00 1.89e-01 3.10e+01 angle pdb=" C GLN W 167 " pdb=" N LYS W 168 " pdb=" CA LYS W 168 " ideal model delta sigma weight residual 122.41 133.83 -11.42 2.09e+00 2.29e-01 2.99e+01 ... (remaining 85564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.26: 34411 18.26 - 36.53: 3105 36.53 - 54.79: 437 54.79 - 73.06: 198 73.06 - 91.32: 96 Dihedral angle restraints: 38247 sinusoidal: 15576 harmonic: 22671 Sorted by residual: dihedral pdb=" CA LEU C 65 " pdb=" C LEU C 65 " pdb=" N GLU C 66 " pdb=" CA GLU C 66 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ARG C 137 " pdb=" C ARG C 137 " pdb=" N HIS C 138 " pdb=" CA HIS C 138 " ideal model delta harmonic sigma weight residual -180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA VAL K 120 " pdb=" C VAL K 120 " pdb=" N TYR K 121 " pdb=" CA TYR K 121 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 38244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 8010 0.064 - 0.128: 1387 0.128 - 0.191: 62 0.191 - 0.255: 11 0.255 - 0.319: 1 Chirality restraints: 9471 Sorted by residual: chirality pdb=" CB ILE G 223 " pdb=" CA ILE G 223 " pdb=" CG1 ILE G 223 " pdb=" CG2 ILE G 223 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA HIS a 135 " pdb=" N HIS a 135 " pdb=" C HIS a 135 " pdb=" CB HIS a 135 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB THR N 173 " pdb=" CA THR N 173 " pdb=" OG1 THR N 173 " pdb=" CG2 THR N 173 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 9468 not shown) Planarity restraints: 11253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP f 126 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO f 127 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO f 127 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO f 127 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 232 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.29e+00 pdb=" C PHE R 232 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE R 232 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO R 233 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 121 " 0.021 2.00e-02 2.50e+03 1.77e-02 6.28e+00 pdb=" CG TYR N 121 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR N 121 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR N 121 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR N 121 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR N 121 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR N 121 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 121 " 0.002 2.00e-02 2.50e+03 ... (remaining 11250 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1764 2.68 - 3.23: 60459 3.23 - 3.79: 95411 3.79 - 4.34: 123148 4.34 - 4.90: 200384 Nonbonded interactions: 481166 Sorted by model distance: nonbonded pdb=" O HIS V 144 " pdb=" N GLN V 148 " model vdw 2.120 3.120 nonbonded pdb=" O HIS D 144 " pdb=" N GLN D 148 " model vdw 2.150 3.120 nonbonded pdb=" O SER Z 210 " pdb=" NH2 ARG a 78 " model vdw 2.154 3.120 nonbonded pdb=" O HIS Z 144 " pdb=" N GLN Z 148 " model vdw 2.163 3.120 nonbonded pdb=" O HIS d 144 " pdb=" N GLN d 148 " model vdw 2.171 3.120 ... (remaining 481161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.090 Extract box with map and model: 1.810 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 93.040 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.600 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: 0.020 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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 : 0.003 0.075 63195 Z= 0.232 Angle : 0.752 13.001 85569 Z= 0.400 Chirality : 0.046 0.319 9471 Planarity : 0.005 0.086 11253 Dihedral : 15.066 91.319 23595 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.03 % Allowed : 0.52 % Favored : 99.45 % 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: -3.02 (0.09), residues: 7821 helix: 1.37 (0.17), residues: 891 sheet: -1.97 (0.09), residues: 3135 loop : -2.89 (0.09), residues: 3795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP P 48 HIS 0.013 0.001 HIS Y 135 PHE 0.041 0.001 PHE N 232 TYR 0.044 0.002 TYR N 121 ARG 0.009 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 956 time to evaluate : 5.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.6111 (pp20) cc_final: 0.4536 (pp20) REVERT: A 169 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7138 (mm-30) REVERT: A 177 LYS cc_start: 0.8617 (mppt) cc_final: 0.8289 (mmtm) REVERT: B 162 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6547 (tp30) REVERT: B 234 ASP cc_start: 0.8329 (p0) cc_final: 0.7849 (p0) REVERT: C 83 TYR cc_start: 0.7687 (t80) cc_final: 0.7320 (t80) REVERT: C 118 MET cc_start: 0.7602 (tmm) cc_final: 0.7220 (tmm) REVERT: C 232 PHE cc_start: 0.6984 (p90) cc_final: 0.6668 (p90) REVERT: D 55 LYS cc_start: 0.8290 (mttm) cc_final: 0.8030 (mmtm) REVERT: F 155 ASP cc_start: 0.8467 (m-30) cc_final: 0.8112 (m-30) REVERT: F 223 ILE cc_start: 0.8284 (mt) cc_final: 0.8025 (mm) REVERT: G 83 TYR cc_start: 0.7775 (t80) cc_final: 0.7214 (t80) REVERT: H 28 LEU cc_start: 0.8047 (mm) cc_final: 0.7682 (mt) REVERT: H 29 GLN cc_start: 0.8045 (pp30) cc_final: 0.7134 (pp30) REVERT: H 48 TRP cc_start: 0.4939 (m-90) cc_final: 0.4375 (m-90) REVERT: H 51 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8270 (tptt) REVERT: I 83 TYR cc_start: 0.6865 (t80) cc_final: 0.6541 (t80) REVERT: J 232 PHE cc_start: 0.7902 (p90) cc_final: 0.7594 (p90) REVERT: K 28 LEU cc_start: 0.8186 (mm) cc_final: 0.7897 (mt) REVERT: K 177 LYS cc_start: 0.7946 (mppt) cc_final: 0.7575 (mmtm) REVERT: K 234 ASP cc_start: 0.7432 (p0) cc_final: 0.7078 (p0) REVERT: L 177 LYS cc_start: 0.8160 (mppt) cc_final: 0.7694 (mmtm) REVERT: M 28 LEU cc_start: 0.7782 (mm) cc_final: 0.7083 (mt) REVERT: M 63 ASP cc_start: 0.8031 (p0) cc_final: 0.7698 (p0) REVERT: M 177 LYS cc_start: 0.8097 (mppt) cc_final: 0.7818 (mmtm) REVERT: N 121 TYR cc_start: 0.7209 (m-80) cc_final: 0.6571 (m-10) REVERT: N 155 ASP cc_start: 0.8501 (m-30) cc_final: 0.8273 (m-30) REVERT: O 55 LYS cc_start: 0.7879 (mptt) cc_final: 0.7616 (mptt) REVERT: O 63 ASP cc_start: 0.8201 (p0) cc_final: 0.7939 (p0) REVERT: O 171 GLU cc_start: 0.7903 (pm20) cc_final: 0.7531 (pp20) REVERT: P 28 LEU cc_start: 0.7990 (tp) cc_final: 0.7606 (tp) REVERT: P 29 GLN cc_start: 0.8529 (pp30) cc_final: 0.7974 (pp30) REVERT: P 162 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7593 (mm-30) REVERT: Q 130 TRP cc_start: 0.8198 (m100) cc_final: 0.7585 (m100) REVERT: Q 171 GLU cc_start: 0.8344 (pm20) cc_final: 0.7355 (pm20) REVERT: R 15 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7983 (tp30) REVERT: R 135 HIS cc_start: 0.6490 (m90) cc_final: 0.6088 (m90) REVERT: R 234 ASP cc_start: 0.7734 (p0) cc_final: 0.7503 (p0) REVERT: S 55 LYS cc_start: 0.8189 (mptt) cc_final: 0.7735 (mmtt) REVERT: S 168 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7818 (mmtm) REVERT: S 234 ASP cc_start: 0.7090 (p0) cc_final: 0.6774 (p0) REVERT: T 168 LYS cc_start: 0.7361 (mtmt) cc_final: 0.7155 (mtmm) REVERT: U 171 GLU cc_start: 0.7801 (pp20) cc_final: 0.7579 (pp20) REVERT: V 28 LEU cc_start: 0.7954 (mp) cc_final: 0.7715 (pp) REVERT: V 128 ASN cc_start: 0.8255 (m-40) cc_final: 0.8013 (m-40) REVERT: V 234 ASP cc_start: 0.7733 (p0) cc_final: 0.7385 (p0) REVERT: W 135 HIS cc_start: 0.6745 (m90) cc_final: 0.6481 (m90) REVERT: W 223 ILE cc_start: 0.7187 (mt) cc_final: 0.6971 (mt) REVERT: X 131 GLN cc_start: 0.8096 (pp30) cc_final: 0.7347 (pt0) REVERT: Y 37 TYR cc_start: 0.7463 (m-80) cc_final: 0.7137 (m-80) REVERT: Y 121 TYR cc_start: 0.6564 (m-10) cc_final: 0.6343 (m-80) REVERT: Y 234 ASP cc_start: 0.7877 (p0) cc_final: 0.7601 (p0) REVERT: Z 177 LYS cc_start: 0.7722 (mppt) cc_final: 0.7355 (mmtm) REVERT: a 79 SER cc_start: 0.7414 (m) cc_final: 0.7132 (t) REVERT: a 118 MET cc_start: 0.8320 (ptm) cc_final: 0.7628 (ttp) REVERT: a 131 GLN cc_start: 0.7874 (pp30) cc_final: 0.7117 (pt0) REVERT: a 135 HIS cc_start: 0.5781 (m90) cc_final: 0.5539 (m90) REVERT: a 171 GLU cc_start: 0.7057 (mp0) cc_final: 0.6729 (mp0) REVERT: a 177 LYS cc_start: 0.7997 (mppt) cc_final: 0.7487 (mmtm) REVERT: b 130 TRP cc_start: 0.8192 (m100) cc_final: 0.7916 (m100) REVERT: d 28 LEU cc_start: 0.6941 (mp) cc_final: 0.6526 (mp) REVERT: d 171 GLU cc_start: 0.7404 (mp0) cc_final: 0.6799 (mp0) REVERT: d 177 LYS cc_start: 0.8342 (mppt) cc_final: 0.8056 (mmtm) REVERT: e 138 HIS cc_start: 0.6893 (p90) cc_final: 0.6531 (p90) REVERT: f 162 GLU cc_start: 0.6612 (mp0) cc_final: 0.6337 (mp0) REVERT: g 192 GLU cc_start: 0.5102 (tt0) cc_final: 0.4616 (tm-30) outliers start: 2 outliers final: 1 residues processed: 958 average time/residue: 0.6140 time to fit residues: 975.7193 Evaluate side-chains 703 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 702 time to evaluate : 5.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 193 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 640 optimal weight: 4.9990 chunk 575 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 307 optimal weight: 8.9990 chunk 594 optimal weight: 10.0000 chunk 230 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 442 optimal weight: 2.9990 chunk 689 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 241 GLN C 138 HIS D 91 GLN E 128 ASN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS G 193 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 GLN I 135 HIS I 138 HIS K 128 ASN L 241 GLN M 148 GLN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 241 GLN ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 HIS ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 GLN ** T 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 165 GLN U 119 ASN ** U 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 176 HIS V 91 GLN ** V 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS a 138 HIS ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 176 HIS ** b 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 165 GLN e 241 GLN f 29 GLN f 241 GLN g 193 GLN g 241 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 63195 Z= 0.307 Angle : 0.707 10.355 85569 Z= 0.360 Chirality : 0.047 0.191 9471 Planarity : 0.005 0.070 11253 Dihedral : 5.561 33.285 8550 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 1.33 % Allowed : 9.70 % Favored : 88.97 % 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: -3.46 (0.09), residues: 7821 helix: -0.00 (0.16), residues: 990 sheet: -2.22 (0.08), residues: 3300 loop : -3.00 (0.09), residues: 3531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP f 130 HIS 0.020 0.001 HIS Y 135 PHE 0.036 0.002 PHE b 232 TYR 0.035 0.002 TYR M 121 ARG 0.006 0.001 ARG e 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 784 time to evaluate : 5.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8445 (pp30) cc_final: 0.7864 (pp30) REVERT: A 83 TYR cc_start: 0.7660 (t80) cc_final: 0.7415 (t80) REVERT: A 95 GLU cc_start: 0.5956 (pp20) cc_final: 0.5515 (pp20) REVERT: A 118 MET cc_start: 0.8140 (ppp) cc_final: 0.7481 (ppp) REVERT: A 169 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7449 (mm-30) REVERT: A 177 LYS cc_start: 0.8846 (mppt) cc_final: 0.8527 (mmtm) REVERT: B 29 GLN cc_start: 0.8245 (pp30) cc_final: 0.7983 (pp30) REVERT: B 234 ASP cc_start: 0.8404 (p0) cc_final: 0.7971 (p0) REVERT: C 55 LYS cc_start: 0.8491 (mttp) cc_final: 0.8177 (mptt) REVERT: C 135 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.7054 (m-70) REVERT: D 29 GLN cc_start: 0.7072 (pp30) cc_final: 0.6537 (pp30) REVERT: D 83 TYR cc_start: 0.8132 (t80) cc_final: 0.7917 (t80) REVERT: F 169 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7362 (mm-30) REVERT: F 223 ILE cc_start: 0.8331 (mt) cc_final: 0.8081 (mm) REVERT: H 28 LEU cc_start: 0.7831 (mm) cc_final: 0.7572 (mt) REVERT: H 29 GLN cc_start: 0.8042 (pp30) cc_final: 0.7107 (pp30) REVERT: H 83 TYR cc_start: 0.7817 (t80) cc_final: 0.7519 (t80) REVERT: I 28 LEU cc_start: 0.7896 (mm) cc_final: 0.7247 (mt) REVERT: I 83 TYR cc_start: 0.7407 (t80) cc_final: 0.6896 (t80) REVERT: I 223 ILE cc_start: 0.8131 (mm) cc_final: 0.7897 (mm) REVERT: K 28 LEU cc_start: 0.8415 (mm) cc_final: 0.8036 (mp) REVERT: K 177 LYS cc_start: 0.8406 (mppt) cc_final: 0.7999 (mmtm) REVERT: K 232 PHE cc_start: 0.7858 (p90) cc_final: 0.7617 (p90) REVERT: K 234 ASP cc_start: 0.7886 (p0) cc_final: 0.7529 (p0) REVERT: L 29 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: M 28 LEU cc_start: 0.7902 (mm) cc_final: 0.7642 (mm) REVERT: M 177 LYS cc_start: 0.8238 (mppt) cc_final: 0.7965 (mmtm) REVERT: N 121 TYR cc_start: 0.7240 (m-80) cc_final: 0.6612 (m-80) REVERT: N 135 HIS cc_start: 0.7366 (m-70) cc_final: 0.7159 (m-70) REVERT: N 155 ASP cc_start: 0.8276 (m-30) cc_final: 0.7997 (m-30) REVERT: O 95 GLU cc_start: 0.6377 (pt0) cc_final: 0.5771 (pm20) REVERT: O 145 LYS cc_start: 0.6161 (mppt) cc_final: 0.5891 (tttm) REVERT: O 171 GLU cc_start: 0.8101 (pm20) cc_final: 0.7544 (pp20) REVERT: O 223 ILE cc_start: 0.8440 (mm) cc_final: 0.8222 (mm) REVERT: P 223 ILE cc_start: 0.8351 (mm) cc_final: 0.8150 (mm) REVERT: Q 28 LEU cc_start: 0.8060 (mm) cc_final: 0.7834 (mm) REVERT: Q 171 GLU cc_start: 0.8200 (pm20) cc_final: 0.7299 (pm20) REVERT: R 135 HIS cc_start: 0.6226 (m90) cc_final: 0.5667 (m90) REVERT: R 169 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7450 (mm-30) REVERT: R 234 ASP cc_start: 0.8092 (p0) cc_final: 0.7841 (p0) REVERT: S 135 HIS cc_start: 0.7281 (m90) cc_final: 0.6805 (m90) REVERT: S 234 ASP cc_start: 0.7265 (p0) cc_final: 0.6928 (p0) REVERT: T 29 GLN cc_start: 0.8567 (pp30) cc_final: 0.8085 (pp30) REVERT: T 128 ASN cc_start: 0.7595 (m-40) cc_final: 0.7333 (m-40) REVERT: T 177 LYS cc_start: 0.8875 (ptpp) cc_final: 0.8556 (ttpp) REVERT: V 136 GLU cc_start: 0.7800 (pt0) cc_final: 0.7558 (pt0) REVERT: V 234 ASP cc_start: 0.7699 (p0) cc_final: 0.7305 (p0) REVERT: W 135 HIS cc_start: 0.6894 (m90) cc_final: 0.6628 (m90) REVERT: W 169 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8133 (mm-30) REVERT: W 177 LYS cc_start: 0.8858 (mppt) cc_final: 0.8634 (mppt) REVERT: W 223 ILE cc_start: 0.7323 (mt) cc_final: 0.7072 (mt) REVERT: X 131 GLN cc_start: 0.7931 (pp30) cc_final: 0.7017 (pt0) REVERT: Y 37 TYR cc_start: 0.7877 (m-80) cc_final: 0.7559 (m-80) REVERT: Y 234 ASP cc_start: 0.8091 (p0) cc_final: 0.7808 (p0) REVERT: Z 177 LYS cc_start: 0.8395 (mppt) cc_final: 0.7959 (mmtm) REVERT: a 118 MET cc_start: 0.8279 (ptm) cc_final: 0.7990 (ptm) REVERT: a 177 LYS cc_start: 0.8141 (mppt) cc_final: 0.7758 (mmtm) REVERT: b 28 LEU cc_start: 0.7396 (tt) cc_final: 0.6798 (mm) REVERT: b 134 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8432 (mm) REVERT: c 167 GLN cc_start: 0.7792 (pm20) cc_final: 0.7266 (pm20) REVERT: d 177 LYS cc_start: 0.8621 (mppt) cc_final: 0.8138 (mmtm) REVERT: d 232 PHE cc_start: 0.7283 (p90) cc_final: 0.6983 (p90) REVERT: e 28 LEU cc_start: 0.8407 (tp) cc_final: 0.8093 (mm) REVERT: e 87 ASP cc_start: 0.8111 (p0) cc_final: 0.7627 (p0) REVERT: e 138 HIS cc_start: 0.7093 (p90) cc_final: 0.6713 (p90) REVERT: e 162 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7521 (mm-30) REVERT: f 236 LYS cc_start: 0.8246 (mmpt) cc_final: 0.7887 (mmpt) REVERT: g 53 ARG cc_start: 0.6723 (mpt180) cc_final: 0.6514 (mpt180) REVERT: g 155 ASP cc_start: 0.8316 (m-30) cc_final: 0.8108 (t70) outliers start: 92 outliers final: 73 residues processed: 835 average time/residue: 0.6054 time to fit residues: 839.2737 Evaluate side-chains 754 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 678 time to evaluate : 5.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 135 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 48 TRP Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 121 TYR Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain Q residue 135 HIS Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 232 PHE Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 118 MET Chi-restraints excluded: chain b residue 134 LEU Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 135 HIS Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 383 optimal weight: 2.9990 chunk 213 optimal weight: 0.3980 chunk 573 optimal weight: 5.9990 chunk 469 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 690 optimal weight: 9.9990 chunk 745 optimal weight: 30.0000 chunk 614 optimal weight: 1.9990 chunk 684 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 553 optimal weight: 0.4980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN K 138 HIS L 128 ASN L 135 HIS L 241 GLN ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 GLN ** T 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 241 GLN ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 135 HIS b 193 GLN c 165 GLN g 81 HIS g 91 GLN g 241 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 63195 Z= 0.225 Angle : 0.641 7.926 85569 Z= 0.326 Chirality : 0.045 0.201 9471 Planarity : 0.004 0.070 11253 Dihedral : 5.304 22.250 8547 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.33 % Allowed : 11.57 % Favored : 86.10 % 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: -3.45 (0.09), residues: 7821 helix: 0.04 (0.16), residues: 990 sheet: -2.22 (0.08), residues: 3300 loop : -3.00 (0.09), residues: 3531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 48 HIS 0.020 0.001 HIS Y 135 PHE 0.023 0.001 PHE d 5 TYR 0.029 0.002 TYR N 121 ARG 0.005 0.000 ARG N 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 764 time to evaluate : 5.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.6936 (tp) cc_final: 0.6646 (pp) REVERT: A 29 GLN cc_start: 0.8396 (pp30) cc_final: 0.7946 (pp30) REVERT: A 83 TYR cc_start: 0.7563 (t80) cc_final: 0.7277 (t80) REVERT: A 95 GLU cc_start: 0.5742 (pp20) cc_final: 0.5436 (pp20) REVERT: A 118 MET cc_start: 0.8146 (ppp) cc_final: 0.7491 (ppp) REVERT: A 169 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7525 (mm-30) REVERT: A 177 LYS cc_start: 0.8635 (mppt) cc_final: 0.8299 (mmtm) REVERT: A 235 LYS cc_start: 0.8069 (tptt) cc_final: 0.7493 (tptt) REVERT: B 29 GLN cc_start: 0.8049 (pp30) cc_final: 0.7797 (pp30) REVERT: B 234 ASP cc_start: 0.8394 (p0) cc_final: 0.8005 (p0) REVERT: C 55 LYS cc_start: 0.8527 (mttp) cc_final: 0.8226 (mptt) REVERT: F 223 ILE cc_start: 0.8515 (mt) cc_final: 0.8281 (mm) REVERT: G 63 ASP cc_start: 0.7808 (p0) cc_final: 0.7116 (p0) REVERT: G 83 TYR cc_start: 0.8168 (t80) cc_final: 0.7344 (t80) REVERT: H 28 LEU cc_start: 0.7776 (mm) cc_final: 0.7506 (mt) REVERT: H 83 TYR cc_start: 0.7759 (t80) cc_final: 0.7392 (t80) REVERT: H 128 ASN cc_start: 0.8532 (t0) cc_final: 0.7657 (m-40) REVERT: I 28 LEU cc_start: 0.7665 (mm) cc_final: 0.7116 (mt) REVERT: I 83 TYR cc_start: 0.7506 (t80) cc_final: 0.6821 (t80) REVERT: I 223 ILE cc_start: 0.8131 (mm) cc_final: 0.7904 (mm) REVERT: J 192 GLU cc_start: 0.7433 (tp30) cc_final: 0.6717 (tm-30) REVERT: K 28 LEU cc_start: 0.8423 (mm) cc_final: 0.7991 (mp) REVERT: K 177 LYS cc_start: 0.8301 (mppt) cc_final: 0.7933 (mmtm) REVERT: K 232 PHE cc_start: 0.7857 (p90) cc_final: 0.7532 (p90) REVERT: K 234 ASP cc_start: 0.7918 (p0) cc_final: 0.7566 (p0) REVERT: L 29 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: L 63 ASP cc_start: 0.8299 (p0) cc_final: 0.8040 (p0) REVERT: L 86 MET cc_start: 0.7686 (tmm) cc_final: 0.7310 (ttt) REVERT: L 95 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6894 (tm-30) REVERT: M 28 LEU cc_start: 0.7907 (mm) cc_final: 0.7569 (mm) REVERT: M 145 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.5059 (tttm) REVERT: M 177 LYS cc_start: 0.8119 (mppt) cc_final: 0.7806 (mmtm) REVERT: N 28 LEU cc_start: 0.7041 (pp) cc_final: 0.6651 (pp) REVERT: N 121 TYR cc_start: 0.7205 (m-80) cc_final: 0.6784 (m-80) REVERT: N 135 HIS cc_start: 0.7418 (m-70) cc_final: 0.6940 (m90) REVERT: O 145 LYS cc_start: 0.6497 (mppt) cc_final: 0.6200 (tttm) REVERT: O 234 ASP cc_start: 0.8910 (p0) cc_final: 0.8355 (p0) REVERT: P 29 GLN cc_start: 0.8356 (pp30) cc_final: 0.7702 (pp30) REVERT: Q 28 LEU cc_start: 0.8162 (mm) cc_final: 0.7804 (mm) REVERT: Q 128 ASN cc_start: 0.8341 (t0) cc_final: 0.8034 (t0) REVERT: Q 137 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7623 (ttp-170) REVERT: R 29 GLN cc_start: 0.8313 (pp30) cc_final: 0.8011 (pp30) REVERT: R 135 HIS cc_start: 0.6287 (m90) cc_final: 0.5733 (m90) REVERT: R 234 ASP cc_start: 0.8098 (p0) cc_final: 0.7840 (p0) REVERT: S 63 ASP cc_start: 0.7618 (p0) cc_final: 0.7415 (p0) REVERT: S 135 HIS cc_start: 0.7201 (m90) cc_final: 0.6682 (m90) REVERT: S 171 GLU cc_start: 0.8184 (pm20) cc_final: 0.7923 (pp20) REVERT: S 234 ASP cc_start: 0.7231 (p0) cc_final: 0.6862 (p0) REVERT: T 55 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8059 (mmtt) REVERT: T 128 ASN cc_start: 0.7444 (m-40) cc_final: 0.7238 (m-40) REVERT: U 28 LEU cc_start: 0.8107 (mm) cc_final: 0.7676 (mt) REVERT: U 55 LYS cc_start: 0.8445 (mptt) cc_final: 0.7956 (mptt) REVERT: V 234 ASP cc_start: 0.7719 (p0) cc_final: 0.7334 (p0) REVERT: W 138 HIS cc_start: 0.7532 (p-80) cc_final: 0.7316 (p-80) REVERT: W 177 LYS cc_start: 0.8611 (mppt) cc_final: 0.8286 (mppt) REVERT: W 223 ILE cc_start: 0.7422 (mt) cc_final: 0.7167 (mt) REVERT: X 5 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7776 (m-10) REVERT: X 131 GLN cc_start: 0.7924 (pp30) cc_final: 0.6803 (pt0) REVERT: Y 37 TYR cc_start: 0.7866 (m-80) cc_final: 0.7514 (m-80) REVERT: Y 131 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7305 (pt0) REVERT: Y 136 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: Y 234 ASP cc_start: 0.7673 (p0) cc_final: 0.7298 (p0) REVERT: Z 169 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7692 (mm-30) REVERT: Z 177 LYS cc_start: 0.8276 (mppt) cc_final: 0.8005 (mmtm) REVERT: a 177 LYS cc_start: 0.8055 (mppt) cc_final: 0.7658 (mmtm) REVERT: c 167 GLN cc_start: 0.7840 (pm20) cc_final: 0.7211 (pm20) REVERT: d 5 PHE cc_start: 0.6005 (m-10) cc_final: 0.5800 (m-10) REVERT: d 171 GLU cc_start: 0.7620 (mp0) cc_final: 0.7135 (mp0) REVERT: d 232 PHE cc_start: 0.7424 (p90) cc_final: 0.7043 (p90) REVERT: e 28 LEU cc_start: 0.8384 (tp) cc_final: 0.8077 (mm) outliers start: 161 outliers final: 114 residues processed: 878 average time/residue: 0.6019 time to fit residues: 879.9731 Evaluate side-chains 815 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 695 time to evaluate : 5.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 48 TRP Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 118 MET Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 135 HIS Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 131 GLN Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 232 PHE Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 208 ILE Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 682 optimal weight: 0.8980 chunk 519 optimal weight: 5.9990 chunk 358 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 329 optimal weight: 0.9990 chunk 463 optimal weight: 6.9990 chunk 692 optimal weight: 1.9990 chunk 733 optimal weight: 0.0970 chunk 362 optimal weight: 2.9990 chunk 656 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 ASN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 GLN L 128 ASN ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 GLN R 148 GLN ** U 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 63195 Z= 0.211 Angle : 0.627 9.358 85569 Z= 0.318 Chirality : 0.045 0.192 9471 Planarity : 0.004 0.073 11253 Dihedral : 5.161 21.923 8547 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 2.74 % Allowed : 13.53 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.42 (0.09), residues: 7821 helix: 0.13 (0.16), residues: 990 sheet: -2.22 (0.08), residues: 3300 loop : -2.98 (0.09), residues: 3531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 48 HIS 0.022 0.001 HIS Y 135 PHE 0.022 0.001 PHE Y 5 TYR 0.025 0.002 TYR O 121 ARG 0.008 0.000 ARG E 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 764 time to evaluate : 5.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: A 28 LEU cc_start: 0.7053 (tp) cc_final: 0.6403 (mm) REVERT: A 29 GLN cc_start: 0.8374 (pp30) cc_final: 0.7906 (pp30) REVERT: A 53 ARG cc_start: 0.6042 (mpt180) cc_final: 0.5842 (mpt180) REVERT: A 95 GLU cc_start: 0.5746 (pp20) cc_final: 0.5442 (pp20) REVERT: A 118 MET cc_start: 0.8004 (ppp) cc_final: 0.7445 (ppp) REVERT: A 121 TYR cc_start: 0.7451 (m-10) cc_final: 0.7005 (m-10) REVERT: A 169 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7553 (mm-30) REVERT: A 235 LYS cc_start: 0.7884 (tptt) cc_final: 0.7356 (tptt) REVERT: B 29 GLN cc_start: 0.8081 (pp30) cc_final: 0.7793 (pp30) REVERT: B 128 ASN cc_start: 0.7608 (t0) cc_final: 0.7065 (m-40) REVERT: B 234 ASP cc_start: 0.8347 (p0) cc_final: 0.7969 (p0) REVERT: C 169 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7299 (mm-30) REVERT: C 232 PHE cc_start: 0.7365 (p90) cc_final: 0.7165 (p90) REVERT: E 163 VAL cc_start: 0.9337 (t) cc_final: 0.9048 (p) REVERT: F 169 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7396 (mm-30) REVERT: F 223 ILE cc_start: 0.8594 (mt) cc_final: 0.8299 (mm) REVERT: G 63 ASP cc_start: 0.7786 (p0) cc_final: 0.7291 (p0) REVERT: G 83 TYR cc_start: 0.8222 (t80) cc_final: 0.7397 (t80) REVERT: H 28 LEU cc_start: 0.8167 (mm) cc_final: 0.7784 (mt) REVERT: H 83 TYR cc_start: 0.7839 (t80) cc_final: 0.7576 (t80) REVERT: H 128 ASN cc_start: 0.8467 (t0) cc_final: 0.8171 (m-40) REVERT: H 171 GLU cc_start: 0.7845 (pm20) cc_final: 0.7614 (pp20) REVERT: I 28 LEU cc_start: 0.7638 (mm) cc_final: 0.7124 (mt) REVERT: I 83 TYR cc_start: 0.7553 (t80) cc_final: 0.6592 (t80) REVERT: I 223 ILE cc_start: 0.8131 (mm) cc_final: 0.7913 (mm) REVERT: J 192 GLU cc_start: 0.7746 (tp30) cc_final: 0.6514 (tm-30) REVERT: K 28 LEU cc_start: 0.8416 (mm) cc_final: 0.7964 (mp) REVERT: K 155 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8180 (m-30) REVERT: K 177 LYS cc_start: 0.8272 (mppt) cc_final: 0.7888 (mmtm) REVERT: K 232 PHE cc_start: 0.7772 (p90) cc_final: 0.7367 (p90) REVERT: K 234 ASP cc_start: 0.7928 (p0) cc_final: 0.7567 (p0) REVERT: L 29 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: M 28 LEU cc_start: 0.8039 (mm) cc_final: 0.7713 (mm) REVERT: N 28 LEU cc_start: 0.7010 (pp) cc_final: 0.6646 (pp) REVERT: O 145 LYS cc_start: 0.6704 (mppt) cc_final: 0.6235 (tttm) REVERT: O 171 GLU cc_start: 0.7977 (pm20) cc_final: 0.7491 (pp20) REVERT: O 234 ASP cc_start: 0.8892 (p0) cc_final: 0.8359 (p0) REVERT: P 29 GLN cc_start: 0.8172 (pp30) cc_final: 0.7769 (pp30) REVERT: Q 28 LEU cc_start: 0.8040 (mm) cc_final: 0.7792 (mm) REVERT: Q 128 ASN cc_start: 0.8288 (t0) cc_final: 0.7961 (t0) REVERT: Q 137 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7877 (mtm-85) REVERT: R 29 GLN cc_start: 0.8317 (pp30) cc_final: 0.7994 (pp30) REVERT: R 135 HIS cc_start: 0.6518 (m90) cc_final: 0.5986 (m90) REVERT: R 139 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7838 (pp) REVERT: R 234 ASP cc_start: 0.8137 (p0) cc_final: 0.7886 (p0) REVERT: S 63 ASP cc_start: 0.7673 (p0) cc_final: 0.7459 (p0) REVERT: S 135 HIS cc_start: 0.7348 (m90) cc_final: 0.6957 (m-70) REVERT: S 234 ASP cc_start: 0.7279 (p0) cc_final: 0.6906 (p0) REVERT: S 235 LYS cc_start: 0.8714 (tptt) cc_final: 0.8318 (tptp) REVERT: T 128 ASN cc_start: 0.7429 (m-40) cc_final: 0.7174 (m-40) REVERT: U 28 LEU cc_start: 0.8105 (mm) cc_final: 0.7683 (mt) REVERT: U 54 TYR cc_start: 0.7910 (m-80) cc_final: 0.7484 (m-80) REVERT: U 55 LYS cc_start: 0.8508 (mptt) cc_final: 0.7968 (mptt) REVERT: V 234 ASP cc_start: 0.7752 (p0) cc_final: 0.7370 (p0) REVERT: W 138 HIS cc_start: 0.7229 (p-80) cc_final: 0.6936 (p-80) REVERT: W 144 HIS cc_start: 0.6564 (OUTLIER) cc_final: 0.6149 (t-90) REVERT: W 177 LYS cc_start: 0.8855 (mppt) cc_final: 0.8591 (mppt) REVERT: W 223 ILE cc_start: 0.7402 (mt) cc_final: 0.7127 (mt) REVERT: X 5 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7668 (m-10) REVERT: X 131 GLN cc_start: 0.7694 (pp30) cc_final: 0.6706 (pt0) REVERT: Y 37 TYR cc_start: 0.7860 (m-80) cc_final: 0.7526 (m-80) REVERT: Y 131 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7342 (pt0) REVERT: Y 234 ASP cc_start: 0.7464 (p0) cc_final: 0.7139 (p0) REVERT: Z 135 HIS cc_start: 0.6735 (m90) cc_final: 0.6246 (m90) REVERT: Z 169 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7739 (mm-30) REVERT: a 177 LYS cc_start: 0.8024 (mppt) cc_final: 0.7634 (mmtm) REVERT: c 167 GLN cc_start: 0.8164 (pm20) cc_final: 0.7793 (pm20) REVERT: d 139 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8391 (tp) REVERT: d 171 GLU cc_start: 0.7641 (mp0) cc_final: 0.7133 (mp0) REVERT: d 232 PHE cc_start: 0.7482 (p90) cc_final: 0.6954 (p90) REVERT: e 28 LEU cc_start: 0.8435 (tp) cc_final: 0.8102 (mm) REVERT: f 128 ASN cc_start: 0.7987 (m-40) cc_final: 0.7636 (m-40) outliers start: 189 outliers final: 135 residues processed: 900 average time/residue: 0.5950 time to fit residues: 894.5866 Evaluate side-chains 846 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 702 time to evaluate : 5.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain K residue 48 TRP Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 PHE Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 135 HIS Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 144 HIS Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 131 GLN Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 232 PHE Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 121 TYR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 135 HIS Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 28 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 166 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 611 optimal weight: 0.9980 chunk 416 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 546 optimal weight: 0.9990 chunk 302 optimal weight: 4.9990 chunk 626 optimal weight: 5.9990 chunk 507 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 374 optimal weight: 6.9990 chunk 658 optimal weight: 0.4980 chunk 185 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 HIS L 128 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 GLN ** W 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 63195 Z= 0.194 Angle : 0.620 9.188 85569 Z= 0.313 Chirality : 0.044 0.186 9471 Planarity : 0.004 0.070 11253 Dihedral : 5.008 21.760 8547 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.89 % Allowed : 14.46 % Favored : 82.66 % 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: -3.34 (0.09), residues: 7821 helix: 0.30 (0.16), residues: 990 sheet: -2.21 (0.08), residues: 3333 loop : -2.91 (0.09), residues: 3498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 48 HIS 0.024 0.001 HIS Y 135 PHE 0.022 0.001 PHE Y 5 TYR 0.030 0.001 TYR L 121 ARG 0.008 0.000 ARG e 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 759 time to evaluate : 5.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7101 (tp) cc_final: 0.6467 (mm) REVERT: A 29 GLN cc_start: 0.8163 (pp30) cc_final: 0.7743 (pp30) REVERT: A 118 MET cc_start: 0.7818 (ppp) cc_final: 0.7419 (ppp) REVERT: A 121 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.7223 (m-80) REVERT: A 169 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7575 (mm-30) REVERT: A 235 LYS cc_start: 0.7840 (tptt) cc_final: 0.7426 (tptt) REVERT: B 28 LEU cc_start: 0.7961 (mp) cc_final: 0.7571 (pp) REVERT: B 29 GLN cc_start: 0.8065 (pp30) cc_final: 0.7785 (pp30) REVERT: B 128 ASN cc_start: 0.7909 (t0) cc_final: 0.7418 (m-40) REVERT: B 234 ASP cc_start: 0.8086 (p0) cc_final: 0.7696 (p0) REVERT: C 138 HIS cc_start: 0.6236 (t70) cc_final: 0.5736 (t-90) REVERT: C 169 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7601 (mm-30) REVERT: C 232 PHE cc_start: 0.7344 (p90) cc_final: 0.7090 (p90) REVERT: F 95 GLU cc_start: 0.6327 (tm-30) cc_final: 0.5688 (tm-30) REVERT: F 223 ILE cc_start: 0.8594 (mt) cc_final: 0.8299 (mm) REVERT: G 63 ASP cc_start: 0.7932 (p0) cc_final: 0.7546 (p0) REVERT: G 83 TYR cc_start: 0.8182 (t80) cc_final: 0.7439 (t80) REVERT: G 128 ASN cc_start: 0.7914 (m-40) cc_final: 0.7697 (m-40) REVERT: H 28 LEU cc_start: 0.8149 (mm) cc_final: 0.7752 (mt) REVERT: H 83 TYR cc_start: 0.7830 (t80) cc_final: 0.7503 (t80) REVERT: H 128 ASN cc_start: 0.8372 (t0) cc_final: 0.8093 (m-40) REVERT: I 28 LEU cc_start: 0.7647 (mm) cc_final: 0.7155 (mt) REVERT: I 83 TYR cc_start: 0.7582 (t80) cc_final: 0.6654 (t80) REVERT: I 95 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6885 (tm-30) REVERT: J 145 LYS cc_start: 0.6643 (tttm) cc_final: 0.6249 (ttpt) REVERT: J 192 GLU cc_start: 0.7722 (tp30) cc_final: 0.6510 (tm-30) REVERT: K 28 LEU cc_start: 0.8408 (mm) cc_final: 0.8157 (mm) REVERT: K 56 CYS cc_start: 0.8871 (t) cc_final: 0.7481 (p) REVERT: K 155 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: K 177 LYS cc_start: 0.8212 (mppt) cc_final: 0.7830 (mmtm) REVERT: K 232 PHE cc_start: 0.7780 (p90) cc_final: 0.7356 (p90) REVERT: K 234 ASP cc_start: 0.8064 (p0) cc_final: 0.7722 (p0) REVERT: L 39 LEU cc_start: 0.9164 (mp) cc_final: 0.8852 (mm) REVERT: L 95 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6918 (tm-30) REVERT: L 139 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8564 (tp) REVERT: M 28 LEU cc_start: 0.7881 (mm) cc_final: 0.7516 (mm) REVERT: M 145 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.4999 (tttm) REVERT: M 177 LYS cc_start: 0.8067 (mppt) cc_final: 0.7817 (mmtm) REVERT: N 135 HIS cc_start: 0.7490 (m-70) cc_final: 0.7067 (m90) REVERT: O 145 LYS cc_start: 0.6660 (mppt) cc_final: 0.6153 (tttm) REVERT: O 171 GLU cc_start: 0.8123 (pm20) cc_final: 0.7531 (pp20) REVERT: O 234 ASP cc_start: 0.8877 (p0) cc_final: 0.8365 (p0) REVERT: P 29 GLN cc_start: 0.8200 (pp30) cc_final: 0.7898 (pp30) REVERT: Q 9 VAL cc_start: 0.8394 (t) cc_final: 0.8186 (p) REVERT: Q 28 LEU cc_start: 0.8302 (mm) cc_final: 0.7992 (mm) REVERT: Q 128 ASN cc_start: 0.8207 (t0) cc_final: 0.7972 (t0) REVERT: Q 137 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7646 (mtm-85) REVERT: R 29 GLN cc_start: 0.8282 (pp30) cc_final: 0.7957 (pp30) REVERT: R 135 HIS cc_start: 0.6630 (m90) cc_final: 0.6153 (m90) REVERT: R 234 ASP cc_start: 0.8113 (p0) cc_final: 0.7859 (p0) REVERT: S 63 ASP cc_start: 0.7671 (p0) cc_final: 0.7429 (p0) REVERT: S 135 HIS cc_start: 0.7346 (m90) cc_final: 0.6895 (m90) REVERT: S 234 ASP cc_start: 0.7447 (p0) cc_final: 0.7116 (p0) REVERT: T 128 ASN cc_start: 0.7398 (m-40) cc_final: 0.7144 (m-40) REVERT: T 232 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6810 (p90) REVERT: U 28 LEU cc_start: 0.8111 (mm) cc_final: 0.7617 (mt) REVERT: U 54 TYR cc_start: 0.7943 (m-80) cc_final: 0.7553 (m-80) REVERT: U 55 LYS cc_start: 0.8523 (mptt) cc_final: 0.7976 (mptt) REVERT: U 130 TRP cc_start: 0.7899 (m100) cc_final: 0.7470 (m100) REVERT: V 234 ASP cc_start: 0.7762 (p0) cc_final: 0.7382 (p0) REVERT: W 135 HIS cc_start: 0.7553 (m-70) cc_final: 0.7072 (m-70) REVERT: W 138 HIS cc_start: 0.7085 (p-80) cc_final: 0.6810 (p-80) REVERT: W 177 LYS cc_start: 0.8830 (mppt) cc_final: 0.8509 (mppt) REVERT: W 223 ILE cc_start: 0.7374 (mt) cc_final: 0.7131 (mt) REVERT: X 5 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7619 (m-10) REVERT: X 131 GLN cc_start: 0.7596 (pp30) cc_final: 0.6677 (pt0) REVERT: Y 37 TYR cc_start: 0.7677 (m-80) cc_final: 0.7440 (m-80) REVERT: Y 131 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: Y 234 ASP cc_start: 0.7479 (p0) cc_final: 0.7148 (p0) REVERT: Z 5 PHE cc_start: 0.7157 (t80) cc_final: 0.6887 (t80) REVERT: Z 135 HIS cc_start: 0.6685 (m90) cc_final: 0.6203 (m90) REVERT: a 139 LEU cc_start: 0.9054 (tp) cc_final: 0.8652 (pp) REVERT: a 177 LYS cc_start: 0.8002 (mppt) cc_final: 0.7625 (mmtm) REVERT: d 28 LEU cc_start: 0.7500 (mp) cc_final: 0.7297 (mp) REVERT: d 145 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.5720 (ptpt) REVERT: d 171 GLU cc_start: 0.7637 (mp0) cc_final: 0.7118 (mp0) REVERT: d 232 PHE cc_start: 0.7537 (p90) cc_final: 0.6968 (p90) REVERT: e 28 LEU cc_start: 0.8442 (tp) cc_final: 0.8149 (mm) REVERT: f 128 ASN cc_start: 0.7956 (m-40) cc_final: 0.7728 (m-40) outliers start: 199 outliers final: 140 residues processed: 911 average time/residue: 0.5814 time to fit residues: 886.4531 Evaluate side-chains 838 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 689 time to evaluate : 5.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 48 TRP Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 22 PHE Chi-restraints excluded: chain L residue 135 HIS Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 208 ILE Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 136 GLU Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 232 PHE Chi-restraints excluded: chain U residue 170 VAL Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 131 GLN Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 229 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 232 PHE Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 121 TYR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 145 LYS Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 135 HIS Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 166 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 246 optimal weight: 0.9990 chunk 660 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 430 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 734 optimal weight: 3.9990 chunk 609 optimal weight: 2.9990 chunk 340 optimal weight: 0.0980 chunk 61 optimal weight: 6.9990 chunk 242 optimal weight: 0.9990 chunk 385 optimal weight: 7.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 ASN L 135 HIS ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN O 135 HIS ** P 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 ASN ** W 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 63195 Z= 0.203 Angle : 0.620 9.708 85569 Z= 0.312 Chirality : 0.044 0.242 9471 Planarity : 0.004 0.052 11253 Dihedral : 4.939 22.042 8547 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 3.09 % Allowed : 15.66 % Favored : 81.25 % 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: -3.23 (0.09), residues: 7821 helix: 0.43 (0.16), residues: 990 sheet: -2.10 (0.09), residues: 3234 loop : -2.89 (0.09), residues: 3597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 130 HIS 0.022 0.001 HIS Y 135 PHE 0.022 0.001 PHE Y 5 TYR 0.027 0.002 TYR a 121 ARG 0.006 0.000 ARG O 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 726 time to evaluate : 5.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7191 (tp) cc_final: 0.6525 (mm) REVERT: A 29 GLN cc_start: 0.8071 (pp30) cc_final: 0.7648 (pp30) REVERT: A 118 MET cc_start: 0.7828 (ppp) cc_final: 0.7431 (ppp) REVERT: A 121 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: A 169 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7636 (mm-30) REVERT: A 235 LYS cc_start: 0.7838 (tptt) cc_final: 0.7407 (tptt) REVERT: B 28 LEU cc_start: 0.7972 (mp) cc_final: 0.7566 (pp) REVERT: B 29 GLN cc_start: 0.8127 (pp30) cc_final: 0.7883 (pp30) REVERT: B 234 ASP cc_start: 0.8100 (p0) cc_final: 0.7724 (p0) REVERT: C 192 GLU cc_start: 0.5511 (tm-30) cc_final: 0.5134 (tm-30) REVERT: F 5 PHE cc_start: 0.6833 (t80) cc_final: 0.6619 (t80) REVERT: F 223 ILE cc_start: 0.8607 (mt) cc_final: 0.8334 (mm) REVERT: G 63 ASP cc_start: 0.7912 (p0) cc_final: 0.7538 (p0) REVERT: G 83 TYR cc_start: 0.8264 (t80) cc_final: 0.7414 (t80) REVERT: G 128 ASN cc_start: 0.7912 (m-40) cc_final: 0.7655 (m-40) REVERT: H 28 LEU cc_start: 0.8023 (mm) cc_final: 0.7759 (mt) REVERT: H 83 TYR cc_start: 0.7878 (t80) cc_final: 0.7588 (t80) REVERT: H 128 ASN cc_start: 0.8346 (t0) cc_final: 0.8102 (m-40) REVERT: I 28 LEU cc_start: 0.7695 (mm) cc_final: 0.7192 (mt) REVERT: I 83 TYR cc_start: 0.7653 (t80) cc_final: 0.6712 (t80) REVERT: J 192 GLU cc_start: 0.7681 (tp30) cc_final: 0.6412 (tm-30) REVERT: K 28 LEU cc_start: 0.8372 (mm) cc_final: 0.8151 (mm) REVERT: K 56 CYS cc_start: 0.8897 (t) cc_final: 0.7677 (p) REVERT: K 177 LYS cc_start: 0.8187 (mppt) cc_final: 0.7823 (mmtm) REVERT: K 232 PHE cc_start: 0.7972 (p90) cc_final: 0.7515 (p90) REVERT: K 234 ASP cc_start: 0.8102 (p0) cc_final: 0.7754 (p0) REVERT: L 29 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: L 39 LEU cc_start: 0.9178 (mp) cc_final: 0.8927 (mp) REVERT: M 28 LEU cc_start: 0.7934 (mm) cc_final: 0.7567 (mm) REVERT: M 145 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.4929 (tttm) REVERT: M 177 LYS cc_start: 0.8070 (mppt) cc_final: 0.7840 (mmtm) REVERT: M 203 LYS cc_start: 0.7779 (tmtt) cc_final: 0.7574 (tmtt) REVERT: N 63 ASP cc_start: 0.7642 (p0) cc_final: 0.7406 (p0) REVERT: O 145 LYS cc_start: 0.6720 (mppt) cc_final: 0.6144 (tttm) REVERT: O 171 GLU cc_start: 0.8111 (pm20) cc_final: 0.7455 (pp20) REVERT: O 234 ASP cc_start: 0.8911 (p0) cc_final: 0.8444 (p0) REVERT: Q 28 LEU cc_start: 0.8321 (mm) cc_final: 0.7973 (mm) REVERT: Q 83 TYR cc_start: 0.7625 (t80) cc_final: 0.7422 (t80) REVERT: Q 128 ASN cc_start: 0.8179 (t0) cc_final: 0.7865 (t0) REVERT: Q 137 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7758 (mtm-85) REVERT: R 28 LEU cc_start: 0.7836 (mm) cc_final: 0.7373 (mt) REVERT: R 29 GLN cc_start: 0.7907 (pp30) cc_final: 0.7618 (pp30) REVERT: R 135 HIS cc_start: 0.6700 (m90) cc_final: 0.6416 (m90) REVERT: R 234 ASP cc_start: 0.8136 (p0) cc_final: 0.7882 (p0) REVERT: S 55 LYS cc_start: 0.8348 (mptt) cc_final: 0.8012 (mmtt) REVERT: S 63 ASP cc_start: 0.7642 (p0) cc_final: 0.7377 (p0) REVERT: S 135 HIS cc_start: 0.7156 (m90) cc_final: 0.6775 (m90) REVERT: S 234 ASP cc_start: 0.7384 (p0) cc_final: 0.7048 (p0) REVERT: T 128 ASN cc_start: 0.7427 (m-40) cc_final: 0.7118 (m-40) REVERT: T 177 LYS cc_start: 0.8776 (ptpp) cc_final: 0.8507 (ttpp) REVERT: U 28 LEU cc_start: 0.8047 (mm) cc_final: 0.7603 (mt) REVERT: U 54 TYR cc_start: 0.7951 (m-80) cc_final: 0.7681 (m-80) REVERT: U 130 TRP cc_start: 0.7905 (m100) cc_final: 0.7500 (m100) REVERT: V 234 ASP cc_start: 0.7858 (p0) cc_final: 0.7474 (p0) REVERT: W 138 HIS cc_start: 0.7146 (p-80) cc_final: 0.6898 (p-80) REVERT: W 177 LYS cc_start: 0.8830 (mppt) cc_final: 0.8537 (mppt) REVERT: X 5 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7618 (m-10) REVERT: X 131 GLN cc_start: 0.7587 (pp30) cc_final: 0.6641 (pt0) REVERT: Y 37 TYR cc_start: 0.7690 (m-80) cc_final: 0.7458 (m-80) REVERT: Y 131 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7384 (pt0) REVERT: Y 234 ASP cc_start: 0.7519 (p0) cc_final: 0.7180 (p0) REVERT: Z 5 PHE cc_start: 0.7251 (t80) cc_final: 0.6828 (t80) REVERT: Z 135 HIS cc_start: 0.6813 (m90) cc_final: 0.6177 (m90) REVERT: a 177 LYS cc_start: 0.8281 (mppt) cc_final: 0.7913 (mmtm) REVERT: d 29 GLN cc_start: 0.7544 (pp30) cc_final: 0.6948 (tm-30) REVERT: d 65 LEU cc_start: 0.8993 (pp) cc_final: 0.8623 (mt) REVERT: d 171 GLU cc_start: 0.7612 (mp0) cc_final: 0.7172 (mp0) REVERT: d 232 PHE cc_start: 0.7655 (p90) cc_final: 0.7054 (p90) REVERT: e 28 LEU cc_start: 0.8608 (tp) cc_final: 0.8193 (mm) REVERT: e 162 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7561 (mm-30) outliers start: 213 outliers final: 165 residues processed: 890 average time/residue: 0.5838 time to fit residues: 878.4905 Evaluate side-chains 857 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 686 time to evaluate : 5.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 48 TRP Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 135 HIS Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 208 ILE Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 136 GLU Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 170 VAL Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 162 GLU Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 131 GLN Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 229 VAL Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 163 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 86 MET Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 121 TYR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 145 LYS Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 135 HIS Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 166 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 708 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 418 optimal weight: 0.0010 chunk 536 optimal weight: 6.9990 chunk 415 optimal weight: 6.9990 chunk 618 optimal weight: 4.9990 chunk 410 optimal weight: 5.9990 chunk 731 optimal weight: 1.9990 chunk 457 optimal weight: 2.9990 chunk 446 optimal weight: 7.9990 chunk 337 optimal weight: 8.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN F 167 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 GLN L 128 ASN L 241 GLN M 176 HIS ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 HIS ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 GLN ** W 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 165 GLN Y 81 HIS ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN d 241 GLN ** f 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 241 GLN g 241 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 63195 Z= 0.263 Angle : 0.652 9.275 85569 Z= 0.331 Chirality : 0.045 0.287 9471 Planarity : 0.004 0.056 11253 Dihedral : 5.192 22.402 8547 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 3.32 % Allowed : 16.44 % Favored : 80.24 % 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: -3.51 (0.09), residues: 7821 helix: 0.37 (0.16), residues: 990 sheet: -2.42 (0.08), residues: 3432 loop : -2.96 (0.09), residues: 3399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 130 HIS 0.024 0.001 HIS Y 135 PHE 0.023 0.001 PHE Y 5 TYR 0.047 0.002 TYR L 121 ARG 0.008 0.000 ARG e 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 719 time to evaluate : 5.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7479 (tp) cc_final: 0.6823 (mm) REVERT: A 29 GLN cc_start: 0.8144 (pp30) cc_final: 0.7704 (pp30) REVERT: A 53 ARG cc_start: 0.5976 (mpt180) cc_final: 0.5728 (mpt180) REVERT: A 169 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 235 LYS cc_start: 0.7619 (tptt) cc_final: 0.7300 (tptt) REVERT: B 28 LEU cc_start: 0.8094 (mp) cc_final: 0.7654 (pp) REVERT: B 29 GLN cc_start: 0.8254 (pp30) cc_final: 0.8034 (pp30) REVERT: B 234 ASP cc_start: 0.7701 (p0) cc_final: 0.7301 (p0) REVERT: C 168 LYS cc_start: 0.7894 (mmmm) cc_final: 0.7666 (mmtm) REVERT: C 169 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7516 (mm-30) REVERT: C 192 GLU cc_start: 0.5719 (tm-30) cc_final: 0.5336 (tm-30) REVERT: F 5 PHE cc_start: 0.6989 (t80) cc_final: 0.6734 (t80) REVERT: F 28 LEU cc_start: 0.8309 (mp) cc_final: 0.8061 (mm) REVERT: F 223 ILE cc_start: 0.8672 (mt) cc_final: 0.8379 (mm) REVERT: G 63 ASP cc_start: 0.7938 (p0) cc_final: 0.7546 (p0) REVERT: G 128 ASN cc_start: 0.7956 (m-40) cc_final: 0.7688 (m-40) REVERT: G 135 HIS cc_start: 0.7472 (m-70) cc_final: 0.7218 (m170) REVERT: G 232 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7879 (p90) REVERT: H 28 LEU cc_start: 0.7746 (mm) cc_final: 0.7513 (mt) REVERT: H 128 ASN cc_start: 0.8388 (t0) cc_final: 0.8132 (m-40) REVERT: I 28 LEU cc_start: 0.7828 (mm) cc_final: 0.7282 (mt) REVERT: I 83 TYR cc_start: 0.7861 (t80) cc_final: 0.6839 (t80) REVERT: J 192 GLU cc_start: 0.7735 (tp30) cc_final: 0.6439 (tm-30) REVERT: K 177 LYS cc_start: 0.8206 (mppt) cc_final: 0.7805 (mmtm) REVERT: K 232 PHE cc_start: 0.8048 (p90) cc_final: 0.7524 (p90) REVERT: K 234 ASP cc_start: 0.8115 (p0) cc_final: 0.7778 (p0) REVERT: L 29 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: L 39 LEU cc_start: 0.9223 (mp) cc_final: 0.8997 (mp) REVERT: L 63 ASP cc_start: 0.8263 (p0) cc_final: 0.7923 (p0) REVERT: L 135 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7509 (t70) REVERT: M 28 LEU cc_start: 0.7893 (mm) cc_final: 0.7566 (mm) REVERT: M 145 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.5026 (tttm) REVERT: N 169 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7340 (mm-30) REVERT: O 63 ASP cc_start: 0.8187 (p0) cc_final: 0.7933 (p0) REVERT: O 171 GLU cc_start: 0.8152 (pm20) cc_final: 0.7450 (pp20) REVERT: O 234 ASP cc_start: 0.8898 (p0) cc_final: 0.8414 (p0) REVERT: Q 28 LEU cc_start: 0.8379 (mm) cc_final: 0.8061 (mm) REVERT: Q 83 TYR cc_start: 0.7766 (t80) cc_final: 0.7519 (t80) REVERT: Q 128 ASN cc_start: 0.8128 (t0) cc_final: 0.7885 (t0) REVERT: Q 200 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8827 (pp) REVERT: R 28 LEU cc_start: 0.7904 (mm) cc_final: 0.7359 (mp) REVERT: R 29 GLN cc_start: 0.7947 (pp30) cc_final: 0.7663 (pp30) REVERT: R 135 HIS cc_start: 0.6721 (m90) cc_final: 0.6412 (m90) REVERT: R 234 ASP cc_start: 0.8214 (p0) cc_final: 0.7964 (p0) REVERT: S 63 ASP cc_start: 0.7716 (p0) cc_final: 0.7463 (p0) REVERT: S 135 HIS cc_start: 0.7232 (m90) cc_final: 0.6808 (m90) REVERT: S 234 ASP cc_start: 0.7444 (p0) cc_final: 0.7096 (p0) REVERT: T 128 ASN cc_start: 0.7337 (m-40) cc_final: 0.6989 (m-40) REVERT: T 177 LYS cc_start: 0.8872 (ptpp) cc_final: 0.8574 (ttpp) REVERT: U 28 LEU cc_start: 0.8158 (mm) cc_final: 0.7675 (mt) REVERT: U 54 TYR cc_start: 0.8005 (m-80) cc_final: 0.7629 (m-80) REVERT: V 234 ASP cc_start: 0.7280 (p0) cc_final: 0.6806 (p0) REVERT: W 138 HIS cc_start: 0.7181 (p-80) cc_final: 0.6979 (p-80) REVERT: W 144 HIS cc_start: 0.6922 (OUTLIER) cc_final: 0.6596 (m-70) REVERT: W 177 LYS cc_start: 0.8869 (mppt) cc_final: 0.8605 (mppt) REVERT: Y 37 TYR cc_start: 0.7827 (m-80) cc_final: 0.7601 (m-80) REVERT: Y 131 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7270 (pt0) REVERT: Y 234 ASP cc_start: 0.7435 (p0) cc_final: 0.7113 (p0) REVERT: Z 135 HIS cc_start: 0.6822 (m90) cc_final: 0.6157 (m90) REVERT: a 177 LYS cc_start: 0.8335 (mppt) cc_final: 0.7970 (mmtm) REVERT: c 208 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8638 (mm) REVERT: d 28 LEU cc_start: 0.8023 (mp) cc_final: 0.7567 (pp) REVERT: d 29 GLN cc_start: 0.8000 (pp30) cc_final: 0.7560 (tm-30) REVERT: d 232 PHE cc_start: 0.7868 (p90) cc_final: 0.7155 (p90) REVERT: e 28 LEU cc_start: 0.8620 (tp) cc_final: 0.8159 (mm) REVERT: e 162 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7534 (mm-30) outliers start: 229 outliers final: 184 residues processed: 897 average time/residue: 0.5954 time to fit residues: 896.1489 Evaluate side-chains 874 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 682 time to evaluate : 5.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 48 TRP Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 118 MET Chi-restraints excluded: chain L residue 135 HIS Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 200 LEU Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 136 GLU Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 170 VAL Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 145 LYS Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 144 HIS Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 131 GLN Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 229 VAL Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 163 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 86 MET Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 145 LYS Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 135 HIS Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 166 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain g residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 452 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 436 optimal weight: 4.9990 chunk 220 optimal weight: 0.0980 chunk 143 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 465 optimal weight: 0.9980 chunk 498 optimal weight: 7.9990 chunk 361 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 575 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 ASN L 135 HIS ** O 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN ** d 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 63195 Z= 0.217 Angle : 0.646 9.347 85569 Z= 0.325 Chirality : 0.045 0.275 9471 Planarity : 0.004 0.053 11253 Dihedral : 5.046 23.842 8547 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 3.10 % Allowed : 17.02 % Favored : 79.88 % 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: -3.17 (0.09), residues: 7821 helix: 0.41 (0.16), residues: 990 sheet: -2.35 (0.09), residues: 2937 loop : -2.55 (0.09), residues: 3894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 130 HIS 0.025 0.001 HIS Y 135 PHE 0.031 0.001 PHE W 49 TYR 0.041 0.002 TYR L 121 ARG 0.008 0.000 ARG e 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 718 time to evaluate : 5.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7543 (tp) cc_final: 0.6897 (mm) REVERT: A 29 GLN cc_start: 0.8076 (pp30) cc_final: 0.7738 (pp30) REVERT: A 53 ARG cc_start: 0.6143 (mpt180) cc_final: 0.5913 (mpt180) REVERT: A 169 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7775 (mm-30) REVERT: A 235 LYS cc_start: 0.7788 (tptt) cc_final: 0.7394 (tptt) REVERT: B 28 LEU cc_start: 0.8034 (mp) cc_final: 0.7633 (pp) REVERT: B 29 GLN cc_start: 0.8243 (pp30) cc_final: 0.7992 (pp30) REVERT: B 234 ASP cc_start: 0.7732 (p0) cc_final: 0.7351 (p0) REVERT: C 192 GLU cc_start: 0.5729 (tm-30) cc_final: 0.5328 (tm-30) REVERT: E 167 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6860 (pp30) REVERT: F 5 PHE cc_start: 0.7168 (t80) cc_final: 0.6878 (t80) REVERT: F 28 LEU cc_start: 0.8131 (mp) cc_final: 0.7878 (mm) REVERT: F 162 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7344 (tm-30) REVERT: F 223 ILE cc_start: 0.8687 (mt) cc_final: 0.8446 (mm) REVERT: G 63 ASP cc_start: 0.7953 (p0) cc_final: 0.7534 (p0) REVERT: G 128 ASN cc_start: 0.7868 (m-40) cc_final: 0.7603 (m-40) REVERT: G 135 HIS cc_start: 0.7683 (m-70) cc_final: 0.7329 (m170) REVERT: G 232 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7849 (p90) REVERT: H 28 LEU cc_start: 0.8081 (mm) cc_final: 0.7826 (mt) REVERT: H 128 ASN cc_start: 0.8363 (t0) cc_final: 0.8099 (m-40) REVERT: I 28 LEU cc_start: 0.7767 (mm) cc_final: 0.7232 (mt) REVERT: I 95 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6878 (tm-30) REVERT: J 192 GLU cc_start: 0.7144 (tp30) cc_final: 0.6618 (tm-30) REVERT: K 56 CYS cc_start: 0.8922 (t) cc_final: 0.7581 (p) REVERT: K 177 LYS cc_start: 0.8159 (mppt) cc_final: 0.7789 (mmtm) REVERT: K 232 PHE cc_start: 0.7971 (p90) cc_final: 0.7416 (p90) REVERT: K 234 ASP cc_start: 0.7720 (p0) cc_final: 0.7394 (p0) REVERT: L 29 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: L 39 LEU cc_start: 0.9214 (mp) cc_final: 0.8975 (mp) REVERT: M 28 LEU cc_start: 0.7797 (mm) cc_final: 0.7452 (mm) REVERT: N 169 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7369 (mm-30) REVERT: O 63 ASP cc_start: 0.8226 (p0) cc_final: 0.7964 (p0) REVERT: O 171 GLU cc_start: 0.8137 (pm20) cc_final: 0.7470 (pp20) REVERT: O 234 ASP cc_start: 0.8884 (p0) cc_final: 0.8409 (p0) REVERT: Q 9 VAL cc_start: 0.8571 (t) cc_final: 0.8366 (p) REVERT: Q 28 LEU cc_start: 0.8319 (mm) cc_final: 0.7987 (mm) REVERT: Q 83 TYR cc_start: 0.7906 (t80) cc_final: 0.7658 (t80) REVERT: Q 128 ASN cc_start: 0.8042 (t0) cc_final: 0.7821 (t0) REVERT: Q 200 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8816 (pp) REVERT: R 28 LEU cc_start: 0.8263 (mm) cc_final: 0.7919 (mt) REVERT: R 29 GLN cc_start: 0.7833 (pp30) cc_final: 0.7543 (pp30) REVERT: R 135 HIS cc_start: 0.6698 (m90) cc_final: 0.6407 (m90) REVERT: R 234 ASP cc_start: 0.8202 (p0) cc_final: 0.7950 (p0) REVERT: S 55 LYS cc_start: 0.8327 (mptt) cc_final: 0.8113 (mmtt) REVERT: S 135 HIS cc_start: 0.7229 (m90) cc_final: 0.6796 (m90) REVERT: S 234 ASP cc_start: 0.7409 (p0) cc_final: 0.7053 (p0) REVERT: S 235 LYS cc_start: 0.8582 (tptp) cc_final: 0.8321 (tptp) REVERT: S 236 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7405 (tptt) REVERT: T 55 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7969 (mmtt) REVERT: T 128 ASN cc_start: 0.7458 (m-40) cc_final: 0.7008 (m-40) REVERT: U 28 LEU cc_start: 0.8067 (mm) cc_final: 0.7586 (mt) REVERT: U 54 TYR cc_start: 0.7994 (m-80) cc_final: 0.7674 (m-80) REVERT: U 169 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6329 (mm-30) REVERT: V 234 ASP cc_start: 0.7346 (p0) cc_final: 0.6851 (p0) REVERT: V 235 LYS cc_start: 0.8024 (tptt) cc_final: 0.7574 (tptt) REVERT: V 236 LYS cc_start: 0.7038 (mmtt) cc_final: 0.6616 (mmtt) REVERT: W 135 HIS cc_start: 0.7280 (m-70) cc_final: 0.7074 (m90) REVERT: W 144 HIS cc_start: 0.6942 (OUTLIER) cc_final: 0.6251 (m-70) REVERT: X 131 GLN cc_start: 0.7975 (pp30) cc_final: 0.6774 (pt0) REVERT: Y 37 TYR cc_start: 0.7786 (m-80) cc_final: 0.7558 (m-80) REVERT: Y 131 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7227 (pt0) REVERT: Y 234 ASP cc_start: 0.7379 (p0) cc_final: 0.7030 (p0) REVERT: Z 135 HIS cc_start: 0.7135 (m90) cc_final: 0.6446 (m90) REVERT: a 177 LYS cc_start: 0.8278 (mppt) cc_final: 0.7921 (mmtm) REVERT: c 208 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8558 (mm) REVERT: d 28 LEU cc_start: 0.8058 (mp) cc_final: 0.7551 (pp) REVERT: d 29 GLN cc_start: 0.8048 (pp30) cc_final: 0.7622 (tm-30) REVERT: d 232 PHE cc_start: 0.7865 (p90) cc_final: 0.7153 (p90) REVERT: e 28 LEU cc_start: 0.8564 (tp) cc_final: 0.8124 (mm) REVERT: e 162 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7516 (mm-30) REVERT: f 155 ASP cc_start: 0.8322 (m-30) cc_final: 0.7705 (t70) outliers start: 214 outliers final: 184 residues processed: 885 average time/residue: 0.5887 time to fit residues: 879.4513 Evaluate side-chains 871 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 680 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 118 MET Chi-restraints excluded: chain L residue 135 HIS Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 135 HIS Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 200 LEU Chi-restraints excluded: chain R residue 48 TRP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 136 GLU Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 170 VAL Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain V residue 145 LYS Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 144 HIS Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain W residue 236 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 170 VAL Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 131 GLN Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 229 VAL Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 163 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 232 PHE Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 86 MET Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 145 LYS Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 135 HIS Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 65 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 166 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain g residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 665 optimal weight: 4.9990 chunk 700 optimal weight: 30.0000 chunk 639 optimal weight: 0.7980 chunk 681 optimal weight: 4.9990 chunk 410 optimal weight: 3.9990 chunk 296 optimal weight: 0.0470 chunk 535 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 616 optimal weight: 5.9990 chunk 644 optimal weight: 3.9990 chunk 679 optimal weight: 0.9980 overall best weight: 1.3480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 ASN L 135 HIS L 241 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 GLN ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 63195 Z= 0.214 Angle : 0.651 9.721 85569 Z= 0.327 Chirality : 0.045 0.252 9471 Planarity : 0.004 0.053 11253 Dihedral : 5.012 25.737 8547 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.99 % Allowed : 17.60 % Favored : 79.41 % 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: -3.43 (0.09), residues: 7821 helix: 0.46 (0.16), residues: 990 sheet: -2.41 (0.08), residues: 3333 loop : -2.88 (0.09), residues: 3498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 130 HIS 0.025 0.001 HIS Y 135 PHE 0.041 0.001 PHE K 5 TYR 0.052 0.001 TYR L 121 ARG 0.010 0.000 ARG c 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 711 time to evaluate : 5.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7557 (tp) cc_final: 0.6898 (mm) REVERT: A 29 GLN cc_start: 0.8078 (pp30) cc_final: 0.7733 (pp30) REVERT: A 83 TYR cc_start: 0.7757 (t80) cc_final: 0.7284 (t80) REVERT: A 169 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7793 (mm-30) REVERT: A 235 LYS cc_start: 0.7715 (tptt) cc_final: 0.7369 (tptt) REVERT: B 28 LEU cc_start: 0.8049 (mp) cc_final: 0.7637 (pp) REVERT: B 234 ASP cc_start: 0.7742 (p0) cc_final: 0.7360 (p0) REVERT: C 169 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7672 (mm-30) REVERT: C 192 GLU cc_start: 0.5762 (tm-30) cc_final: 0.5352 (tm-30) REVERT: C 232 PHE cc_start: 0.7582 (p90) cc_final: 0.7271 (p90) REVERT: F 5 PHE cc_start: 0.7398 (t80) cc_final: 0.7124 (t80) REVERT: F 162 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7354 (tm-30) REVERT: F 169 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7557 (mm-30) REVERT: F 223 ILE cc_start: 0.8559 (mt) cc_final: 0.8303 (mm) REVERT: G 63 ASP cc_start: 0.7958 (p0) cc_final: 0.7534 (p0) REVERT: G 128 ASN cc_start: 0.7841 (m-40) cc_final: 0.7578 (m-40) REVERT: H 28 LEU cc_start: 0.8062 (mm) cc_final: 0.7822 (mt) REVERT: H 128 ASN cc_start: 0.8345 (t0) cc_final: 0.8081 (m-40) REVERT: H 171 GLU cc_start: 0.7834 (pm20) cc_final: 0.7578 (pp20) REVERT: H 234 ASP cc_start: 0.7541 (p0) cc_final: 0.7149 (p0) REVERT: I 28 LEU cc_start: 0.7795 (mm) cc_final: 0.7178 (mt) REVERT: J 192 GLU cc_start: 0.7673 (tp30) cc_final: 0.6441 (tm-30) REVERT: K 177 LYS cc_start: 0.8145 (mppt) cc_final: 0.7775 (mmtm) REVERT: K 232 PHE cc_start: 0.7952 (p90) cc_final: 0.7349 (p90) REVERT: K 234 ASP cc_start: 0.7615 (p0) cc_final: 0.7297 (p0) REVERT: L 29 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8019 (tm-30) REVERT: L 39 LEU cc_start: 0.9218 (mp) cc_final: 0.8994 (mp) REVERT: L 55 LYS cc_start: 0.8465 (mptt) cc_final: 0.8142 (mmtt) REVERT: L 63 ASP cc_start: 0.8245 (p0) cc_final: 0.8030 (p0) REVERT: M 28 LEU cc_start: 0.7770 (mm) cc_final: 0.7421 (mm) REVERT: N 203 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8748 (mtpp) REVERT: N 234 ASP cc_start: 0.8879 (p0) cc_final: 0.8638 (p0) REVERT: O 171 GLU cc_start: 0.8094 (pm20) cc_final: 0.7418 (pp20) REVERT: O 234 ASP cc_start: 0.8887 (p0) cc_final: 0.8423 (p0) REVERT: Q 9 VAL cc_start: 0.8572 (t) cc_final: 0.8335 (p) REVERT: Q 28 LEU cc_start: 0.8298 (mm) cc_final: 0.7759 (mt) REVERT: Q 83 TYR cc_start: 0.7927 (t80) cc_final: 0.7677 (t80) REVERT: Q 128 ASN cc_start: 0.8012 (t0) cc_final: 0.7765 (t0) REVERT: R 28 LEU cc_start: 0.8289 (mm) cc_final: 0.7928 (mt) REVERT: R 29 GLN cc_start: 0.7803 (pp30) cc_final: 0.7523 (pp30) REVERT: R 135 HIS cc_start: 0.6717 (m90) cc_final: 0.6405 (m90) REVERT: R 234 ASP cc_start: 0.8204 (p0) cc_final: 0.7949 (p0) REVERT: S 55 LYS cc_start: 0.8369 (mptt) cc_final: 0.8143 (mmtt) REVERT: S 63 ASP cc_start: 0.7649 (p0) cc_final: 0.7199 (p0) REVERT: S 135 HIS cc_start: 0.7275 (m90) cc_final: 0.6779 (m90) REVERT: S 234 ASP cc_start: 0.7437 (p0) cc_final: 0.7054 (p0) REVERT: S 236 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7522 (tptt) REVERT: T 128 ASN cc_start: 0.7458 (m-40) cc_final: 0.7125 (m-40) REVERT: T 162 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7691 (tm-30) REVERT: U 28 LEU cc_start: 0.7980 (mm) cc_final: 0.7527 (mt) REVERT: U 54 TYR cc_start: 0.7982 (m-80) cc_final: 0.7647 (m-80) REVERT: V 234 ASP cc_start: 0.7461 (p0) cc_final: 0.7039 (p0) REVERT: V 235 LYS cc_start: 0.8049 (tptt) cc_final: 0.7734 (tptt) REVERT: V 236 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6672 (mmtt) REVERT: W 135 HIS cc_start: 0.7369 (m-70) cc_final: 0.7154 (m90) REVERT: W 144 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.6195 (m-70) REVERT: X 131 GLN cc_start: 0.7658 (pp30) cc_final: 0.6564 (pt0) REVERT: Y 37 TYR cc_start: 0.7794 (m-80) cc_final: 0.7548 (m-80) REVERT: Y 131 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7336 (pt0) REVERT: Y 234 ASP cc_start: 0.7532 (p0) cc_final: 0.7162 (p0) REVERT: Z 5 PHE cc_start: 0.7267 (t80) cc_final: 0.6815 (t80) REVERT: Z 135 HIS cc_start: 0.7139 (m90) cc_final: 0.6424 (m90) REVERT: a 177 LYS cc_start: 0.8193 (mppt) cc_final: 0.7950 (mmtm) REVERT: b 135 HIS cc_start: 0.7075 (m90) cc_final: 0.6869 (m90) REVERT: c 28 LEU cc_start: 0.7809 (mm) cc_final: 0.7528 (mt) REVERT: c 208 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8523 (mm) REVERT: d 28 LEU cc_start: 0.8046 (mp) cc_final: 0.7537 (pp) REVERT: d 29 GLN cc_start: 0.8105 (pp30) cc_final: 0.7697 (tm-30) REVERT: d 232 PHE cc_start: 0.7865 (p90) cc_final: 0.7184 (p90) REVERT: e 162 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7489 (mm-30) REVERT: f 155 ASP cc_start: 0.8535 (m-30) cc_final: 0.7999 (t70) outliers start: 206 outliers final: 180 residues processed: 870 average time/residue: 0.5704 time to fit residues: 840.2384 Evaluate side-chains 870 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 685 time to evaluate : 5.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 203 LYS Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 135 HIS Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 48 TRP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 136 GLU Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 170 VAL Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain V residue 145 LYS Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 162 GLU Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 144 HIS Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain W residue 236 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 170 VAL Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 131 GLN Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 229 VAL Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 157 VAL Chi-restraints excluded: chain Z residue 163 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 232 PHE Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 86 MET Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 135 HIS Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 166 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain g residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 447 optimal weight: 9.9990 chunk 720 optimal weight: 2.9990 chunk 439 optimal weight: 0.5980 chunk 341 optimal weight: 5.9990 chunk 501 optimal weight: 2.9990 chunk 756 optimal weight: 0.0010 chunk 695 optimal weight: 0.0770 chunk 602 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 465 optimal weight: 5.9990 chunk 369 optimal weight: 6.9990 overall best weight: 0.8346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN L 128 ASN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 GLN ** P 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 149 GLN ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 35 GLN f 135 HIS f 165 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 63195 Z= 0.196 Angle : 0.656 11.521 85569 Z= 0.327 Chirality : 0.045 0.254 9471 Planarity : 0.004 0.052 11253 Dihedral : 4.879 28.124 8547 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.60 % Allowed : 18.15 % Favored : 79.25 % 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: -3.25 (0.09), residues: 7821 helix: 0.53 (0.16), residues: 990 sheet: -2.19 (0.09), residues: 3234 loop : -2.85 (0.09), residues: 3597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 130 HIS 0.027 0.001 HIS Y 135 PHE 0.041 0.001 PHE K 5 TYR 0.032 0.001 TYR O 121 ARG 0.010 0.000 ARG c 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 725 time to evaluate : 5.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7744 (tp) cc_final: 0.7267 (mm) REVERT: A 29 GLN cc_start: 0.8018 (pp30) cc_final: 0.7684 (pp30) REVERT: A 128 ASN cc_start: 0.8066 (t0) cc_final: 0.7847 (t0) REVERT: A 169 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 235 LYS cc_start: 0.7712 (tptt) cc_final: 0.7511 (tptt) REVERT: B 28 LEU cc_start: 0.8108 (mp) cc_final: 0.7704 (pp) REVERT: B 234 ASP cc_start: 0.7725 (p0) cc_final: 0.7358 (p0) REVERT: C 192 GLU cc_start: 0.5756 (tm-30) cc_final: 0.5339 (tm-30) REVERT: E 162 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7214 (tm-30) REVERT: F 28 LEU cc_start: 0.7990 (mm) cc_final: 0.7749 (pp) REVERT: F 162 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7393 (tm-30) REVERT: F 169 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7264 (mm-30) REVERT: F 223 ILE cc_start: 0.8553 (mt) cc_final: 0.8312 (mm) REVERT: G 63 ASP cc_start: 0.7926 (p0) cc_final: 0.7553 (p0) REVERT: G 83 TYR cc_start: 0.7903 (t80) cc_final: 0.7301 (t80) REVERT: G 128 ASN cc_start: 0.7993 (m-40) cc_final: 0.7745 (m-40) REVERT: H 28 LEU cc_start: 0.8003 (mm) cc_final: 0.7772 (mt) REVERT: H 83 TYR cc_start: 0.7915 (t80) cc_final: 0.7584 (t80) REVERT: H 128 ASN cc_start: 0.8428 (t0) cc_final: 0.8224 (m-40) REVERT: I 28 LEU cc_start: 0.7715 (mm) cc_final: 0.7137 (mt) REVERT: I 171 GLU cc_start: 0.7727 (pp20) cc_final: 0.7399 (pp20) REVERT: J 128 ASN cc_start: 0.7917 (m-40) cc_final: 0.7689 (m-40) REVERT: J 192 GLU cc_start: 0.7625 (tp30) cc_final: 0.6437 (tm-30) REVERT: K 56 CYS cc_start: 0.8923 (t) cc_final: 0.7555 (p) REVERT: K 86 MET cc_start: 0.7796 (ttm) cc_final: 0.7489 (ttp) REVERT: K 168 LYS cc_start: 0.7795 (mmmm) cc_final: 0.7162 (mtmm) REVERT: K 177 LYS cc_start: 0.8128 (mppt) cc_final: 0.7791 (mmtm) REVERT: K 232 PHE cc_start: 0.7819 (p90) cc_final: 0.7203 (p90) REVERT: K 234 ASP cc_start: 0.7564 (p0) cc_final: 0.7255 (p0) REVERT: L 29 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: L 39 LEU cc_start: 0.9194 (mp) cc_final: 0.8913 (mm) REVERT: L 55 LYS cc_start: 0.8479 (mptt) cc_final: 0.8191 (mmtt) REVERT: L 137 ARG cc_start: 0.7447 (mtm180) cc_final: 0.7053 (ptt180) REVERT: M 28 LEU cc_start: 0.7671 (mm) cc_final: 0.7361 (mm) REVERT: N 203 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8590 (mtpp) REVERT: N 234 ASP cc_start: 0.8865 (p0) cc_final: 0.8639 (p0) REVERT: O 83 TYR cc_start: 0.7697 (t80) cc_final: 0.7476 (t80) REVERT: O 121 TYR cc_start: 0.7122 (m-80) cc_final: 0.6868 (m-80) REVERT: O 171 GLU cc_start: 0.8054 (pm20) cc_final: 0.7438 (pp20) REVERT: O 234 ASP cc_start: 0.8874 (p0) cc_final: 0.8416 (p0) REVERT: Q 9 VAL cc_start: 0.8556 (t) cc_final: 0.8314 (p) REVERT: Q 28 LEU cc_start: 0.8232 (mm) cc_final: 0.7704 (mt) REVERT: Q 83 TYR cc_start: 0.7925 (t80) cc_final: 0.7649 (t80) REVERT: Q 128 ASN cc_start: 0.8235 (t0) cc_final: 0.8010 (t0) REVERT: R 28 LEU cc_start: 0.8289 (mm) cc_final: 0.7942 (mt) REVERT: R 29 GLN cc_start: 0.7665 (pp30) cc_final: 0.7384 (pp30) REVERT: R 135 HIS cc_start: 0.6692 (m90) cc_final: 0.6395 (m90) REVERT: R 234 ASP cc_start: 0.8170 (p0) cc_final: 0.7919 (p0) REVERT: S 55 LYS cc_start: 0.8310 (mptt) cc_final: 0.8053 (mmtt) REVERT: S 63 ASP cc_start: 0.7254 (p0) cc_final: 0.6757 (p0) REVERT: S 135 HIS cc_start: 0.7335 (m90) cc_final: 0.6865 (m90) REVERT: S 234 ASP cc_start: 0.7175 (p0) cc_final: 0.6849 (p0) REVERT: T 128 ASN cc_start: 0.7366 (m-40) cc_final: 0.7021 (m-40) REVERT: T 162 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7696 (tm-30) REVERT: U 28 LEU cc_start: 0.7948 (mm) cc_final: 0.7559 (mt) REVERT: U 54 TYR cc_start: 0.7906 (m-80) cc_final: 0.7547 (m-80) REVERT: U 169 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7744 (mm-30) REVERT: V 28 LEU cc_start: 0.8071 (mp) cc_final: 0.7741 (pp) REVERT: V 139 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8825 (tp) REVERT: V 234 ASP cc_start: 0.7424 (p0) cc_final: 0.7022 (p0) REVERT: V 235 LYS cc_start: 0.7813 (tptt) cc_final: 0.7546 (tptt) REVERT: V 236 LYS cc_start: 0.7170 (mmtt) cc_final: 0.6824 (mmtt) REVERT: W 118 MET cc_start: 0.7974 (ptp) cc_final: 0.7761 (ptp) REVERT: W 135 HIS cc_start: 0.7458 (m-70) cc_final: 0.7234 (m90) REVERT: W 144 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.6098 (m-70) REVERT: W 169 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7783 (mm-30) REVERT: W 177 LYS cc_start: 0.8770 (mppt) cc_final: 0.8456 (mmtm) REVERT: X 53 ARG cc_start: 0.7453 (mpt180) cc_final: 0.7232 (mpt180) REVERT: X 130 TRP cc_start: 0.7714 (m100) cc_final: 0.7478 (m100) REVERT: X 131 GLN cc_start: 0.7987 (pp30) cc_final: 0.6561 (pt0) REVERT: Y 37 TYR cc_start: 0.7720 (m-80) cc_final: 0.7439 (m-80) REVERT: Y 131 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7345 (pt0) REVERT: Y 234 ASP cc_start: 0.7520 (p0) cc_final: 0.7157 (p0) REVERT: Z 5 PHE cc_start: 0.7229 (t80) cc_final: 0.6786 (t80) REVERT: Z 135 HIS cc_start: 0.7108 (m90) cc_final: 0.6426 (m90) REVERT: a 139 LEU cc_start: 0.9152 (tp) cc_final: 0.8751 (pp) REVERT: a 177 LYS cc_start: 0.8184 (mppt) cc_final: 0.7940 (mmtm) REVERT: b 28 LEU cc_start: 0.6727 (tt) cc_final: 0.6188 (mp) REVERT: b 135 HIS cc_start: 0.7074 (m90) cc_final: 0.6837 (m90) REVERT: c 28 LEU cc_start: 0.7813 (mm) cc_final: 0.7564 (mt) REVERT: c 208 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8729 (mm) REVERT: d 28 LEU cc_start: 0.8012 (mp) cc_final: 0.7480 (pp) REVERT: d 29 GLN cc_start: 0.8069 (pp30) cc_final: 0.7684 (tm-30) REVERT: d 232 PHE cc_start: 0.7888 (p90) cc_final: 0.7178 (p90) REVERT: e 162 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7432 (mm-30) REVERT: f 155 ASP cc_start: 0.8512 (m-30) cc_final: 0.7839 (t70) outliers start: 179 outliers final: 162 residues processed: 866 average time/residue: 0.5885 time to fit residues: 858.2515 Evaluate side-chains 855 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 687 time to evaluate : 5.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 203 LYS Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 48 TRP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 136 GLU Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain V residue 139 LEU Chi-restraints excluded: chain V residue 145 LYS Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 144 HIS Chi-restraints excluded: chain W residue 145 LYS Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain W residue 236 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 131 GLN Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 229 VAL Chi-restraints excluded: chain Z residue 157 VAL Chi-restraints excluded: chain Z residue 163 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 232 PHE Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 86 MET Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 135 HIS Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 166 THR Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain g residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 478 optimal weight: 2.9990 chunk 641 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 555 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 167 optimal weight: 0.0570 chunk 603 optimal weight: 7.9990 chunk 252 optimal weight: 0.9990 chunk 619 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 HIS L 128 ASN L 241 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 241 GLN ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 91 GLN c 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.126031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.103331 restraints weight = 149990.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.104300 restraints weight = 104647.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.104377 restraints weight = 82184.070| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 63195 Z= 0.285 Angle : 0.700 10.496 85569 Z= 0.354 Chirality : 0.046 0.242 9471 Planarity : 0.004 0.053 11253 Dihedral : 5.228 29.544 8547 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 2.71 % Allowed : 18.24 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.09), residues: 7821 helix: 0.42 (0.16), residues: 990 sheet: -2.55 (0.08), residues: 3432 loop : -2.95 (0.09), residues: 3399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 130 HIS 0.028 0.001 HIS Y 135 PHE 0.039 0.002 PHE K 5 TYR 0.042 0.002 TYR O 121 ARG 0.010 0.001 ARG c 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13553.06 seconds wall clock time: 237 minutes 6.82 seconds (14226.82 seconds total)