Starting phenix.real_space_refine on Fri Mar 15 05:54:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/03_2024/6a7f_6993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/03_2024/6a7f_6993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/03_2024/6a7f_6993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/03_2024/6a7f_6993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/03_2024/6a7f_6993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/03_2024/6a7f_6993.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.007 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 30 5.16 5 C 7050 2.51 5 N 1740 2.21 5 O 2010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10830 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "B" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "C" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "D" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "E" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "F" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "G" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "H" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "L" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "M" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "O" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "P" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "Q" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "R" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "S" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "T" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "U" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "V" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "W" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "X" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "Y" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "Z" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "a" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "b" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "c" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "d" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Time building chain proxies: 6.28, per 1000 atoms: 0.58 Number of scatterers: 10830 At special positions: 0 Unit cell: (76.7, 76.7, 165.1, 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 30 16.00 O 2010 8.00 N 1740 7.00 C 7050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.78 Conformation dependent library (CDL) restraints added in 1.9 seconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 95.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Proline residue: A 30 - end of helix removed outlier: 4.020A pdb=" N ALA A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Proline residue: B 30 - end of helix removed outlier: 4.020A pdb=" N ALA B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) Proline residue: C 30 - end of helix removed outlier: 4.021A pdb=" N ALA C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG C 43 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) Proline residue: D 30 - end of helix removed outlier: 4.021A pdb=" N ALA D 38 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 42 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) Proline residue: E 30 - end of helix removed outlier: 4.021A pdb=" N ALA E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG E 43 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS E 46 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) Proline residue: F 30 - end of helix removed outlier: 4.020A pdb=" N ALA F 38 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS F 46 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) Proline residue: G 30 - end of helix removed outlier: 4.022A pdb=" N ALA G 38 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG G 43 " --> pdb=" O GLY G 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS G 46 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) Proline residue: H 30 - end of helix removed outlier: 4.021A pdb=" N ALA H 38 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG H 43 " --> pdb=" O GLY H 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS H 46 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Proline residue: I 30 - end of helix removed outlier: 4.021A pdb=" N ALA I 38 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG I 43 " --> pdb=" O GLY I 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS I 46 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 53 " --> pdb=" O SER I 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) Proline residue: J 30 - end of helix removed outlier: 4.021A pdb=" N ALA J 38 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG J 43 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS J 46 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) Proline residue: K 30 - end of helix removed outlier: 4.021A pdb=" N ALA K 38 " --> pdb=" O THR K 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE K 42 " --> pdb=" O ALA K 38 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS K 46 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) Proline residue: L 30 - end of helix removed outlier: 4.022A pdb=" N ALA L 38 " --> pdb=" O THR L 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG L 43 " --> pdb=" O GLY L 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS L 46 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL L 53 " --> pdb=" O SER L 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP M 23 " --> pdb=" O THR M 19 " (cutoff:3.500A) Proline residue: M 30 - end of helix removed outlier: 4.021A pdb=" N ALA M 38 " --> pdb=" O THR M 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE M 42 " --> pdb=" O ALA M 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG M 43 " --> pdb=" O GLY M 39 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS M 46 " --> pdb=" O ILE M 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP N 23 " --> pdb=" O THR N 19 " (cutoff:3.500A) Proline residue: N 30 - end of helix removed outlier: 4.020A pdb=" N ALA N 38 " --> pdb=" O THR N 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE N 42 " --> pdb=" O ALA N 38 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG N 43 " --> pdb=" O GLY N 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS N 46 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL N 53 " --> pdb=" O SER N 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP O 23 " --> pdb=" O THR O 19 " (cutoff:3.500A) Proline residue: O 30 - end of helix removed outlier: 4.022A pdb=" N ALA O 38 " --> pdb=" O THR O 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE O 42 " --> pdb=" O ALA O 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG O 43 " --> pdb=" O GLY O 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS O 46 " --> pdb=" O ILE O 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL O 53 " --> pdb=" O SER O 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP P 23 " --> pdb=" O THR P 19 " (cutoff:3.500A) Proline residue: P 30 - end of helix removed outlier: 4.021A pdb=" N ALA P 38 " --> pdb=" O THR P 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE P 42 " --> pdb=" O ALA P 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG P 43 " --> pdb=" O GLY P 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS P 46 " --> pdb=" O ILE P 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL P 53 " --> pdb=" O SER P 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP Q 23 " --> pdb=" O THR Q 19 " (cutoff:3.500A) Proline residue: Q 30 - end of helix removed outlier: 4.022A pdb=" N ALA Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Q 42 " --> pdb=" O ALA Q 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG Q 43 " --> pdb=" O GLY Q 39 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS Q 46 " --> pdb=" O ILE Q 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL Q 53 " --> pdb=" O SER Q 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP R 23 " --> pdb=" O THR R 19 " (cutoff:3.500A) Proline residue: R 30 - end of helix removed outlier: 4.021A pdb=" N ALA R 38 " --> pdb=" O THR R 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL R 53 " --> pdb=" O SER R 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP S 23 " --> pdb=" O THR S 19 " (cutoff:3.500A) Proline residue: S 30 - end of helix removed outlier: 4.021A pdb=" N ALA S 38 " --> pdb=" O THR S 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE S 42 " --> pdb=" O ALA S 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG S 43 " --> pdb=" O GLY S 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS S 46 " --> pdb=" O ILE S 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL S 53 " --> pdb=" O SER S 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP T 23 " --> pdb=" O THR T 19 " (cutoff:3.500A) Proline residue: T 30 - end of helix removed outlier: 4.021A pdb=" N ALA T 38 " --> pdb=" O THR T 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE T 42 " --> pdb=" O ALA T 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG T 43 " --> pdb=" O GLY T 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS T 46 " --> pdb=" O ILE T 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL T 53 " --> pdb=" O SER T 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP U 23 " --> pdb=" O THR U 19 " (cutoff:3.500A) Proline residue: U 30 - end of helix removed outlier: 4.021A pdb=" N ALA U 38 " --> pdb=" O THR U 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE U 42 " --> pdb=" O ALA U 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG U 43 " --> pdb=" O GLY U 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS U 46 " --> pdb=" O ILE U 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL U 53 " --> pdb=" O SER U 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP V 23 " --> pdb=" O THR V 19 " (cutoff:3.500A) Proline residue: V 30 - end of helix removed outlier: 4.022A pdb=" N ALA V 38 " --> pdb=" O THR V 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE V 42 " --> pdb=" O ALA V 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG V 43 " --> pdb=" O GLY V 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS V 46 " --> pdb=" O ILE V 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL V 53 " --> pdb=" O SER V 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP W 23 " --> pdb=" O THR W 19 " (cutoff:3.500A) Proline residue: W 30 - end of helix removed outlier: 4.021A pdb=" N ALA W 38 " --> pdb=" O THR W 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE W 42 " --> pdb=" O ALA W 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG W 43 " --> pdb=" O GLY W 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS W 46 " --> pdb=" O ILE W 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL W 53 " --> pdb=" O SER W 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP X 23 " --> pdb=" O THR X 19 " (cutoff:3.500A) Proline residue: X 30 - end of helix removed outlier: 4.022A pdb=" N ALA X 38 " --> pdb=" O THR X 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE X 42 " --> pdb=" O ALA X 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG X 43 " --> pdb=" O GLY X 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS X 46 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL X 53 " --> pdb=" O SER X 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP Y 23 " --> pdb=" O THR Y 19 " (cutoff:3.500A) Proline residue: Y 30 - end of helix removed outlier: 4.021A pdb=" N ALA Y 38 " --> pdb=" O THR Y 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Y 42 " --> pdb=" O ALA Y 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG Y 43 " --> pdb=" O GLY Y 39 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS Y 46 " --> pdb=" O ILE Y 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL Y 53 " --> pdb=" O SER Y 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP Z 23 " --> pdb=" O THR Z 19 " (cutoff:3.500A) Proline residue: Z 30 - end of helix removed outlier: 4.021A pdb=" N ALA Z 38 " --> pdb=" O THR Z 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Z 42 " --> pdb=" O ALA Z 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG Z 43 " --> pdb=" O GLY Z 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS Z 46 " --> pdb=" O ILE Z 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL Z 53 " --> pdb=" O SER Z 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 53 removed outlier: 3.629A pdb=" N ASP a 23 " --> pdb=" O THR a 19 " (cutoff:3.500A) Proline residue: a 30 - end of helix removed outlier: 4.020A pdb=" N ALA a 38 " --> pdb=" O THR a 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE a 42 " --> pdb=" O ALA a 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG a 43 " --> pdb=" O GLY a 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS a 46 " --> pdb=" O ILE a 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL a 53 " --> pdb=" O SER a 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP b 23 " --> pdb=" O THR b 19 " (cutoff:3.500A) Proline residue: b 30 - end of helix removed outlier: 4.020A pdb=" N ALA b 38 " --> pdb=" O THR b 34 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG b 43 " --> pdb=" O GLY b 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS b 46 " --> pdb=" O ILE b 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL b 53 " --> pdb=" O SER b 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP c 23 " --> pdb=" O THR c 19 " (cutoff:3.500A) Proline residue: c 30 - end of helix removed outlier: 4.020A pdb=" N ALA c 38 " --> pdb=" O THR c 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE c 42 " --> pdb=" O ALA c 38 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG c 43 " --> pdb=" O GLY c 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS c 46 " --> pdb=" O ILE c 42 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL c 53 " --> pdb=" O SER c 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP d 23 " --> pdb=" O THR d 19 " (cutoff:3.500A) Proline residue: d 30 - end of helix removed outlier: 4.021A pdb=" N ALA d 38 " --> pdb=" O THR d 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE d 42 " --> pdb=" O ALA d 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG d 43 " --> pdb=" O GLY d 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS d 46 " --> pdb=" O ILE d 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL d 53 " --> pdb=" O SER d 49 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2880 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: 2.78 Time building geometry restraints manager: 7.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3199 1.33 - 1.45: 1403 1.45 - 1.56: 6318 1.56 - 1.67: 0 1.67 - 1.79: 60 Bond restraints: 10980 Sorted by residual: bond pdb=" CB VAL X 32 " pdb=" CG2 VAL X 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.79e+00 bond pdb=" CB VAL M 32 " pdb=" CG2 VAL M 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB VAL d 32 " pdb=" CG2 VAL d 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB VAL H 32 " pdb=" CG2 VAL H 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CB VAL c 32 " pdb=" CG2 VAL c 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.73e+00 ... (remaining 10975 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.30: 180 106.30 - 113.19: 6759 113.19 - 120.09: 3934 120.09 - 126.99: 3947 126.99 - 133.89: 120 Bond angle restraints: 14940 Sorted by residual: angle pdb=" N TRP I 29 " pdb=" CA TRP I 29 " pdb=" C TRP I 29 " ideal model delta sigma weight residual 113.45 117.78 -4.33 1.39e+00 5.18e-01 9.70e+00 angle pdb=" N TRP F 29 " pdb=" CA TRP F 29 " pdb=" C TRP F 29 " ideal model delta sigma weight residual 113.45 117.77 -4.32 1.39e+00 5.18e-01 9.68e+00 angle pdb=" N TRP U 29 " pdb=" CA TRP U 29 " pdb=" C TRP U 29 " ideal model delta sigma weight residual 113.45 117.77 -4.32 1.39e+00 5.18e-01 9.66e+00 angle pdb=" N TRP J 29 " pdb=" CA TRP J 29 " pdb=" C TRP J 29 " ideal model delta sigma weight residual 113.45 117.76 -4.31 1.39e+00 5.18e-01 9.63e+00 angle pdb=" N TRP a 29 " pdb=" CA TRP a 29 " pdb=" C TRP a 29 " ideal model delta sigma weight residual 113.45 117.76 -4.31 1.39e+00 5.18e-01 9.62e+00 ... (remaining 14935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 6120 14.33 - 28.65: 420 28.65 - 42.98: 30 42.98 - 57.30: 0 57.30 - 71.63: 30 Dihedral angle restraints: 6600 sinusoidal: 2430 harmonic: 4170 Sorted by residual: dihedral pdb=" CA THR G 7 " pdb=" C THR G 7 " pdb=" N ASN G 8 " pdb=" CA ASN G 8 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR R 7 " pdb=" C THR R 7 " pdb=" N ASN R 8 " pdb=" CA ASN R 8 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR C 7 " pdb=" C THR C 7 " pdb=" N ASN C 8 " pdb=" CA ASN C 8 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1023 0.042 - 0.083: 614 0.083 - 0.125: 209 0.125 - 0.166: 104 0.166 - 0.208: 30 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA TRP I 29 " pdb=" N TRP I 29 " pdb=" C TRP I 29 " pdb=" CB TRP I 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TRP Q 29 " pdb=" N TRP Q 29 " pdb=" C TRP Q 29 " pdb=" CB TRP Q 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA TRP d 29 " pdb=" N TRP d 29 " pdb=" C TRP d 29 " pdb=" CB TRP d 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1977 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL T 41 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C VAL T 41 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL T 41 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE T 42 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL W 41 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C VAL W 41 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL W 41 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE W 42 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL b 41 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C VAL b 41 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL b 41 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE b 42 " -0.011 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3091 2.80 - 3.32: 11247 3.32 - 3.85: 18366 3.85 - 4.37: 20225 4.37 - 4.90: 35192 Nonbonded interactions: 88121 Sorted by model distance: nonbonded pdb=" NZ LYS C 46 " pdb=" O LYS I 51 " model vdw 2.271 2.520 nonbonded pdb=" NZ LYS W 46 " pdb=" O VAL c 53 " model vdw 2.288 2.520 nonbonded pdb=" NZ LYS T 46 " pdb=" O VAL U 53 " model vdw 2.328 2.520 nonbonded pdb=" NZ LYS O 46 " pdb=" O VAL P 53 " model vdw 2.332 2.520 nonbonded pdb=" O ALA a 13 " pdb=" OG SER a 16 " model vdw 2.339 2.440 ... (remaining 88116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.010 Extract box with map and model: 3.310 Check model and map are aligned: 0.200 Set scattering table: 0.090 Process input model: 33.010 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.014 0.064 10980 Z= 0.903 Angle : 1.172 6.672 14940 Z= 0.615 Chirality : 0.064 0.208 1980 Planarity : 0.008 0.044 1740 Dihedral : 11.202 71.631 3840 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.18), residues: 1350 helix: -1.19 (0.11), residues: 1320 sheet: None (None), residues: 0 loop : -0.50 (0.01), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 29 PHE 0.008 0.003 PHE Y 48 TYR 0.003 0.001 TYR G 9 ARG 0.006 0.002 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 833 time to evaluate : 1.270 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: A 14 MET cc_start: 0.9213 (mmt) cc_final: 0.8863 (mmt) REVERT: A 23 ASP cc_start: 0.8373 (m-30) cc_final: 0.8085 (m-30) REVERT: A 27 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8831 (tp-100) REVERT: A 47 LYS cc_start: 0.9241 (tttt) cc_final: 0.8748 (tppt) REVERT: B 42 ILE cc_start: 0.9521 (tt) cc_final: 0.9248 (tp) REVERT: B 47 LYS cc_start: 0.8973 (tttt) cc_final: 0.8658 (mmtt) REVERT: B 51 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8607 (mttt) REVERT: C 9 TYR cc_start: 0.7565 (m-80) cc_final: 0.7326 (m-80) REVERT: C 42 ILE cc_start: 0.9470 (tt) cc_final: 0.9252 (tt) REVERT: C 47 LYS cc_start: 0.9055 (tttt) cc_final: 0.8539 (tptt) REVERT: D 23 ASP cc_start: 0.8346 (m-30) cc_final: 0.8017 (m-30) REVERT: D 47 LYS cc_start: 0.9197 (tttt) cc_final: 0.8818 (tptt) REVERT: E 15 ASP cc_start: 0.8656 (m-30) cc_final: 0.8454 (m-30) REVERT: E 20 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8663 (mm-40) REVERT: E 23 ASP cc_start: 0.8251 (m-30) cc_final: 0.7862 (m-30) REVERT: F 8 ASN cc_start: 0.8166 (t0) cc_final: 0.7146 (t0) REVERT: F 9 TYR cc_start: 0.7269 (m-80) cc_final: 0.7068 (m-80) REVERT: F 11 THR cc_start: 0.8286 (p) cc_final: 0.7624 (p) REVERT: F 23 ASP cc_start: 0.8463 (m-30) cc_final: 0.8232 (m-30) REVERT: F 51 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8413 (mtpp) REVERT: G 7 THR cc_start: 0.8273 (p) cc_final: 0.7934 (p) REVERT: G 8 ASN cc_start: 0.8012 (t0) cc_final: 0.6751 (m110) REVERT: G 23 ASP cc_start: 0.8490 (m-30) cc_final: 0.8082 (t70) REVERT: G 27 GLN cc_start: 0.8939 (tp-100) cc_final: 0.8531 (tp-100) REVERT: G 40 LEU cc_start: 0.9460 (mt) cc_final: 0.9216 (mt) REVERT: G 44 LEU cc_start: 0.9175 (mt) cc_final: 0.8916 (mm) REVERT: G 51 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8630 (mtpp) REVERT: H 9 TYR cc_start: 0.7680 (m-80) cc_final: 0.7168 (m-80) REVERT: H 19 THR cc_start: 0.8734 (p) cc_final: 0.8234 (p) REVERT: H 27 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8570 (tp-100) REVERT: H 51 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8522 (mtpp) REVERT: I 9 TYR cc_start: 0.8034 (m-80) cc_final: 0.7647 (m-80) REVERT: I 22 ILE cc_start: 0.8599 (mt) cc_final: 0.8280 (mm) REVERT: I 27 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8468 (tp40) REVERT: I 42 ILE cc_start: 0.9383 (tt) cc_final: 0.9075 (tt) REVERT: I 48 PHE cc_start: 0.8802 (m-80) cc_final: 0.8492 (m-80) REVERT: J 9 TYR cc_start: 0.7627 (m-80) cc_final: 0.7395 (m-80) REVERT: J 27 GLN cc_start: 0.9021 (tp-100) cc_final: 0.8704 (tp-100) REVERT: J 51 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8733 (mtpp) REVERT: K 14 MET cc_start: 0.8519 (mmt) cc_final: 0.8016 (mmm) REVERT: K 47 LYS cc_start: 0.8333 (tttt) cc_final: 0.8028 (ttmm) REVERT: K 51 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8393 (mmmm) REVERT: L 14 MET cc_start: 0.8784 (mmt) cc_final: 0.8200 (mmm) REVERT: L 27 GLN cc_start: 0.9196 (tp-100) cc_final: 0.8958 (tp-100) REVERT: L 47 LYS cc_start: 0.8460 (tttt) cc_final: 0.8066 (ttmm) REVERT: L 48 PHE cc_start: 0.9030 (m-80) cc_final: 0.8697 (m-80) REVERT: L 51 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8415 (mmmm) REVERT: M 27 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8517 (tp-100) REVERT: M 44 LEU cc_start: 0.9220 (mt) cc_final: 0.8966 (mm) REVERT: M 47 LYS cc_start: 0.8423 (tttt) cc_final: 0.7859 (ttmm) REVERT: M 50 SER cc_start: 0.8485 (t) cc_final: 0.7994 (p) REVERT: M 51 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8200 (mmmm) REVERT: N 8 ASN cc_start: 0.7876 (t0) cc_final: 0.7366 (m-40) REVERT: N 27 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8518 (tp40) REVERT: N 47 LYS cc_start: 0.8508 (tttt) cc_final: 0.8168 (ttmm) REVERT: O 47 LYS cc_start: 0.8522 (tttt) cc_final: 0.8077 (ttmm) REVERT: P 15 ASP cc_start: 0.8433 (m-30) cc_final: 0.8038 (m-30) REVERT: P 47 LYS cc_start: 0.8756 (tttt) cc_final: 0.8391 (ttmm) REVERT: Q 8 ASN cc_start: 0.8056 (t0) cc_final: 0.7833 (m110) REVERT: Q 11 THR cc_start: 0.8462 (p) cc_final: 0.8228 (p) REVERT: Q 15 ASP cc_start: 0.8497 (m-30) cc_final: 0.8270 (m-30) REVERT: Q 40 LEU cc_start: 0.9270 (mt) cc_final: 0.9030 (mt) REVERT: Q 42 ILE cc_start: 0.9294 (tt) cc_final: 0.8998 (tp) REVERT: Q 47 LYS cc_start: 0.8444 (tttt) cc_final: 0.8166 (ttmm) REVERT: Q 50 SER cc_start: 0.8939 (t) cc_final: 0.8725 (t) REVERT: R 14 MET cc_start: 0.8904 (mmt) cc_final: 0.8633 (mmt) REVERT: R 40 LEU cc_start: 0.9348 (mt) cc_final: 0.9098 (mp) REVERT: S 15 ASP cc_start: 0.8499 (m-30) cc_final: 0.8092 (m-30) REVERT: S 40 LEU cc_start: 0.9190 (mt) cc_final: 0.8906 (mp) REVERT: S 43 ARG cc_start: 0.8164 (ttt180) cc_final: 0.7925 (ttt180) REVERT: T 22 ILE cc_start: 0.8345 (mt) cc_final: 0.7996 (mm) REVERT: T 47 LYS cc_start: 0.8481 (tttt) cc_final: 0.8178 (ttmm) REVERT: U 8 ASN cc_start: 0.7409 (t0) cc_final: 0.6156 (t0) REVERT: U 9 TYR cc_start: 0.7665 (m-80) cc_final: 0.7396 (m-80) REVERT: U 20 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8920 (mm-40) REVERT: U 47 LYS cc_start: 0.8692 (tttt) cc_final: 0.8239 (ttpt) REVERT: U 51 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7837 (mptp) REVERT: V 8 ASN cc_start: 0.7551 (t0) cc_final: 0.6269 (t0) REVERT: V 9 TYR cc_start: 0.7745 (m-80) cc_final: 0.7266 (m-80) REVERT: V 15 ASP cc_start: 0.8903 (m-30) cc_final: 0.8701 (m-30) REVERT: W 8 ASN cc_start: 0.7522 (t0) cc_final: 0.6374 (t0) REVERT: W 15 ASP cc_start: 0.8820 (m-30) cc_final: 0.8591 (m-30) REVERT: W 47 LYS cc_start: 0.8618 (tttt) cc_final: 0.8379 (ttmm) REVERT: X 15 ASP cc_start: 0.8859 (m-30) cc_final: 0.8638 (m-30) REVERT: Y 8 ASN cc_start: 0.7577 (t0) cc_final: 0.5856 (t0) REVERT: Y 9 TYR cc_start: 0.7655 (m-80) cc_final: 0.7452 (m-80) REVERT: Y 15 ASP cc_start: 0.8931 (m-30) cc_final: 0.8615 (m-30) REVERT: Z 18 LYS cc_start: 0.8464 (tttt) cc_final: 0.7960 (mptt) REVERT: Z 20 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8999 (mm-40) REVERT: Z 23 ASP cc_start: 0.8326 (m-30) cc_final: 0.8062 (t0) REVERT: Z 40 LEU cc_start: 0.9048 (mt) cc_final: 0.8789 (mt) REVERT: a 18 LYS cc_start: 0.8443 (tttt) cc_final: 0.7740 (mptt) REVERT: b 15 ASP cc_start: 0.8733 (m-30) cc_final: 0.8400 (m-30) REVERT: b 18 LYS cc_start: 0.8297 (tttt) cc_final: 0.8021 (mptt) REVERT: c 15 ASP cc_start: 0.8716 (m-30) cc_final: 0.8418 (m-30) REVERT: c 18 LYS cc_start: 0.8306 (tttt) cc_final: 0.8041 (mptt) REVERT: c 25 ILE cc_start: 0.8552 (mt) cc_final: 0.8294 (mt) REVERT: d 18 LYS cc_start: 0.8472 (tttt) cc_final: 0.7821 (mmtt) REVERT: d 22 ILE cc_start: 0.8606 (mt) cc_final: 0.8373 (mm) outliers start: 0 outliers final: 0 residues processed: 833 average time/residue: 0.2308 time to fit residues: 260.6932 Evaluate side-chains 662 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 662 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10980 Z= 0.209 Angle : 0.562 7.222 14940 Z= 0.293 Chirality : 0.040 0.133 1980 Planarity : 0.005 0.030 1740 Dihedral : 4.323 11.977 1440 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.25 % Allowed : 18.86 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1350 helix: 0.54 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : 2.80 (0.37), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 29 PHE 0.011 0.001 PHE b 48 TYR 0.005 0.001 TYR Y 9 ARG 0.002 0.001 ARG W 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 820 time to evaluate : 1.158 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 20 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8381 (mm-40) REVERT: A 27 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8742 (tp-100) REVERT: A 42 ILE cc_start: 0.8919 (tp) cc_final: 0.8600 (tt) REVERT: A 47 LYS cc_start: 0.9213 (tttt) cc_final: 0.8736 (tppt) REVERT: A 49 SER cc_start: 0.9226 (t) cc_final: 0.8731 (p) REVERT: B 27 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8323 (tt0) REVERT: B 42 ILE cc_start: 0.9411 (tt) cc_final: 0.9042 (tp) REVERT: B 47 LYS cc_start: 0.8929 (tttt) cc_final: 0.8578 (mmtt) REVERT: B 51 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8729 (mtpt) REVERT: C 9 TYR cc_start: 0.7443 (m-80) cc_final: 0.7219 (m-80) REVERT: C 20 GLN cc_start: 0.9041 (tp40) cc_final: 0.8401 (mt0) REVERT: C 23 ASP cc_start: 0.8395 (t0) cc_final: 0.8035 (p0) REVERT: C 47 LYS cc_start: 0.9093 (tttt) cc_final: 0.8509 (tptt) REVERT: D 23 ASP cc_start: 0.8399 (m-30) cc_final: 0.8108 (m-30) REVERT: D 42 ILE cc_start: 0.9152 (tp) cc_final: 0.8860 (tt) REVERT: D 46 LYS cc_start: 0.8916 (mttm) cc_final: 0.8715 (mttp) REVERT: D 47 LYS cc_start: 0.9131 (tttt) cc_final: 0.8793 (tptt) REVERT: D 51 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8677 (mttt) REVERT: E 20 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8833 (mm-40) REVERT: E 42 ILE cc_start: 0.9084 (tp) cc_final: 0.8804 (tt) REVERT: F 8 ASN cc_start: 0.7674 (t0) cc_final: 0.7097 (t0) REVERT: F 27 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8553 (tp40) REVERT: F 51 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8520 (mtpp) REVERT: G 9 TYR cc_start: 0.7062 (m-80) cc_final: 0.6860 (m-80) REVERT: G 20 GLN cc_start: 0.9132 (mm-40) cc_final: 0.7857 (mm-40) REVERT: G 40 LEU cc_start: 0.9469 (mt) cc_final: 0.9250 (mt) REVERT: G 51 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8637 (mtpp) REVERT: H 9 TYR cc_start: 0.7673 (m-80) cc_final: 0.7016 (m-80) REVERT: H 11 THR cc_start: 0.8218 (p) cc_final: 0.7894 (p) REVERT: H 19 THR cc_start: 0.8503 (p) cc_final: 0.8111 (p) REVERT: H 27 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8847 (tp40) REVERT: H 43 ARG cc_start: 0.8576 (mtp180) cc_final: 0.8200 (ttm170) REVERT: H 51 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8556 (mtpp) REVERT: I 23 ASP cc_start: 0.8323 (t70) cc_final: 0.8111 (p0) REVERT: I 27 GLN cc_start: 0.8974 (tp-100) cc_final: 0.8378 (tp-100) REVERT: I 42 ILE cc_start: 0.9374 (tt) cc_final: 0.9174 (tt) REVERT: I 50 SER cc_start: 0.8374 (t) cc_final: 0.7940 (p) REVERT: I 51 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8559 (mtpp) REVERT: J 23 ASP cc_start: 0.8354 (t70) cc_final: 0.8118 (p0) REVERT: J 26 SER cc_start: 0.8472 (p) cc_final: 0.8182 (p) REVERT: J 27 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8600 (tp-100) REVERT: J 48 PHE cc_start: 0.9242 (m-80) cc_final: 0.8824 (m-80) REVERT: J 51 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8721 (mtpp) REVERT: K 14 MET cc_start: 0.8692 (mmt) cc_final: 0.8109 (mmt) REVERT: K 18 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7727 (ttmm) REVERT: K 47 LYS cc_start: 0.8371 (tttt) cc_final: 0.7830 (ttmm) REVERT: K 50 SER cc_start: 0.8358 (t) cc_final: 0.7783 (p) REVERT: K 51 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8498 (mmmm) REVERT: L 47 LYS cc_start: 0.8432 (tttt) cc_final: 0.8059 (ttmm) REVERT: L 51 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8516 (mmmm) REVERT: M 14 MET cc_start: 0.8487 (mmm) cc_final: 0.7823 (mmt) REVERT: M 15 ASP cc_start: 0.8468 (m-30) cc_final: 0.8214 (m-30) REVERT: M 27 GLN cc_start: 0.9025 (tp-100) cc_final: 0.8593 (tp40) REVERT: M 47 LYS cc_start: 0.8421 (tttt) cc_final: 0.8134 (ttmm) REVERT: M 51 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8303 (mmmm) REVERT: N 8 ASN cc_start: 0.7876 (t0) cc_final: 0.7088 (m-40) REVERT: N 47 LYS cc_start: 0.8495 (tttt) cc_final: 0.8050 (ttmm) REVERT: N 50 SER cc_start: 0.8403 (t) cc_final: 0.7981 (p) REVERT: O 14 MET cc_start: 0.8656 (mmm) cc_final: 0.8202 (mmt) REVERT: O 27 GLN cc_start: 0.8866 (tp40) cc_final: 0.8442 (tp40) REVERT: P 15 ASP cc_start: 0.8161 (m-30) cc_final: 0.7827 (m-30) REVERT: P 27 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8405 (tp40) REVERT: P 47 LYS cc_start: 0.8684 (tttt) cc_final: 0.8398 (ttmm) REVERT: Q 15 ASP cc_start: 0.8362 (m-30) cc_final: 0.8117 (m-30) REVERT: Q 27 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8500 (tp40) REVERT: Q 40 LEU cc_start: 0.9284 (mt) cc_final: 0.9065 (mt) REVERT: Q 42 ILE cc_start: 0.9368 (tt) cc_final: 0.9118 (tp) REVERT: S 15 ASP cc_start: 0.8267 (m-30) cc_final: 0.7973 (m-30) REVERT: T 15 ASP cc_start: 0.8301 (m-30) cc_final: 0.8076 (m-30) REVERT: T 22 ILE cc_start: 0.8236 (mt) cc_final: 0.8030 (mm) REVERT: T 27 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8470 (tp-100) REVERT: T 47 LYS cc_start: 0.8465 (tttt) cc_final: 0.8200 (ttmm) REVERT: U 15 ASP cc_start: 0.8618 (m-30) cc_final: 0.8388 (m-30) REVERT: U 18 LYS cc_start: 0.8755 (ttpp) cc_final: 0.8041 (ttmm) REVERT: U 40 LEU cc_start: 0.9113 (mp) cc_final: 0.8689 (mt) REVERT: V 8 ASN cc_start: 0.6976 (t0) cc_final: 0.6583 (t0) REVERT: V 47 LYS cc_start: 0.8751 (tttm) cc_final: 0.8432 (ttmm) REVERT: W 27 GLN cc_start: 0.8975 (tp40) cc_final: 0.8718 (tp40) REVERT: W 43 ARG cc_start: 0.8425 (ttm170) cc_final: 0.8127 (ttp80) REVERT: X 49 SER cc_start: 0.9022 (t) cc_final: 0.8807 (t) REVERT: X 51 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8397 (mttp) REVERT: Y 8 ASN cc_start: 0.6825 (t0) cc_final: 0.5996 (t0) REVERT: Y 18 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8237 (ttmm) REVERT: Y 43 ARG cc_start: 0.7977 (ttp-170) cc_final: 0.7653 (ttm170) REVERT: Y 47 LYS cc_start: 0.8664 (tttm) cc_final: 0.8354 (ttmm) REVERT: Z 18 LYS cc_start: 0.8314 (tttt) cc_final: 0.7940 (mptt) REVERT: Z 23 ASP cc_start: 0.8309 (m-30) cc_final: 0.8062 (t0) REVERT: Z 46 LYS cc_start: 0.8038 (mttt) cc_final: 0.7674 (mtmt) REVERT: a 18 LYS cc_start: 0.8463 (tttt) cc_final: 0.7896 (mptt) REVERT: b 15 ASP cc_start: 0.8789 (m-30) cc_final: 0.8466 (m-30) REVERT: b 18 LYS cc_start: 0.8321 (tttt) cc_final: 0.7972 (mptt) REVERT: b 24 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8776 (tp) REVERT: c 14 MET cc_start: 0.8229 (mmm) cc_final: 0.8022 (mmm) REVERT: c 15 ASP cc_start: 0.8638 (m-30) cc_final: 0.8359 (m-30) REVERT: c 18 LYS cc_start: 0.8425 (tttt) cc_final: 0.7997 (mptt) REVERT: c 43 ARG cc_start: 0.8730 (ttt-90) cc_final: 0.8459 (ttp80) REVERT: d 15 ASP cc_start: 0.8547 (m-30) cc_final: 0.8238 (m-30) REVERT: d 18 LYS cc_start: 0.8351 (tttt) cc_final: 0.7743 (mmtt) outliers start: 40 outliers final: 26 residues processed: 822 average time/residue: 0.2195 time to fit residues: 249.0908 Evaluate side-chains 749 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 722 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain d residue 9 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN R 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10980 Z= 0.224 Angle : 0.563 5.969 14940 Z= 0.290 Chirality : 0.041 0.138 1980 Planarity : 0.004 0.043 1740 Dihedral : 4.083 11.480 1440 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.90 % Allowed : 23.09 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1350 helix: 1.13 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.30 (0.46), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Z 29 PHE 0.012 0.001 PHE c 48 TYR 0.004 0.001 TYR F 9 ARG 0.006 0.000 ARG U 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 766 time to evaluate : 1.352 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 27 GLN cc_start: 0.9128 (tp-100) cc_final: 0.8398 (tt0) REVERT: A 42 ILE cc_start: 0.8900 (tp) cc_final: 0.8494 (tt) REVERT: A 47 LYS cc_start: 0.9182 (tttt) cc_final: 0.8786 (mmtt) REVERT: A 49 SER cc_start: 0.9058 (t) cc_final: 0.8730 (m) REVERT: A 51 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8688 (mtpt) REVERT: B 20 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8371 (mm-40) REVERT: B 42 ILE cc_start: 0.9378 (tt) cc_final: 0.9019 (tp) REVERT: B 45 PHE cc_start: 0.9323 (t80) cc_final: 0.8946 (t80) REVERT: B 47 LYS cc_start: 0.8944 (tttt) cc_final: 0.8527 (mmtt) REVERT: B 51 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8743 (mttt) REVERT: C 9 TYR cc_start: 0.7505 (m-80) cc_final: 0.7159 (m-80) REVERT: C 20 GLN cc_start: 0.9018 (tp40) cc_final: 0.8381 (mt0) REVERT: C 23 ASP cc_start: 0.8413 (t0) cc_final: 0.8119 (p0) REVERT: C 47 LYS cc_start: 0.9060 (tttt) cc_final: 0.8458 (tptt) REVERT: D 23 ASP cc_start: 0.8410 (m-30) cc_final: 0.8087 (m-30) REVERT: D 42 ILE cc_start: 0.8792 (tp) cc_final: 0.8575 (tt) REVERT: D 47 LYS cc_start: 0.9126 (tttt) cc_final: 0.8821 (tptt) REVERT: D 51 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8669 (mttt) REVERT: E 20 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8587 (mm-40) REVERT: E 42 ILE cc_start: 0.9046 (tp) cc_final: 0.8696 (tt) REVERT: F 8 ASN cc_start: 0.8000 (t0) cc_final: 0.7575 (t0) REVERT: G 51 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8669 (mtpp) REVERT: H 9 TYR cc_start: 0.7460 (m-80) cc_final: 0.6962 (m-80) REVERT: H 43 ARG cc_start: 0.8593 (mtp180) cc_final: 0.8143 (ttm170) REVERT: H 51 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8593 (mtpp) REVERT: I 22 ILE cc_start: 0.8723 (mt) cc_final: 0.8518 (mm) REVERT: I 27 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8399 (tp40) REVERT: I 42 ILE cc_start: 0.9377 (tt) cc_final: 0.9144 (tt) REVERT: I 50 SER cc_start: 0.8518 (t) cc_final: 0.8036 (p) REVERT: I 51 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8506 (mtpp) REVERT: J 27 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8588 (tp-100) REVERT: J 42 ILE cc_start: 0.9504 (tt) cc_final: 0.9185 (tp) REVERT: J 48 PHE cc_start: 0.9269 (m-80) cc_final: 0.8637 (m-80) REVERT: J 51 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8751 (mtpp) REVERT: K 14 MET cc_start: 0.8689 (mmt) cc_final: 0.8184 (mmt) REVERT: K 18 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7904 (ttmm) REVERT: K 47 LYS cc_start: 0.8330 (tttt) cc_final: 0.7781 (ttmm) REVERT: K 50 SER cc_start: 0.8480 (t) cc_final: 0.7826 (p) REVERT: K 51 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8556 (mmmm) REVERT: L 14 MET cc_start: 0.8770 (mmt) cc_final: 0.8423 (mmt) REVERT: L 20 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8852 (mm-40) REVERT: L 47 LYS cc_start: 0.8418 (tttt) cc_final: 0.7782 (ttmm) REVERT: L 50 SER cc_start: 0.8651 (t) cc_final: 0.8176 (p) REVERT: L 51 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8421 (mmmm) REVERT: M 14 MET cc_start: 0.8351 (mmm) cc_final: 0.7870 (mmt) REVERT: M 15 ASP cc_start: 0.8488 (m-30) cc_final: 0.8246 (m-30) REVERT: M 27 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8653 (tp40) REVERT: M 47 LYS cc_start: 0.8445 (tttt) cc_final: 0.8144 (ttmm) REVERT: N 8 ASN cc_start: 0.7892 (t0) cc_final: 0.6778 (t0) REVERT: N 18 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7760 (ttmt) REVERT: N 47 LYS cc_start: 0.8436 (tttt) cc_final: 0.7902 (ttmm) REVERT: N 50 SER cc_start: 0.8649 (t) cc_final: 0.8189 (p) REVERT: N 51 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8366 (mtpp) REVERT: O 8 ASN cc_start: 0.8277 (t0) cc_final: 0.7349 (t0) REVERT: O 14 MET cc_start: 0.8718 (mmm) cc_final: 0.8037 (mmt) REVERT: O 27 GLN cc_start: 0.8928 (tp40) cc_final: 0.8502 (tp40) REVERT: P 15 ASP cc_start: 0.8130 (m-30) cc_final: 0.7846 (m-30) REVERT: P 27 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8455 (tp40) REVERT: P 47 LYS cc_start: 0.8789 (tttt) cc_final: 0.8574 (ttmm) REVERT: Q 15 ASP cc_start: 0.8302 (m-30) cc_final: 0.7931 (m-30) REVERT: Q 27 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8439 (tp40) REVERT: Q 40 LEU cc_start: 0.9325 (mt) cc_final: 0.9052 (mt) REVERT: Q 42 ILE cc_start: 0.9330 (tt) cc_final: 0.9038 (tp) REVERT: S 15 ASP cc_start: 0.8253 (m-30) cc_final: 0.7973 (m-30) REVERT: T 27 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8401 (tp-100) REVERT: T 47 LYS cc_start: 0.8541 (tttt) cc_final: 0.8295 (ttmm) REVERT: U 15 ASP cc_start: 0.8636 (m-30) cc_final: 0.8330 (m-30) REVERT: U 18 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8058 (ttmm) REVERT: U 51 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7461 (mttm) REVERT: V 8 ASN cc_start: 0.6921 (t0) cc_final: 0.6178 (t0) REVERT: W 27 GLN cc_start: 0.8965 (tp40) cc_final: 0.8755 (tp-100) REVERT: W 43 ARG cc_start: 0.8436 (ttm170) cc_final: 0.8158 (ttp80) REVERT: X 9 TYR cc_start: 0.7694 (m-80) cc_final: 0.7071 (m-80) REVERT: X 49 SER cc_start: 0.9074 (t) cc_final: 0.8634 (p) REVERT: Y 9 TYR cc_start: 0.7756 (m-80) cc_final: 0.7457 (m-80) REVERT: Y 43 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7677 (ttp80) REVERT: Y 47 LYS cc_start: 0.8740 (tttm) cc_final: 0.8496 (ttmm) REVERT: Z 18 LYS cc_start: 0.8261 (tttt) cc_final: 0.7901 (mptt) REVERT: Z 23 ASP cc_start: 0.8284 (m-30) cc_final: 0.8057 (t0) REVERT: Z 46 LYS cc_start: 0.7881 (mttt) cc_final: 0.7611 (mttt) REVERT: a 18 LYS cc_start: 0.8319 (tttt) cc_final: 0.7827 (mptt) REVERT: a 43 ARG cc_start: 0.8762 (ttp80) cc_final: 0.8544 (ttp80) REVERT: b 15 ASP cc_start: 0.8663 (m-30) cc_final: 0.8422 (m-30) REVERT: b 18 LYS cc_start: 0.8378 (tttt) cc_final: 0.7903 (mptt) REVERT: c 15 ASP cc_start: 0.8532 (m-30) cc_final: 0.8293 (m-30) REVERT: c 18 LYS cc_start: 0.8477 (tttt) cc_final: 0.8034 (mptt) REVERT: d 18 LYS cc_start: 0.8334 (tttt) cc_final: 0.7740 (mmtt) outliers start: 48 outliers final: 40 residues processed: 772 average time/residue: 0.2165 time to fit residues: 231.6208 Evaluate side-chains 763 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 723 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain d residue 9 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN R 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10980 Z= 0.228 Angle : 0.569 6.634 14940 Z= 0.291 Chirality : 0.042 0.143 1980 Planarity : 0.004 0.027 1740 Dihedral : 3.966 12.093 1440 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.82 % Allowed : 25.61 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.24), residues: 1350 helix: 1.37 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.46 (0.47), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 29 PHE 0.011 0.001 PHE Q 48 TYR 0.005 0.001 TYR X 9 ARG 0.004 0.000 ARG U 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 764 time to evaluate : 1.320 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 27 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8474 (mt0) REVERT: A 42 ILE cc_start: 0.8889 (tp) cc_final: 0.8483 (tt) REVERT: A 47 LYS cc_start: 0.9178 (tttt) cc_final: 0.8683 (tppt) REVERT: A 49 SER cc_start: 0.9047 (t) cc_final: 0.8714 (m) REVERT: A 51 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8676 (mtpt) REVERT: B 45 PHE cc_start: 0.9343 (t80) cc_final: 0.9030 (t80) REVERT: B 47 LYS cc_start: 0.8937 (tttt) cc_final: 0.8528 (mmtt) REVERT: B 51 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8713 (mtpt) REVERT: C 9 TYR cc_start: 0.7494 (m-80) cc_final: 0.7027 (m-80) REVERT: C 20 GLN cc_start: 0.9019 (tp40) cc_final: 0.8367 (mt0) REVERT: C 23 ASP cc_start: 0.8562 (t0) cc_final: 0.8130 (p0) REVERT: C 45 PHE cc_start: 0.9279 (t80) cc_final: 0.9018 (t80) REVERT: C 47 LYS cc_start: 0.9058 (tttt) cc_final: 0.8467 (tptt) REVERT: D 23 ASP cc_start: 0.8405 (m-30) cc_final: 0.8093 (m-30) REVERT: D 47 LYS cc_start: 0.9036 (tttt) cc_final: 0.8752 (tptt) REVERT: D 51 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8756 (mttt) REVERT: E 19 THR cc_start: 0.8712 (p) cc_final: 0.8327 (p) REVERT: E 20 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8392 (mm-40) REVERT: E 51 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8689 (mtpt) REVERT: F 8 ASN cc_start: 0.7938 (t0) cc_final: 0.7385 (m110) REVERT: F 42 ILE cc_start: 0.9282 (tt) cc_final: 0.9016 (tp) REVERT: F 51 LYS cc_start: 0.8987 (mtpp) cc_final: 0.8643 (mtpp) REVERT: G 51 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8669 (mtpp) REVERT: H 9 TYR cc_start: 0.7492 (m-80) cc_final: 0.7041 (m-80) REVERT: H 43 ARG cc_start: 0.8526 (mtp180) cc_final: 0.8110 (ttm170) REVERT: H 51 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8573 (mtpp) REVERT: I 27 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8176 (tp40) REVERT: I 42 ILE cc_start: 0.9363 (tt) cc_final: 0.9105 (tt) REVERT: I 50 SER cc_start: 0.8633 (t) cc_final: 0.8193 (p) REVERT: I 51 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8651 (mtpp) REVERT: J 23 ASP cc_start: 0.7791 (p0) cc_final: 0.7401 (p0) REVERT: J 27 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8530 (tp-100) REVERT: J 48 PHE cc_start: 0.9216 (m-80) cc_final: 0.8660 (m-80) REVERT: K 14 MET cc_start: 0.8724 (mmt) cc_final: 0.8294 (mmt) REVERT: K 18 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7854 (ttmm) REVERT: K 47 LYS cc_start: 0.8292 (tttt) cc_final: 0.7764 (ttmm) REVERT: K 50 SER cc_start: 0.8299 (t) cc_final: 0.7666 (p) REVERT: K 51 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8577 (mmmm) REVERT: L 14 MET cc_start: 0.8759 (mmt) cc_final: 0.8387 (mmt) REVERT: L 20 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8920 (mm-40) REVERT: L 47 LYS cc_start: 0.8464 (tttt) cc_final: 0.7847 (ttmm) REVERT: L 50 SER cc_start: 0.8436 (t) cc_final: 0.7925 (p) REVERT: L 51 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8472 (mmmm) REVERT: M 14 MET cc_start: 0.8378 (mmm) cc_final: 0.8152 (mmt) REVERT: M 15 ASP cc_start: 0.8521 (m-30) cc_final: 0.8264 (m-30) REVERT: M 27 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8638 (tp40) REVERT: M 47 LYS cc_start: 0.8399 (tttt) cc_final: 0.8189 (ttmm) REVERT: N 8 ASN cc_start: 0.7575 (t0) cc_final: 0.6976 (m-40) REVERT: N 18 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7795 (ttmm) REVERT: N 47 LYS cc_start: 0.8420 (tttt) cc_final: 0.7906 (ttmm) REVERT: N 50 SER cc_start: 0.8656 (t) cc_final: 0.8207 (p) REVERT: N 51 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8357 (mtpp) REVERT: O 8 ASN cc_start: 0.7702 (t0) cc_final: 0.7158 (t0) REVERT: O 14 MET cc_start: 0.8754 (mmm) cc_final: 0.8153 (mmt) REVERT: O 27 GLN cc_start: 0.8917 (tp40) cc_final: 0.8465 (tp40) REVERT: P 15 ASP cc_start: 0.8181 (m-30) cc_final: 0.7947 (m-30) REVERT: P 27 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8383 (tp40) REVERT: P 47 LYS cc_start: 0.8862 (tttt) cc_final: 0.8603 (ttmm) REVERT: Q 15 ASP cc_start: 0.8261 (m-30) cc_final: 0.7964 (m-30) REVERT: Q 27 GLN cc_start: 0.8860 (tp-100) cc_final: 0.8385 (tp40) REVERT: Q 40 LEU cc_start: 0.9268 (mt) cc_final: 0.9047 (mt) REVERT: S 15 ASP cc_start: 0.8221 (m-30) cc_final: 0.7891 (m-30) REVERT: T 15 ASP cc_start: 0.8356 (m-30) cc_final: 0.8122 (m-30) REVERT: T 27 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8416 (tp-100) REVERT: U 15 ASP cc_start: 0.8614 (m-30) cc_final: 0.8326 (m-30) REVERT: V 8 ASN cc_start: 0.6899 (t0) cc_final: 0.5971 (t0) REVERT: V 32 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8333 (p) REVERT: W 43 ARG cc_start: 0.8483 (ttm170) cc_final: 0.8221 (ttp80) REVERT: W 51 LYS cc_start: 0.8546 (mttp) cc_final: 0.8336 (mttp) REVERT: X 32 VAL cc_start: 0.8751 (t) cc_final: 0.8511 (p) REVERT: X 49 SER cc_start: 0.9075 (t) cc_final: 0.8649 (p) REVERT: Y 47 LYS cc_start: 0.8736 (tttm) cc_final: 0.8413 (ttmm) REVERT: Z 18 LYS cc_start: 0.8249 (tttt) cc_final: 0.7869 (mptt) REVERT: Z 23 ASP cc_start: 0.8379 (m-30) cc_final: 0.8168 (t0) REVERT: Z 46 LYS cc_start: 0.8095 (mttt) cc_final: 0.7757 (mtmt) REVERT: a 18 LYS cc_start: 0.8276 (tttt) cc_final: 0.7805 (mptt) REVERT: b 15 ASP cc_start: 0.8655 (m-30) cc_final: 0.8433 (m-30) REVERT: b 18 LYS cc_start: 0.8333 (tttt) cc_final: 0.7718 (mptt) REVERT: b 33 THR cc_start: 0.8351 (t) cc_final: 0.7952 (p) REVERT: c 11 THR cc_start: 0.8785 (p) cc_final: 0.8376 (p) REVERT: c 15 ASP cc_start: 0.8538 (m-30) cc_final: 0.8306 (m-30) REVERT: c 18 LYS cc_start: 0.8557 (tttt) cc_final: 0.8061 (mptt) REVERT: d 18 LYS cc_start: 0.8317 (tttt) cc_final: 0.7719 (mmtt) outliers start: 47 outliers final: 42 residues processed: 768 average time/residue: 0.2143 time to fit residues: 229.3643 Evaluate side-chains 777 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 734 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain d residue 9 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 0.0770 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN F 27 GLN R 27 GLN S 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10980 Z= 0.196 Angle : 0.555 6.192 14940 Z= 0.282 Chirality : 0.041 0.156 1980 Planarity : 0.004 0.027 1740 Dihedral : 3.894 11.112 1440 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.98 % Allowed : 27.15 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.24), residues: 1350 helix: 1.54 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.25 (0.38), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 29 PHE 0.017 0.001 PHE U 48 TYR 0.007 0.001 TYR L 9 ARG 0.003 0.000 ARG U 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 770 time to evaluate : 1.172 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 27 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8439 (mt0) REVERT: A 42 ILE cc_start: 0.9111 (tp) cc_final: 0.8698 (tt) REVERT: A 47 LYS cc_start: 0.9192 (tttt) cc_final: 0.8725 (tppt) REVERT: A 49 SER cc_start: 0.8978 (t) cc_final: 0.8678 (m) REVERT: A 51 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8707 (mtpt) REVERT: B 47 LYS cc_start: 0.8931 (tttt) cc_final: 0.8521 (mmtt) REVERT: B 51 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8690 (mtpt) REVERT: C 9 TYR cc_start: 0.7479 (m-80) cc_final: 0.7019 (m-80) REVERT: C 20 GLN cc_start: 0.8991 (tp40) cc_final: 0.8342 (mt0) REVERT: C 23 ASP cc_start: 0.8560 (t0) cc_final: 0.8178 (p0) REVERT: C 45 PHE cc_start: 0.9253 (t80) cc_final: 0.9013 (t80) REVERT: C 47 LYS cc_start: 0.9040 (tttt) cc_final: 0.8457 (tptt) REVERT: D 23 ASP cc_start: 0.8404 (m-30) cc_final: 0.8098 (m-30) REVERT: D 47 LYS cc_start: 0.8987 (tttt) cc_final: 0.8672 (tptt) REVERT: D 51 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8693 (mttt) REVERT: E 8 ASN cc_start: 0.8313 (t0) cc_final: 0.7813 (t0) REVERT: E 51 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8612 (mtpt) REVERT: F 8 ASN cc_start: 0.7801 (t0) cc_final: 0.7104 (m110) REVERT: F 9 TYR cc_start: 0.7757 (m-80) cc_final: 0.7326 (m-80) REVERT: F 42 ILE cc_start: 0.9229 (tt) cc_final: 0.8971 (tp) REVERT: F 51 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8686 (mtpp) REVERT: G 27 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8435 (mm-40) REVERT: G 51 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8666 (mtpp) REVERT: H 9 TYR cc_start: 0.7417 (m-80) cc_final: 0.7003 (m-80) REVERT: H 43 ARG cc_start: 0.8538 (mtp180) cc_final: 0.8103 (ttm170) REVERT: H 50 SER cc_start: 0.8487 (t) cc_final: 0.8228 (m) REVERT: H 51 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8546 (mtpp) REVERT: I 27 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8178 (tp40) REVERT: I 42 ILE cc_start: 0.9331 (tt) cc_final: 0.9083 (tt) REVERT: I 50 SER cc_start: 0.8643 (t) cc_final: 0.8198 (p) REVERT: I 51 LYS cc_start: 0.9016 (mmtm) cc_final: 0.8643 (mtpp) REVERT: J 23 ASP cc_start: 0.7811 (p0) cc_final: 0.7413 (p0) REVERT: J 27 GLN cc_start: 0.9043 (tp-100) cc_final: 0.8606 (tp-100) REVERT: J 48 PHE cc_start: 0.9182 (m-80) cc_final: 0.8612 (m-80) REVERT: K 14 MET cc_start: 0.8729 (mmt) cc_final: 0.8280 (mmt) REVERT: K 15 ASP cc_start: 0.8408 (m-30) cc_final: 0.8092 (m-30) REVERT: K 18 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7840 (ttmm) REVERT: K 47 LYS cc_start: 0.8278 (tttt) cc_final: 0.7752 (ttmm) REVERT: K 50 SER cc_start: 0.8465 (t) cc_final: 0.7799 (p) REVERT: K 51 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8591 (mmmm) REVERT: L 14 MET cc_start: 0.8739 (mmt) cc_final: 0.8412 (mmt) REVERT: L 20 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8923 (mm-40) REVERT: L 47 LYS cc_start: 0.8451 (tttt) cc_final: 0.7867 (ttmm) REVERT: L 50 SER cc_start: 0.8579 (t) cc_final: 0.8103 (p) REVERT: L 51 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8495 (mmmm) REVERT: M 14 MET cc_start: 0.8420 (mmm) cc_final: 0.8096 (mmt) REVERT: M 15 ASP cc_start: 0.8519 (m-30) cc_final: 0.8296 (m-30) REVERT: M 27 GLN cc_start: 0.9027 (tp-100) cc_final: 0.8660 (tp40) REVERT: N 8 ASN cc_start: 0.7380 (t0) cc_final: 0.7103 (m-40) REVERT: N 18 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7822 (ttmm) REVERT: N 47 LYS cc_start: 0.8389 (tttt) cc_final: 0.7947 (ttmm) REVERT: N 50 SER cc_start: 0.8643 (t) cc_final: 0.8199 (p) REVERT: N 51 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8026 (mtpp) REVERT: O 8 ASN cc_start: 0.7658 (t0) cc_final: 0.7294 (t0) REVERT: O 14 MET cc_start: 0.8711 (mmm) cc_final: 0.8340 (mmt) REVERT: P 15 ASP cc_start: 0.8173 (m-30) cc_final: 0.7946 (m-30) REVERT: P 27 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8371 (tp40) REVERT: P 47 LYS cc_start: 0.8847 (tttt) cc_final: 0.8596 (ttmm) REVERT: Q 15 ASP cc_start: 0.8247 (m-30) cc_final: 0.7995 (m-30) REVERT: Q 27 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8368 (tp40) REVERT: Q 42 ILE cc_start: 0.9300 (tt) cc_final: 0.9084 (tp) REVERT: S 15 ASP cc_start: 0.8181 (m-30) cc_final: 0.7801 (m-30) REVERT: S 51 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8617 (ttmm) REVERT: T 15 ASP cc_start: 0.8288 (m-30) cc_final: 0.8063 (m-30) REVERT: T 27 GLN cc_start: 0.8765 (tp-100) cc_final: 0.8444 (tp-100) REVERT: U 14 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8204 (ttm) REVERT: U 15 ASP cc_start: 0.8487 (m-30) cc_final: 0.8137 (m-30) REVERT: W 43 ARG cc_start: 0.8430 (ttm170) cc_final: 0.8182 (ttp80) REVERT: W 51 LYS cc_start: 0.8508 (mttp) cc_final: 0.8293 (mttp) REVERT: X 49 SER cc_start: 0.9136 (t) cc_final: 0.8718 (p) REVERT: Y 18 LYS cc_start: 0.8307 (ttmm) cc_final: 0.8040 (tttp) REVERT: Z 18 LYS cc_start: 0.8323 (tttt) cc_final: 0.7983 (mptt) REVERT: Z 46 LYS cc_start: 0.7895 (mttt) cc_final: 0.7634 (mtmt) REVERT: a 18 LYS cc_start: 0.8260 (tttt) cc_final: 0.7797 (mptt) REVERT: b 15 ASP cc_start: 0.8695 (m-30) cc_final: 0.8334 (m-30) REVERT: b 18 LYS cc_start: 0.8349 (tttt) cc_final: 0.7682 (mptt) REVERT: c 15 ASP cc_start: 0.8495 (m-30) cc_final: 0.8258 (m-30) REVERT: c 18 LYS cc_start: 0.8560 (tttt) cc_final: 0.7978 (mptt) REVERT: c 27 GLN cc_start: 0.8960 (mm110) cc_final: 0.8745 (mm-40) REVERT: c 48 PHE cc_start: 0.8808 (m-80) cc_final: 0.8532 (m-80) REVERT: d 18 LYS cc_start: 0.8261 (tttt) cc_final: 0.7708 (mptt) outliers start: 49 outliers final: 36 residues processed: 778 average time/residue: 0.2062 time to fit residues: 224.4055 Evaluate side-chains 770 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 732 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 14 MET Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain d residue 9 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN F 27 GLN I 8 ASN R 27 GLN S 27 GLN V 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10980 Z= 0.210 Angle : 0.569 7.096 14940 Z= 0.290 Chirality : 0.041 0.180 1980 Planarity : 0.004 0.026 1740 Dihedral : 3.873 11.430 1440 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.39 % Allowed : 28.78 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.24), residues: 1350 helix: 1.54 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.61 (0.36), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 29 PHE 0.020 0.001 PHE U 48 TYR 0.009 0.001 TYR L 9 ARG 0.004 0.000 ARG S 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 753 time to evaluate : 1.236 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 27 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8430 (mt0) REVERT: A 42 ILE cc_start: 0.9010 (tp) cc_final: 0.8596 (tt) REVERT: A 47 LYS cc_start: 0.9133 (tttt) cc_final: 0.8660 (tppt) REVERT: A 49 SER cc_start: 0.8910 (t) cc_final: 0.8599 (m) REVERT: A 51 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8710 (mtpt) REVERT: B 47 LYS cc_start: 0.8928 (tttt) cc_final: 0.8513 (mmtt) REVERT: B 51 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8776 (mtpt) REVERT: C 9 TYR cc_start: 0.7527 (m-80) cc_final: 0.7073 (m-80) REVERT: C 20 GLN cc_start: 0.8994 (tp40) cc_final: 0.8340 (mt0) REVERT: C 23 ASP cc_start: 0.8556 (t0) cc_final: 0.8189 (p0) REVERT: C 45 PHE cc_start: 0.9228 (t80) cc_final: 0.9018 (t80) REVERT: C 47 LYS cc_start: 0.9039 (tttt) cc_final: 0.8442 (tptt) REVERT: D 23 ASP cc_start: 0.8424 (m-30) cc_final: 0.8148 (m-30) REVERT: D 37 VAL cc_start: 0.9011 (p) cc_final: 0.8763 (m) REVERT: D 47 LYS cc_start: 0.8978 (tttt) cc_final: 0.8666 (tptt) REVERT: D 51 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8697 (mttt) REVERT: E 8 ASN cc_start: 0.8088 (t0) cc_final: 0.7508 (t0) REVERT: E 19 THR cc_start: 0.8647 (p) cc_final: 0.8048 (p) REVERT: E 51 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8632 (mtpt) REVERT: F 8 ASN cc_start: 0.7673 (t0) cc_final: 0.7044 (m110) REVERT: F 9 TYR cc_start: 0.7688 (m-80) cc_final: 0.7361 (m-80) REVERT: F 42 ILE cc_start: 0.9229 (tt) cc_final: 0.9026 (tp) REVERT: F 51 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8631 (mtpp) REVERT: G 27 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8582 (mm-40) REVERT: G 51 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8686 (mtpp) REVERT: H 9 TYR cc_start: 0.7679 (m-80) cc_final: 0.7029 (m-80) REVERT: H 43 ARG cc_start: 0.8520 (mtp180) cc_final: 0.8150 (ttm170) REVERT: H 51 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8514 (mtpp) REVERT: I 23 ASP cc_start: 0.8324 (t70) cc_final: 0.8049 (p0) REVERT: I 27 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8061 (tp40) REVERT: I 42 ILE cc_start: 0.9326 (tt) cc_final: 0.9060 (tt) REVERT: I 50 SER cc_start: 0.8732 (t) cc_final: 0.8291 (p) REVERT: I 51 LYS cc_start: 0.9010 (mmtm) cc_final: 0.8642 (mtpp) REVERT: J 12 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8284 (tm-30) REVERT: J 23 ASP cc_start: 0.7850 (p0) cc_final: 0.7527 (p0) REVERT: J 27 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8553 (tp-100) REVERT: K 14 MET cc_start: 0.8682 (mmt) cc_final: 0.8229 (mmt) REVERT: K 15 ASP cc_start: 0.8405 (m-30) cc_final: 0.8108 (m-30) REVERT: K 18 LYS cc_start: 0.8102 (ttmm) cc_final: 0.7830 (ttmm) REVERT: K 47 LYS cc_start: 0.8280 (tttt) cc_final: 0.7767 (ttmm) REVERT: K 50 SER cc_start: 0.8559 (t) cc_final: 0.7935 (p) REVERT: K 51 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8546 (mmmt) REVERT: L 14 MET cc_start: 0.8737 (mmt) cc_final: 0.8395 (mmt) REVERT: L 20 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8941 (mm-40) REVERT: L 47 LYS cc_start: 0.8460 (tttt) cc_final: 0.7870 (ttmm) REVERT: L 50 SER cc_start: 0.8603 (t) cc_final: 0.8111 (p) REVERT: L 51 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8555 (mmmm) REVERT: M 14 MET cc_start: 0.8434 (mmm) cc_final: 0.8128 (mmt) REVERT: M 15 ASP cc_start: 0.8489 (m-30) cc_final: 0.8279 (m-30) REVERT: M 27 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8642 (tp40) REVERT: M 51 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8897 (mtpp) REVERT: N 8 ASN cc_start: 0.7384 (t0) cc_final: 0.7099 (m-40) REVERT: N 18 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7829 (ttmm) REVERT: N 43 ARG cc_start: 0.8284 (ttp80) cc_final: 0.8078 (ttp-170) REVERT: N 47 LYS cc_start: 0.8388 (tttt) cc_final: 0.7901 (ttmm) REVERT: N 50 SER cc_start: 0.8648 (t) cc_final: 0.8201 (p) REVERT: N 51 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8367 (mtpp) REVERT: O 14 MET cc_start: 0.8623 (mmm) cc_final: 0.8325 (mmt) REVERT: P 15 ASP cc_start: 0.8175 (m-30) cc_final: 0.7929 (m-30) REVERT: P 27 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8447 (tp40) REVERT: P 47 LYS cc_start: 0.8847 (tttt) cc_final: 0.8591 (ttmm) REVERT: Q 15 ASP cc_start: 0.8302 (m-30) cc_final: 0.7997 (m-30) REVERT: Q 27 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8443 (tp40) REVERT: Q 42 ILE cc_start: 0.9306 (tt) cc_final: 0.9075 (tp) REVERT: S 15 ASP cc_start: 0.8185 (m-30) cc_final: 0.7801 (m-30) REVERT: S 51 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8586 (ttmm) REVERT: T 15 ASP cc_start: 0.8282 (m-30) cc_final: 0.8041 (m-30) REVERT: T 27 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8510 (tp-100) REVERT: U 8 ASN cc_start: 0.6759 (t0) cc_final: 0.5727 (t0) REVERT: U 14 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8208 (ttm) REVERT: U 15 ASP cc_start: 0.8656 (m-30) cc_final: 0.8333 (m-30) REVERT: W 18 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8174 (ttmm) REVERT: W 43 ARG cc_start: 0.8427 (ttm170) cc_final: 0.8172 (ttp80) REVERT: W 51 LYS cc_start: 0.8517 (mttp) cc_final: 0.8303 (mttp) REVERT: X 49 SER cc_start: 0.9167 (t) cc_final: 0.8712 (p) REVERT: Z 18 LYS cc_start: 0.8265 (tttt) cc_final: 0.7912 (mptt) REVERT: Z 46 LYS cc_start: 0.7836 (mttt) cc_final: 0.7607 (mtmt) REVERT: Z 47 LYS cc_start: 0.8828 (ttmm) cc_final: 0.8521 (tttm) REVERT: a 18 LYS cc_start: 0.8252 (tttt) cc_final: 0.7795 (mptt) REVERT: b 15 ASP cc_start: 0.8681 (m-30) cc_final: 0.8337 (m-30) REVERT: b 18 LYS cc_start: 0.8616 (tttt) cc_final: 0.7881 (mptt) REVERT: c 15 ASP cc_start: 0.8505 (m-30) cc_final: 0.8279 (m-30) REVERT: c 18 LYS cc_start: 0.8567 (tttt) cc_final: 0.7923 (mptt) REVERT: c 48 PHE cc_start: 0.8833 (m-80) cc_final: 0.8547 (m-80) REVERT: d 18 LYS cc_start: 0.8241 (tttt) cc_final: 0.7676 (mptt) outliers start: 54 outliers final: 41 residues processed: 762 average time/residue: 0.2120 time to fit residues: 225.5432 Evaluate side-chains 767 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 724 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 14 MET Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 50 SER Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN O 8 ASN R 27 GLN S 27 GLN V 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10980 Z= 0.215 Angle : 0.587 6.589 14940 Z= 0.300 Chirality : 0.042 0.185 1980 Planarity : 0.004 0.026 1740 Dihedral : 3.892 11.306 1440 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 3.98 % Allowed : 30.33 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.24), residues: 1350 helix: 1.56 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.69 (0.41), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 29 PHE 0.018 0.001 PHE U 48 TYR 0.009 0.001 TYR O 9 ARG 0.002 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 748 time to evaluate : 1.337 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: A 27 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8431 (mt0) REVERT: A 42 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8577 (tt) REVERT: A 47 LYS cc_start: 0.9129 (tttt) cc_final: 0.8655 (tppt) REVERT: A 49 SER cc_start: 0.8938 (t) cc_final: 0.8647 (m) REVERT: A 51 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8726 (mtpt) REVERT: B 42 ILE cc_start: 0.9299 (tt) cc_final: 0.8962 (tp) REVERT: B 47 LYS cc_start: 0.8927 (tttt) cc_final: 0.8519 (mmtt) REVERT: B 51 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8803 (mttt) REVERT: C 9 TYR cc_start: 0.7518 (m-80) cc_final: 0.7041 (m-80) REVERT: C 20 GLN cc_start: 0.9003 (tp40) cc_final: 0.8345 (mt0) REVERT: C 23 ASP cc_start: 0.8566 (t0) cc_final: 0.8195 (p0) REVERT: C 45 PHE cc_start: 0.9236 (t80) cc_final: 0.9021 (t80) REVERT: C 47 LYS cc_start: 0.9020 (tttt) cc_final: 0.8406 (tptt) REVERT: D 23 ASP cc_start: 0.8420 (m-30) cc_final: 0.8137 (m-30) REVERT: D 37 VAL cc_start: 0.8928 (p) cc_final: 0.8701 (m) REVERT: D 47 LYS cc_start: 0.8969 (tttt) cc_final: 0.8706 (tptt) REVERT: D 51 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8692 (mttt) REVERT: E 8 ASN cc_start: 0.8105 (t0) cc_final: 0.7565 (t0) REVERT: E 46 LYS cc_start: 0.8504 (mttm) cc_final: 0.8265 (mttp) REVERT: E 47 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7693 (ttpt) REVERT: E 51 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8648 (mttt) REVERT: F 9 TYR cc_start: 0.7677 (m-80) cc_final: 0.7393 (m-80) REVERT: F 42 ILE cc_start: 0.9233 (tt) cc_final: 0.8935 (tp) REVERT: F 51 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8677 (mtpp) REVERT: G 27 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8420 (mm-40) REVERT: G 51 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8686 (mtpp) REVERT: H 9 TYR cc_start: 0.7419 (m-80) cc_final: 0.6868 (m-80) REVERT: H 43 ARG cc_start: 0.8519 (mtp180) cc_final: 0.8063 (ttm170) REVERT: H 51 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8513 (mtpp) REVERT: I 23 ASP cc_start: 0.8516 (t70) cc_final: 0.8087 (p0) REVERT: I 27 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8081 (tp-100) REVERT: I 42 ILE cc_start: 0.9306 (tt) cc_final: 0.9036 (tt) REVERT: I 50 SER cc_start: 0.8736 (t) cc_final: 0.8278 (p) REVERT: I 51 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8621 (mtpp) REVERT: J 12 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8283 (tm-30) REVERT: J 23 ASP cc_start: 0.7848 (p0) cc_final: 0.7522 (p0) REVERT: J 27 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8508 (tp-100) REVERT: K 14 MET cc_start: 0.8672 (mmt) cc_final: 0.8220 (mmt) REVERT: K 15 ASP cc_start: 0.8417 (m-30) cc_final: 0.8117 (m-30) REVERT: K 18 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7831 (ttmm) REVERT: K 47 LYS cc_start: 0.8248 (tttt) cc_final: 0.7772 (ttmm) REVERT: K 50 SER cc_start: 0.8560 (t) cc_final: 0.7928 (p) REVERT: K 51 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8543 (mmmt) REVERT: L 14 MET cc_start: 0.8764 (mmt) cc_final: 0.8285 (mmt) REVERT: L 20 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8908 (mm-40) REVERT: L 47 LYS cc_start: 0.8422 (tttt) cc_final: 0.7845 (ttmm) REVERT: L 50 SER cc_start: 0.8834 (t) cc_final: 0.8347 (p) REVERT: L 51 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8493 (mmmm) REVERT: M 15 ASP cc_start: 0.8550 (m-30) cc_final: 0.8260 (m-30) REVERT: M 27 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8676 (tp40) REVERT: M 47 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8165 (ttmm) REVERT: M 50 SER cc_start: 0.8665 (t) cc_final: 0.8250 (p) REVERT: M 51 LYS cc_start: 0.9080 (mtpp) cc_final: 0.8772 (mtpp) REVERT: N 8 ASN cc_start: 0.7339 (t0) cc_final: 0.6937 (m-40) REVERT: N 18 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7802 (ttmm) REVERT: N 47 LYS cc_start: 0.8344 (tttt) cc_final: 0.7854 (ttmm) REVERT: N 50 SER cc_start: 0.8647 (t) cc_final: 0.8208 (p) REVERT: N 51 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8382 (mtpp) REVERT: O 14 MET cc_start: 0.8606 (mmm) cc_final: 0.8287 (mmt) REVERT: P 15 ASP cc_start: 0.8125 (m-30) cc_final: 0.7875 (m-30) REVERT: P 27 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8429 (tp40) REVERT: P 47 LYS cc_start: 0.8785 (tttt) cc_final: 0.8539 (ttmm) REVERT: Q 15 ASP cc_start: 0.8305 (m-30) cc_final: 0.8012 (m-30) REVERT: Q 27 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8507 (tp40) REVERT: S 15 ASP cc_start: 0.8177 (m-30) cc_final: 0.7806 (m-30) REVERT: S 51 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8591 (ttmm) REVERT: T 27 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8554 (tp-100) REVERT: T 48 PHE cc_start: 0.9208 (m-80) cc_final: 0.8916 (m-80) REVERT: U 8 ASN cc_start: 0.6123 (t0) cc_final: 0.5574 (t0) REVERT: U 15 ASP cc_start: 0.8634 (m-30) cc_final: 0.8244 (m-30) REVERT: W 18 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8134 (ttmm) REVERT: W 43 ARG cc_start: 0.8470 (ttm170) cc_final: 0.8177 (ttp80) REVERT: W 51 LYS cc_start: 0.8520 (mttp) cc_final: 0.8305 (mttp) REVERT: X 49 SER cc_start: 0.9221 (t) cc_final: 0.8738 (p) REVERT: X 51 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8260 (ttmm) REVERT: Z 18 LYS cc_start: 0.8268 (tttt) cc_final: 0.7912 (mptt) REVERT: Z 46 LYS cc_start: 0.8007 (mttt) cc_final: 0.7719 (mtmt) REVERT: Z 47 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8549 (tttm) REVERT: a 18 LYS cc_start: 0.8227 (tttt) cc_final: 0.7788 (mptt) REVERT: b 18 LYS cc_start: 0.8600 (tttt) cc_final: 0.7857 (mptt) REVERT: b 51 LYS cc_start: 0.8432 (mttm) cc_final: 0.8227 (mttm) REVERT: c 15 ASP cc_start: 0.8484 (m-30) cc_final: 0.8276 (m-30) REVERT: c 18 LYS cc_start: 0.8562 (tttt) cc_final: 0.7922 (mptt) REVERT: d 18 LYS cc_start: 0.8179 (tttt) cc_final: 0.7630 (mptt) REVERT: d 51 LYS cc_start: 0.8484 (mptt) cc_final: 0.8247 (mptt) outliers start: 49 outliers final: 39 residues processed: 755 average time/residue: 0.2129 time to fit residues: 223.1980 Evaluate side-chains 765 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 724 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 44 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 44 LEU Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN F 8 ASN F 27 GLN O 8 ASN R 27 GLN S 27 GLN V 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10980 Z= 0.207 Angle : 0.596 6.799 14940 Z= 0.304 Chirality : 0.042 0.178 1980 Planarity : 0.004 0.026 1740 Dihedral : 3.907 11.794 1440 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 3.90 % Allowed : 31.30 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.24), residues: 1350 helix: 1.57 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.93 (0.41), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 29 PHE 0.019 0.001 PHE U 48 TYR 0.008 0.001 TYR O 9 ARG 0.003 0.000 ARG F 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 753 time to evaluate : 1.259 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: A 27 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8407 (mt0) REVERT: A 42 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8570 (tt) REVERT: A 47 LYS cc_start: 0.9116 (tttt) cc_final: 0.8627 (tppt) REVERT: A 49 SER cc_start: 0.8926 (t) cc_final: 0.8635 (m) REVERT: A 51 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8723 (mtpt) REVERT: B 12 GLU cc_start: 0.7559 (mp0) cc_final: 0.7348 (mp0) REVERT: B 27 GLN cc_start: 0.8800 (tp-100) cc_final: 0.8173 (tt0) REVERT: B 42 ILE cc_start: 0.9311 (tt) cc_final: 0.8940 (tp) REVERT: B 47 LYS cc_start: 0.8899 (tttt) cc_final: 0.8488 (mmtt) REVERT: B 51 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8775 (mttt) REVERT: C 9 TYR cc_start: 0.7522 (m-80) cc_final: 0.7043 (m-80) REVERT: C 20 GLN cc_start: 0.8980 (tp40) cc_final: 0.8329 (mt0) REVERT: C 23 ASP cc_start: 0.8559 (t0) cc_final: 0.8192 (p0) REVERT: C 47 LYS cc_start: 0.9004 (tttt) cc_final: 0.8402 (tptt) REVERT: D 23 ASP cc_start: 0.8413 (m-30) cc_final: 0.8143 (m-30) REVERT: D 37 VAL cc_start: 0.8982 (p) cc_final: 0.8734 (m) REVERT: D 47 LYS cc_start: 0.8980 (tttt) cc_final: 0.8719 (tptt) REVERT: D 51 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8729 (mttt) REVERT: E 8 ASN cc_start: 0.8263 (t0) cc_final: 0.7725 (t0) REVERT: E 47 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7690 (ttpt) REVERT: E 51 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8669 (mttt) REVERT: F 9 TYR cc_start: 0.7726 (m-80) cc_final: 0.7443 (m-80) REVERT: F 42 ILE cc_start: 0.9243 (tt) cc_final: 0.8939 (tp) REVERT: F 51 LYS cc_start: 0.8921 (mtpp) cc_final: 0.8711 (mtpp) REVERT: G 27 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8394 (mm-40) REVERT: G 49 SER cc_start: 0.8822 (p) cc_final: 0.8503 (p) REVERT: G 51 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8686 (mtpp) REVERT: H 9 TYR cc_start: 0.7321 (m-80) cc_final: 0.6891 (m-80) REVERT: H 43 ARG cc_start: 0.8516 (mtp180) cc_final: 0.8022 (ttm170) REVERT: H 48 PHE cc_start: 0.9080 (m-80) cc_final: 0.8880 (m-80) REVERT: H 51 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8483 (mtpp) REVERT: I 19 THR cc_start: 0.9130 (t) cc_final: 0.8925 (p) REVERT: I 42 ILE cc_start: 0.9327 (tt) cc_final: 0.8934 (tt) REVERT: I 50 SER cc_start: 0.8740 (t) cc_final: 0.8284 (p) REVERT: I 51 LYS cc_start: 0.8972 (mmtm) cc_final: 0.8629 (mtpp) REVERT: J 23 ASP cc_start: 0.7893 (p0) cc_final: 0.7559 (p0) REVERT: J 27 GLN cc_start: 0.8934 (tp-100) cc_final: 0.8463 (tp-100) REVERT: K 14 MET cc_start: 0.8640 (mmt) cc_final: 0.8206 (mmt) REVERT: K 15 ASP cc_start: 0.8430 (m-30) cc_final: 0.8135 (m-30) REVERT: K 18 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7830 (ttmm) REVERT: K 43 ARG cc_start: 0.8597 (mtp180) cc_final: 0.7997 (ttm170) REVERT: K 47 LYS cc_start: 0.8246 (tttt) cc_final: 0.7771 (ttmm) REVERT: K 50 SER cc_start: 0.8631 (t) cc_final: 0.7987 (p) REVERT: K 51 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8549 (mmmt) REVERT: L 14 MET cc_start: 0.8689 (mmt) cc_final: 0.8241 (mmt) REVERT: L 20 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8943 (mm-40) REVERT: L 47 LYS cc_start: 0.8406 (tttt) cc_final: 0.7840 (ttmm) REVERT: L 50 SER cc_start: 0.8830 (t) cc_final: 0.8337 (p) REVERT: L 51 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8470 (mmmm) REVERT: M 14 MET cc_start: 0.8325 (mmm) cc_final: 0.7925 (mmt) REVERT: M 15 ASP cc_start: 0.8500 (m-30) cc_final: 0.8257 (m-30) REVERT: M 27 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8706 (tp40) REVERT: N 8 ASN cc_start: 0.7424 (t0) cc_final: 0.7056 (m-40) REVERT: N 18 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7803 (ttmm) REVERT: N 47 LYS cc_start: 0.8293 (tttt) cc_final: 0.7924 (ttmm) REVERT: N 50 SER cc_start: 0.8641 (t) cc_final: 0.8215 (p) REVERT: N 51 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8109 (mtpp) REVERT: O 14 MET cc_start: 0.8574 (mmm) cc_final: 0.8240 (mmt) REVERT: O 51 LYS cc_start: 0.9209 (mtpp) cc_final: 0.8815 (mtpt) REVERT: P 15 ASP cc_start: 0.8124 (m-30) cc_final: 0.7861 (m-30) REVERT: P 27 GLN cc_start: 0.8900 (tp-100) cc_final: 0.8428 (tp40) REVERT: P 47 LYS cc_start: 0.8793 (tttt) cc_final: 0.8576 (ttmm) REVERT: Q 15 ASP cc_start: 0.8305 (m-30) cc_final: 0.8026 (m-30) REVERT: Q 27 GLN cc_start: 0.8885 (tp-100) cc_final: 0.8488 (tp40) REVERT: S 15 ASP cc_start: 0.8179 (m-30) cc_final: 0.7785 (m-30) REVERT: S 51 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8490 (ttmm) REVERT: T 27 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8563 (tp-100) REVERT: T 48 PHE cc_start: 0.9228 (m-80) cc_final: 0.8888 (m-80) REVERT: U 15 ASP cc_start: 0.8692 (m-30) cc_final: 0.8282 (m-30) REVERT: W 8 ASN cc_start: 0.6413 (t0) cc_final: 0.5753 (t0) REVERT: W 18 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8182 (ttmm) REVERT: W 43 ARG cc_start: 0.8467 (ttm170) cc_final: 0.8181 (ttp80) REVERT: X 47 LYS cc_start: 0.8806 (tttm) cc_final: 0.8531 (ttmm) REVERT: X 49 SER cc_start: 0.9223 (t) cc_final: 0.8747 (p) REVERT: X 51 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8223 (ttmm) REVERT: Z 18 LYS cc_start: 0.8299 (tttt) cc_final: 0.7942 (mptt) REVERT: Z 28 THR cc_start: 0.9169 (m) cc_final: 0.8771 (p) REVERT: Z 46 LYS cc_start: 0.8001 (mttt) cc_final: 0.7714 (mtmt) REVERT: a 18 LYS cc_start: 0.8211 (tttt) cc_final: 0.7786 (mptt) REVERT: b 18 LYS cc_start: 0.8576 (tttt) cc_final: 0.7801 (mptt) REVERT: b 51 LYS cc_start: 0.8193 (mttm) cc_final: 0.7980 (mttm) REVERT: c 15 ASP cc_start: 0.8480 (m-30) cc_final: 0.8278 (m-30) REVERT: c 18 LYS cc_start: 0.8573 (tttt) cc_final: 0.7951 (mptt) REVERT: d 18 LYS cc_start: 0.8331 (tttt) cc_final: 0.7770 (mptt) REVERT: d 51 LYS cc_start: 0.8460 (mptt) cc_final: 0.8216 (mptt) outliers start: 48 outliers final: 34 residues processed: 761 average time/residue: 0.2240 time to fit residues: 237.7393 Evaluate side-chains 769 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 733 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 44 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 50 SER Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 GLN F 8 ASN F 27 GLN O 8 ASN R 27 GLN S 27 GLN V 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10980 Z= 0.254 Angle : 0.621 6.691 14940 Z= 0.319 Chirality : 0.044 0.186 1980 Planarity : 0.004 0.026 1740 Dihedral : 3.996 12.686 1440 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 3.33 % Allowed : 32.76 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.24), residues: 1350 helix: 1.50 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 4.24 (0.43), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 29 PHE 0.023 0.002 PHE c 48 TYR 0.009 0.001 TYR X 9 ARG 0.006 0.000 ARG F 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 718 time to evaluate : 1.357 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 27 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8439 (mt0) REVERT: A 42 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8545 (tt) REVERT: A 47 LYS cc_start: 0.9097 (tttt) cc_final: 0.8626 (tppt) REVERT: A 49 SER cc_start: 0.8914 (t) cc_final: 0.8626 (m) REVERT: A 51 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8732 (mtpt) REVERT: B 42 ILE cc_start: 0.9308 (tt) cc_final: 0.8951 (tp) REVERT: B 47 LYS cc_start: 0.8873 (tttt) cc_final: 0.8468 (mmtt) REVERT: B 51 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8780 (mttt) REVERT: C 9 TYR cc_start: 0.7572 (m-80) cc_final: 0.7064 (m-80) REVERT: C 20 GLN cc_start: 0.9024 (tp40) cc_final: 0.8357 (mt0) REVERT: C 23 ASP cc_start: 0.8569 (t0) cc_final: 0.8195 (p0) REVERT: C 47 LYS cc_start: 0.9013 (tttt) cc_final: 0.8409 (tptt) REVERT: D 23 ASP cc_start: 0.8422 (m-30) cc_final: 0.8173 (m-30) REVERT: D 37 VAL cc_start: 0.9025 (p) cc_final: 0.8776 (m) REVERT: D 47 LYS cc_start: 0.8987 (tttt) cc_final: 0.8622 (tptt) REVERT: D 51 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8744 (mttt) REVERT: E 8 ASN cc_start: 0.8243 (t0) cc_final: 0.7708 (t0) REVERT: E 47 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7689 (ttpt) REVERT: E 51 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8652 (mttt) REVERT: F 9 TYR cc_start: 0.7740 (m-80) cc_final: 0.7354 (m-80) REVERT: F 51 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8706 (mtpp) REVERT: G 27 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8367 (mm-40) REVERT: G 49 SER cc_start: 0.8831 (p) cc_final: 0.8513 (p) REVERT: G 51 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8690 (mtpp) REVERT: H 9 TYR cc_start: 0.7319 (m-80) cc_final: 0.6900 (m-80) REVERT: H 43 ARG cc_start: 0.8503 (mtp180) cc_final: 0.7972 (ttm170) REVERT: H 51 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8514 (mtpp) REVERT: I 27 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8488 (mm-40) REVERT: I 42 ILE cc_start: 0.9358 (tt) cc_final: 0.9098 (tt) REVERT: I 50 SER cc_start: 0.8758 (t) cc_final: 0.8307 (p) REVERT: I 51 LYS cc_start: 0.9009 (mmtm) cc_final: 0.8672 (mtpp) REVERT: J 23 ASP cc_start: 0.7904 (p0) cc_final: 0.7582 (p0) REVERT: J 27 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8533 (tp-100) REVERT: K 14 MET cc_start: 0.8640 (mmt) cc_final: 0.8209 (mmt) REVERT: K 15 ASP cc_start: 0.8420 (m-30) cc_final: 0.8193 (m-30) REVERT: K 18 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7826 (ttmm) REVERT: K 47 LYS cc_start: 0.8251 (tttt) cc_final: 0.7770 (ttmm) REVERT: K 50 SER cc_start: 0.8553 (t) cc_final: 0.8026 (p) REVERT: K 51 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8566 (mmmt) REVERT: L 20 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8935 (mm-40) REVERT: L 47 LYS cc_start: 0.8411 (tttt) cc_final: 0.7846 (ttmm) REVERT: L 50 SER cc_start: 0.8847 (t) cc_final: 0.8365 (p) REVERT: L 51 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8529 (mmmm) REVERT: M 14 MET cc_start: 0.8315 (mmm) cc_final: 0.7865 (mmt) REVERT: M 15 ASP cc_start: 0.8481 (m-30) cc_final: 0.8250 (m-30) REVERT: M 27 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8702 (tp40) REVERT: N 18 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7782 (ttmm) REVERT: N 47 LYS cc_start: 0.8311 (tttt) cc_final: 0.7840 (ttmm) REVERT: N 50 SER cc_start: 0.8654 (t) cc_final: 0.8224 (p) REVERT: N 51 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8391 (mtpp) REVERT: O 14 MET cc_start: 0.8641 (mmm) cc_final: 0.8122 (mmt) REVERT: P 15 ASP cc_start: 0.8197 (m-30) cc_final: 0.7926 (m-30) REVERT: P 47 LYS cc_start: 0.8796 (tttt) cc_final: 0.8571 (ttmm) REVERT: Q 15 ASP cc_start: 0.8154 (m-30) cc_final: 0.7847 (m-30) REVERT: Q 27 GLN cc_start: 0.8877 (tp-100) cc_final: 0.8653 (tp40) REVERT: S 15 ASP cc_start: 0.8203 (m-30) cc_final: 0.7808 (m-30) REVERT: S 51 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8554 (ttmm) REVERT: T 27 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8496 (tp-100) REVERT: U 15 ASP cc_start: 0.8709 (m-30) cc_final: 0.8293 (m-30) REVERT: W 8 ASN cc_start: 0.6392 (t0) cc_final: 0.5373 (t0) REVERT: W 18 LYS cc_start: 0.8490 (ttpt) cc_final: 0.8162 (ttmm) REVERT: W 49 SER cc_start: 0.9052 (m) cc_final: 0.8753 (p) REVERT: X 9 TYR cc_start: 0.7513 (m-80) cc_final: 0.7302 (m-80) REVERT: X 47 LYS cc_start: 0.8843 (tttm) cc_final: 0.8589 (ttmm) REVERT: X 49 SER cc_start: 0.9194 (t) cc_final: 0.8697 (p) REVERT: X 51 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8199 (ttmm) REVERT: Z 18 LYS cc_start: 0.8309 (tttt) cc_final: 0.7946 (mptt) REVERT: Z 28 THR cc_start: 0.9091 (m) cc_final: 0.8705 (p) REVERT: Z 46 LYS cc_start: 0.7919 (mttt) cc_final: 0.7578 (mtmt) REVERT: a 18 LYS cc_start: 0.8197 (tttt) cc_final: 0.7772 (mptt) REVERT: b 18 LYS cc_start: 0.8567 (tttt) cc_final: 0.7789 (mptt) REVERT: b 51 LYS cc_start: 0.8210 (mttm) cc_final: 0.7999 (mttm) REVERT: c 18 LYS cc_start: 0.8563 (tttt) cc_final: 0.7935 (mptt) REVERT: d 18 LYS cc_start: 0.8364 (tttt) cc_final: 0.7773 (mptt) REVERT: d 51 LYS cc_start: 0.8457 (mptt) cc_final: 0.8226 (mptt) outliers start: 41 outliers final: 35 residues processed: 725 average time/residue: 0.2179 time to fit residues: 219.3062 Evaluate side-chains 748 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 711 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 44 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 50 SER Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 0.0060 chunk 101 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 8 ASN F 27 GLN N 8 ASN O 8 ASN R 27 GLN S 27 GLN V 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10980 Z= 0.202 Angle : 0.624 7.484 14940 Z= 0.320 Chirality : 0.043 0.185 1980 Planarity : 0.004 0.030 1740 Dihedral : 4.010 12.627 1440 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 3.01 % Allowed : 33.66 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.24), residues: 1350 helix: 1.46 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 4.23 (0.46), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 29 PHE 0.021 0.001 PHE c 48 TYR 0.008 0.001 TYR X 9 ARG 0.003 0.000 ARG c 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 753 time to evaluate : 1.587 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: A 27 GLN cc_start: 0.8983 (tp-100) cc_final: 0.8437 (mt0) REVERT: A 37 VAL cc_start: 0.9074 (t) cc_final: 0.8725 (m) REVERT: A 42 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8544 (tt) REVERT: A 47 LYS cc_start: 0.9067 (tttt) cc_final: 0.8599 (tppt) REVERT: A 49 SER cc_start: 0.8897 (t) cc_final: 0.8614 (m) REVERT: A 51 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8722 (mtpt) REVERT: B 27 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8193 (tt0) REVERT: B 42 ILE cc_start: 0.9274 (tt) cc_final: 0.8917 (tp) REVERT: B 47 LYS cc_start: 0.8864 (tttt) cc_final: 0.8455 (mmtt) REVERT: B 51 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8775 (mttt) REVERT: C 9 TYR cc_start: 0.7529 (m-80) cc_final: 0.7048 (m-80) REVERT: C 20 GLN cc_start: 0.8976 (tp40) cc_final: 0.8323 (mt0) REVERT: C 23 ASP cc_start: 0.8563 (t0) cc_final: 0.8189 (p0) REVERT: C 47 LYS cc_start: 0.8998 (tttt) cc_final: 0.8398 (tptt) REVERT: D 23 ASP cc_start: 0.8404 (m-30) cc_final: 0.8154 (m-30) REVERT: D 37 VAL cc_start: 0.8981 (p) cc_final: 0.8723 (m) REVERT: D 47 LYS cc_start: 0.8978 (tttt) cc_final: 0.8668 (tptt) REVERT: D 51 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8727 (mttt) REVERT: E 8 ASN cc_start: 0.8189 (t0) cc_final: 0.7656 (t0) REVERT: E 47 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7633 (ttpp) REVERT: E 51 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8649 (mttt) REVERT: F 9 TYR cc_start: 0.7682 (m-80) cc_final: 0.7372 (m-80) REVERT: F 51 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8771 (mtpp) REVERT: G 27 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8364 (mm-40) REVERT: G 49 SER cc_start: 0.8800 (p) cc_final: 0.8467 (p) REVERT: G 51 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8666 (mtpp) REVERT: H 9 TYR cc_start: 0.7315 (m-80) cc_final: 0.6964 (m-80) REVERT: H 43 ARG cc_start: 0.8560 (mtp180) cc_final: 0.8136 (ttm170) REVERT: H 51 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8510 (mtpp) REVERT: I 42 ILE cc_start: 0.9335 (tt) cc_final: 0.8983 (tt) REVERT: I 50 SER cc_start: 0.8755 (t) cc_final: 0.8301 (p) REVERT: I 51 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8661 (mtpp) REVERT: J 23 ASP cc_start: 0.7904 (p0) cc_final: 0.7578 (p0) REVERT: J 27 GLN cc_start: 0.8917 (tp-100) cc_final: 0.8441 (tp-100) REVERT: K 14 MET cc_start: 0.8640 (mmt) cc_final: 0.8201 (mmt) REVERT: K 15 ASP cc_start: 0.8473 (m-30) cc_final: 0.8176 (m-30) REVERT: K 18 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7837 (ttmm) REVERT: K 43 ARG cc_start: 0.8579 (mtp180) cc_final: 0.8038 (ttm170) REVERT: K 47 LYS cc_start: 0.8233 (tttt) cc_final: 0.7771 (ttmm) REVERT: K 50 SER cc_start: 0.8643 (t) cc_final: 0.8126 (p) REVERT: K 51 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8577 (mmmt) REVERT: L 14 MET cc_start: 0.8654 (mmt) cc_final: 0.8185 (mmm) REVERT: L 20 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8923 (mm-40) REVERT: L 47 LYS cc_start: 0.8392 (tttt) cc_final: 0.7829 (ttmm) REVERT: L 50 SER cc_start: 0.8836 (t) cc_final: 0.8329 (p) REVERT: L 51 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8478 (mmmm) REVERT: M 14 MET cc_start: 0.8201 (mmm) cc_final: 0.7863 (mmt) REVERT: M 27 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8667 (tp40) REVERT: N 8 ASN cc_start: 0.7188 (OUTLIER) cc_final: 0.6906 (m-40) REVERT: N 18 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7778 (ttmm) REVERT: N 47 LYS cc_start: 0.8218 (tttt) cc_final: 0.8007 (ttmm) REVERT: O 14 MET cc_start: 0.8623 (mmm) cc_final: 0.8084 (mmt) REVERT: O 51 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8755 (mtpp) REVERT: P 15 ASP cc_start: 0.8172 (m-30) cc_final: 0.7899 (m-30) REVERT: P 27 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8596 (tp40) REVERT: Q 15 ASP cc_start: 0.8051 (m-30) cc_final: 0.7644 (m-30) REVERT: Q 27 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8491 (tp40) REVERT: S 15 ASP cc_start: 0.8165 (m-30) cc_final: 0.7759 (m-30) REVERT: S 27 GLN cc_start: 0.8810 (tp40) cc_final: 0.8572 (tp40) REVERT: S 51 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8486 (ttmm) REVERT: T 27 GLN cc_start: 0.8925 (tp-100) cc_final: 0.8486 (tp40) REVERT: U 15 ASP cc_start: 0.8713 (m-30) cc_final: 0.8359 (m-30) REVERT: W 18 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8097 (ttmm) REVERT: W 43 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8171 (ttp80) REVERT: W 49 SER cc_start: 0.9036 (m) cc_final: 0.8721 (p) REVERT: X 47 LYS cc_start: 0.8841 (tttm) cc_final: 0.8553 (ttmm) REVERT: X 49 SER cc_start: 0.9163 (t) cc_final: 0.8703 (p) REVERT: X 51 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8224 (ttmm) REVERT: Z 18 LYS cc_start: 0.8263 (tttt) cc_final: 0.7897 (mptt) REVERT: Z 28 THR cc_start: 0.9080 (m) cc_final: 0.8669 (p) REVERT: Z 46 LYS cc_start: 0.8025 (mttt) cc_final: 0.7668 (mtmt) REVERT: a 18 LYS cc_start: 0.8210 (tttt) cc_final: 0.7772 (mptt) REVERT: b 18 LYS cc_start: 0.8556 (tttt) cc_final: 0.7801 (mptt) REVERT: b 46 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8121 (ttmt) REVERT: b 51 LYS cc_start: 0.8128 (mttm) cc_final: 0.7913 (mttm) REVERT: c 18 LYS cc_start: 0.8552 (tttt) cc_final: 0.7932 (mptt) REVERT: d 18 LYS cc_start: 0.8270 (tttt) cc_final: 0.7650 (mptt) REVERT: d 51 LYS cc_start: 0.8408 (mptt) cc_final: 0.8181 (mptt) outliers start: 37 outliers final: 29 residues processed: 759 average time/residue: 0.2201 time to fit residues: 229.7120 Evaluate side-chains 762 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 730 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 44 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 50 SER Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 17 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN F 8 ASN F 27 GLN N 8 ASN O 8 ASN R 27 GLN V 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.101351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088199 restraints weight = 20001.139| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.98 r_work: 0.3167 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10980 Z= 0.205 Angle : 0.625 7.203 14940 Z= 0.322 Chirality : 0.043 0.186 1980 Planarity : 0.004 0.026 1740 Dihedral : 4.031 13.946 1440 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 3.01 % Allowed : 35.04 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.24), residues: 1350 helix: 1.43 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 4.69 (0.47), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 29 PHE 0.014 0.001 PHE U 48 TYR 0.014 0.001 TYR N 9 ARG 0.005 0.000 ARG F 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3684.87 seconds wall clock time: 66 minutes 14.72 seconds (3974.72 seconds total)